Publications 2023

@article{polacek_automation_2023,
	title = {Automation of tree-ring detection and measurements using deep learning},
	volume = {14},
	copyright = {© 2023 GMI - Gregor Mendel Institute of Molecular Plant Biology. Methods in Ecology and Evolution published by John Wiley \& Sons Ltd on behalf of British Ecological Society.},
	issn = {2041-210X},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/2041-210X.14183},
	doi = {10.1111/2041-210X.14183},
	abstract = {Core samples from trees are a critical reservoir of ecological information, informing our understanding of past climates, as well as contemporary ecosystem responses to global change. Manual measurements of annual growth rings in trees are slow, labour-intensive and subject to human bias, hindering the generation of big datasets. We present an alternative, neural network-based implementation that automates detection and measurement of tree-ring boundaries from coniferous species. We trained our Mask R-CNN extensively on over 8000 manually annotated ring boundaries from microscope-imaged Norway Spruce Picea abies increment cores. We assessed the performance of the trained model after post-processing on real-world data generated from our core processing pipeline. The CNN after post-processing performed well, with recognition of over 98\% of ring boundaries (recall) with a precision in detection of 96\% when tested on real-world data. Additionally, we have implemented automatic measurements based on minimum distance between rings. With minimal editing for missed ring detections, these measurements were 98\% correlated with human measurements of the same samples. Tests on other three conifer species demonstrate that the CNN generalizes well to other species with similar structure. We demonstrate the efficacy of automating the measurement of growth increment in tree core samples. Our CNN-based system provides high predictive performance in terms of both tree-ring detection and growth rate determination. Our application is readily deployable as a Docker container and requires only basic command line skills. Additionally, an easy re-training option allows users to expand capabilities to other wood types. Application outputs include both editable annotations of predictions as well as ring-width measurements in a commonly used .pos format, facilitating the efficient generation of large ring-width measurement datasets from increment core samples, an important source of environmental data.},
	language = {en},
	number = {9},
	urldate = {2024-03-22},
	journal = {Methods in Ecology and Evolution},
	author = {Poláček, Miroslav and Arizpe, Alexis and Hüther, Patrick and Weidlich, Lisa and Steindl, Sonja and Swarts, Kelly},
	year = {2023},
	note = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1111/2041-210X.14183},
	keywords = {automation, computer vision, mask R-CNN, phenotyping, tree rings},
	pages = {2233--2242},
}

Core samples from trees are a critical reservoir of ecological information, informing our understanding of past climates, as well as contemporary ecosystem responses to global change. Manual measurements of annual growth rings in trees are slow, labour-intensive and subject to human bias, hindering the generation of big datasets. We present an alternative, neural network-based implementation that automates detection and measurement of tree-ring boundaries from coniferous species. We trained our Mask R-CNN extensively on over 8000 manually annotated ring boundaries from microscope-imaged Norway Spruce Picea abies increment cores. We assessed the performance of the trained model after post-processing on real-world data generated from our core processing pipeline. The CNN after post-processing performed well, with recognition of over 98% of ring boundaries (recall) with a precision in detection of 96% when tested on real-world data. Additionally, we have implemented automatic measurements based on minimum distance between rings. With minimal editing for missed ring detections, these measurements were 98% correlated with human measurements of the same samples. Tests on other three conifer species demonstrate that the CNN generalizes well to other species with similar structure. We demonstrate the efficacy of automating the measurement of growth increment in tree core samples. Our CNN-based system provides high predictive performance in terms of both tree-ring detection and growth rate determination. Our application is readily deployable as a Docker container and requires only basic command line skills. Additionally, an easy re-training option allows users to expand capabilities to other wood types. Application outputs include both editable annotations of predictions as well as ring-width measurements in a commonly used .pos format, facilitating the efficient generation of large ring-width measurement datasets from increment core samples, an important source of environmental data.

@article{vallebueno-estrada_domestication_2023,
	title = {Domestication and lowland adaptation of coastal preceramic maize from {Paredones}, {Peru}},
	volume = {12},
	issn = {2050-084X},
	url = {https://doi.org/10.7554/eLife.83149},
	doi = {10.7554/eLife.83149},
	abstract = {Archaeological cobs from Paredones and Huaca Prieta (Peru) represent some of the oldest maize known to date, yet they present relevant phenotypic traits corresponding to domesticated maize. This contrasts with the earliest Mexican macro-specimens from Guila Naquitz and San Marcos, which are phenotypically intermediate for these traits, even though they date more recently in time. To gain insights into the origins of ancient Peruvian maize, we sequenced DNA from three Paredones specimens dating {\textasciitilde}6700–5000 calibrated years before present (BP), conducting comparative analyses with two teosinte subspecies (Zea mays ssp. mexicana and parviglumis) and extant maize, that include highland and lowland landraces from Mesoamerica and South America. We show that Paredones maize originated from the same domestication event as Mexican maize and was domesticated by {\textasciitilde}6700 BP, implying rapid dispersal followed by improvement. Paredones maize shows no relevant gene flow from mexicana, smaller than that observed in teosinte parviglumis. Thus, Paredones samples represent the only maize without confounding mexicana variation found to date. It also harbors significantly fewer alleles previously found to be adaptive to highlands, but not of alleles adaptive to lowlands, supporting a lowland migration route. Our overall results imply that Paredones maize originated in Mesoamerica, arrived in Peru without mexicana introgression through a rapid lowland migration route, and underwent improvements in both Mesoamerica and South America.},
	urldate = {2024-03-22},
	journal = {eLife},
	author = {Vallebueno-Estrada, Miguel and Hernández-Robles, Guillermo G and González-Orozco, Eduardo and Lopez-Valdivia, Ivan and Rosales Tham, Teresa and Vásquez Sánchez, Víctor and Swarts, Kelly and Dillehay, Tom D and Vielle-Calzada, Jean-Philippe and Montiel, Rafael},
	editor = {Weigel, Detlef},
	month = apr,
	year = {2023},
	note = {Publisher: eLife Sciences Publications, Ltd},
	keywords = {domestication, lowlands, paleogenomics, paredones},
	pages = {e83149},
}

Archaeological cobs from Paredones and Huaca Prieta (Peru) represent some of the oldest maize known to date, yet they present relevant phenotypic traits corresponding to domesticated maize. This contrasts with the earliest Mexican macro-specimens from Guila Naquitz and San Marcos, which are phenotypically intermediate for these traits, even though they date more recently in time. To gain insights into the origins of ancient Peruvian maize, we sequenced DNA from three Paredones specimens dating ~6700–5000 calibrated years before present (BP), conducting comparative analyses with two teosinte subspecies (Zea mays ssp. mexicana and parviglumis) and extant maize, that include highland and lowland landraces from Mesoamerica and South America. We show that Paredones maize originated from the same domestication event as Mexican maize and was domesticated by ~6700 BP, implying rapid dispersal followed by improvement. Paredones maize shows no relevant gene flow from mexicana, smaller than that observed in teosinte parviglumis. Thus, Paredones samples represent the only maize without confounding mexicana variation found to date. It also harbors significantly fewer alleles previously found to be adaptive to highlands, but not of alleles adaptive to lowlands, supporting a lowland migration route. Our overall results imply that Paredones maize originated in Mesoamerica, arrived in Peru without mexicana introgression through a rapid lowland migration route, and underwent improvements in both Mesoamerica and South America.

@article{guerreiro_unveiling_2023,
	title = {Unveiling the intricate mechanisms of plant defense},
	volume = {1},
	issn = {2813-821X},
	url = {https://www.frontiersin.org/articles/10.3389/fphgy.2023.1285373},
	doi = {10.3389/fphgy.2023.1285373},
	abstract = {Plants may lack mobility, but they are not defenseless against the constant threats posed by pathogens and pests. Pattern Recognition Receptors (PRRs), which are located on the plasma membrane, enable plants to effectively recognize intruders. These receptors function by sensing elicitors or fragments of the cell wall that arise from damage. Recent studies underscore the significance of maintaining cell wall integrity in the coordination of defense mechanisms following the detection of parasitism. Pathogen invasion often triggers alterations in cell wall structure, which leads to the release of molecules like β-glucans and oligogalacturonides. These small molecules are then recognized by PRRs, which stimulate downstream signaling pathways that involve both receptor-like kinases and calcium-dependent signaling. Here, we present the latest insights into plant signaling that play a vital role in immunity: the maintenance of cell wall integrity; the intricate interplay between receptor-like kinases; and the involvement of calcium ions. The goal of the review is to provide readers with a deeper understanding of the intricate mechanisms underlying plant defense strategies.},
	urldate = {2024-02-08},
	journal = {Frontiers in Plant Physiology},
	author = {Guerreiro, Julie and Marhavý, Peter},
	year = {2023},
}

Plants may lack mobility, but they are not defenseless against the constant threats posed by pathogens and pests. Pattern Recognition Receptors (PRRs), which are located on the plasma membrane, enable plants to effectively recognize intruders. These receptors function by sensing elicitors or fragments of the cell wall that arise from damage. Recent studies underscore the significance of maintaining cell wall integrity in the coordination of defense mechanisms following the detection of parasitism. Pathogen invasion often triggers alterations in cell wall structure, which leads to the release of molecules like β-glucans and oligogalacturonides. These small molecules are then recognized by PRRs, which stimulate downstream signaling pathways that involve both receptor-like kinases and calcium-dependent signaling. Here, we present the latest insights into plant signaling that play a vital role in immunity: the maintenance of cell wall integrity; the intricate interplay between receptor-like kinases; and the involvement of calcium ions. The goal of the review is to provide readers with a deeper understanding of the intricate mechanisms underlying plant defense strategies.

@article{bacete_dynamics_2023,
	title = {Dynamics and mechanics of plant cell walls: insights into plant growth, defence, and stress response},
	volume = {113},
	issn = {1573-5028},
	shorttitle = {Dynamics and mechanics of plant cell walls},
	url = {https://doi.org/10.1007/s11103-023-01395-9},
	doi = {10.1007/s11103-023-01395-9},
	language = {en},
	number = {6},
	urldate = {2024-01-04},
	journal = {Plant Molecular Biology},
	author = {Bacete, Laura and Mélida, Hugo},
	month = dec,
	year = {2023},
	pages = {329--330},
}

@article{skalicky_fluorescence-activated_2023,
	title = {Fluorescence-activated multi-organelle mapping of subcellular plant hormone distribution},
	volume = {116},
	copyright = {© 2023 The Authors. 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.16456},
	doi = {10.1111/tpj.16456},
	abstract = {Auxins and cytokinins are two major families of phytohormones that control most aspects of plant growth, development and plasticity. Their distribution in plants has been described, but the importance of cell- and subcellular-type specific phytohormone homeostasis remains undefined. Herein, we revealed auxin and cytokinin distribution maps showing their different organelle-specific allocations within the Arabidopsis plant cell. To do so, we have developed Fluorescence-Activated multi-Organelle Sorting (FAmOS), an innovative subcellular fractionation technique based on flow cytometric principles. FAmOS allows the simultaneous sorting of four differently labelled organelles based on their individual light scatter and fluorescence parameters while ensuring hormone metabolic stability. Our data showed different subcellular distribution of auxin and cytokinins, revealing the formation of phytohormone gradients that have been suggested by the subcellular localization of auxin and cytokinin transporters, receptors and metabolic enzymes. Both hormones showed enrichment in vacuoles, while cytokinins were also accumulated in the endoplasmic reticulum.},
	language = {en},
	number = {6},
	urldate = {2023-12-22},
	journal = {The Plant Journal},
	author = {Skalický, Vladimír and Antoniadi, Ioanna and Pěnčík, Aleš and Chamrád, Ivo and Lenobel, René and Kubeš, Martin F. and Zatloukal, Marek and Žukauskaitė, Asta and Strnad, Miroslav and Ljung, Karin and Novák, Ondřej},
	month = sep,
	year = {2023},
	note = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1111/tpj.16456},
	keywords = {Arabidopsis thaliana, Auxin, LC–MS/MS, cytokinin, flow cytometry, subcellular fractionation, subcellular homeostasis, technical advances},
	pages = {1825--1841},
}

Auxins and cytokinins are two major families of phytohormones that control most aspects of plant growth, development and plasticity. Their distribution in plants has been described, but the importance of cell- and subcellular-type specific phytohormone homeostasis remains undefined. Herein, we revealed auxin and cytokinin distribution maps showing their different organelle-specific allocations within the Arabidopsis plant cell. To do so, we have developed Fluorescence-Activated multi-Organelle Sorting (FAmOS), an innovative subcellular fractionation technique based on flow cytometric principles. FAmOS allows the simultaneous sorting of four differently labelled organelles based on their individual light scatter and fluorescence parameters while ensuring hormone metabolic stability. Our data showed different subcellular distribution of auxin and cytokinins, revealing the formation of phytohormone gradients that have been suggested by the subcellular localization of auxin and cytokinin transporters, receptors and metabolic enzymes. Both hormones showed enrichment in vacuoles, while cytokinins were also accumulated in the endoplasmic reticulum.

@article{sharma_regulation_2023,
	title = {Regulation of {PIN} polarity in response to abiotic stress},
	volume = {76},
	issn = {1369-5266},
	url = {https://www.sciencedirect.com/science/article/pii/S1369526623001103},
	doi = {10.1016/j.pbi.2023.102445},
	abstract = {Plants have evolved robust adaptive mechanisms to withstand the ever-changing environment. Tightly regulated distribution of the hormone auxin throughout the plant body controls an impressive variety of developmental processes that tailor plant growth and morphology to environmental conditions. The proper flow and directionality of auxin between cells is mainly governed by asymmetrically localized efflux carriers – PINs – ensuring proper coordination of developmental processes in plants. Discerning the molecular players and cellular dynamics involved in the establishment and maintenance of PINs in specific membrane domains, as well as their ability to readjust in response to abiotic stressors is essential for understanding how plants balance adaptability and stability. While much is known about how PINs get polarized, there is still limited knowledge about how abiotic stresses alter PIN polarity by acting on these systems. In this review, we focus on the current understanding of mechanisms involved in (re)establishing and maintaining PIN polarity under abiotic stresses.},
	urldate = {2023-12-22},
	journal = {Current Opinion in Plant Biology},
	author = {Sharma, Manvi and Marhava, Petra},
	month = dec,
	year = {2023},
	pages = {102445},
}

Plants have evolved robust adaptive mechanisms to withstand the ever-changing environment. Tightly regulated distribution of the hormone auxin throughout the plant body controls an impressive variety of developmental processes that tailor plant growth and morphology to environmental conditions. The proper flow and directionality of auxin between cells is mainly governed by asymmetrically localized efflux carriers – PINs – ensuring proper coordination of developmental processes in plants. Discerning the molecular players and cellular dynamics involved in the establishment and maintenance of PINs in specific membrane domains, as well as their ability to readjust in response to abiotic stressors is essential for understanding how plants balance adaptability and stability. While much is known about how PINs get polarized, there is still limited knowledge about how abiotic stresses alter PIN polarity by acting on these systems. In this review, we focus on the current understanding of mechanisms involved in (re)establishing and maintaining PIN polarity under abiotic stresses.

@article{bas_preparation_2023,
	title = {Preparation and {Characterization} of {Softwood} and {Hardwood} {Nanofibril} {Hydrogels}: {Toward} {Wound} {Dressing} {Applications}},
	volume = {24},
	issn = {1525-7797},
	shorttitle = {Preparation and {Characterization} of {Softwood} and {Hardwood} {Nanofibril} {Hydrogels}},
	url = {https://doi.org/10.1021/acs.biomac.3c00596},
	doi = {10.1021/acs.biomac.3c00596},
	abstract = {Hydrogels of cellulose nanofibrils (CNFs) are promising wound dressing candidates due to their biocompatibility, high water absorption, and transparency. Herein, two different commercially available wood species, softwood and hardwood, were subjected to TEMPO-mediated oxidation to proceed with delignification and oxidation in a one-pot process, and thereafter, nanofibrils were isolated using a high-pressure microfluidizer. Furthermore, transparent nanofibril hydrogel networks were prepared by vacuum filtration. Nanofibril properties and network performance correlated with oxidation were investigated and compared with commercially available TEMPO-oxidized pulp nanofibrils and their networks. Softwood nanofibril hydrogel networks exhibited the best mechanical properties, and in vitro toxicological risk assessment showed no detrimental effect for any of the studied hydrogels on human fibroblast or keratinocyte cells. This study demonstrates a straightforward processing route for direct oxidation of different wood species to obtain nanofibril hydrogels for potential use as wound dressings, with softwood having the most potential.},
	number = {12},
	urldate = {2023-12-22},
	journal = {Biomacromolecules},
	author = {Baş, Yağmur and Berglund, Linn and Niittylä, Totte and Zattarin, Elisa and Aili, Daniel and Sotra, Zeljana and Rinklake, Ivana and Junker, Johan and Rakar, Jonathan and Oksman, Kristiina},
	month = dec,
	year = {2023},
	note = {Publisher: American Chemical Society},
	pages = {5605--5619},
}

Hydrogels of cellulose nanofibrils (CNFs) are promising wound dressing candidates due to their biocompatibility, high water absorption, and transparency. Herein, two different commercially available wood species, softwood and hardwood, were subjected to TEMPO-mediated oxidation to proceed with delignification and oxidation in a one-pot process, and thereafter, nanofibrils were isolated using a high-pressure microfluidizer. Furthermore, transparent nanofibril hydrogel networks were prepared by vacuum filtration. Nanofibril properties and network performance correlated with oxidation were investigated and compared with commercially available TEMPO-oxidized pulp nanofibrils and their networks. Softwood nanofibril hydrogel networks exhibited the best mechanical properties, and in vitro toxicological risk assessment showed no detrimental effect for any of the studied hydrogels on human fibroblast or keratinocyte cells. This study demonstrates a straightforward processing route for direct oxidation of different wood species to obtain nanofibril hydrogels for potential use as wound dressings, with softwood having the most potential.

@article{soni_interplay_2023,
	title = {The interplay between cell wall integrity and cell cycle progression in plants},
	volume = {113},
	issn = {1573-5028},
	url = {https://doi.org/10.1007/s11103-023-01394-w},
	doi = {10.1007/s11103-023-01394-w},
	abstract = {Plant cell walls are dynamic structures that play crucial roles in growth, development, and stress responses. Despite our growing understanding of cell wall biology, the connections between cell wall integrity (CWI) and cell cycle progression in plants remain poorly understood. This review aims to explore the intricate relationship between CWI and cell cycle progression in plants, drawing insights from studies in yeast and mammals. We provide an overview of the plant cell cycle, highlight the role of endoreplication in cell wall composition, and discuss recent findings on the molecular mechanisms linking CWI perception to cell wall biosynthesis and gene expression regulation. Furthermore, we address future perspectives and unanswered questions in the field, such as the identification of specific CWI sensing mechanisms and the role of CWI maintenance in the growth-defense trade-off. Elucidating these connections could have significant implications for crop improvement and sustainable agriculture.},
	language = {en},
	number = {6},
	urldate = {2023-12-22},
	journal = {Plant Molecular Biology},
	author = {Soni, Nancy and Bacete, Laura},
	month = dec,
	year = {2023},
	keywords = {Auxin, Cell cycle progression, Cell wall sensing, Cytokinin, Endoreplication, Growth-defense trade-off, Plant cell wall integrity},
	pages = {367--382},
}

Plant cell walls are dynamic structures that play crucial roles in growth, development, and stress responses. Despite our growing understanding of cell wall biology, the connections between cell wall integrity (CWI) and cell cycle progression in plants remain poorly understood. This review aims to explore the intricate relationship between CWI and cell cycle progression in plants, drawing insights from studies in yeast and mammals. We provide an overview of the plant cell cycle, highlight the role of endoreplication in cell wall composition, and discuss recent findings on the molecular mechanisms linking CWI perception to cell wall biosynthesis and gene expression regulation. Furthermore, we address future perspectives and unanswered questions in the field, such as the identification of specific CWI sensing mechanisms and the role of CWI maintenance in the growth-defense trade-off. Elucidating these connections could have significant implications for crop improvement and sustainable agriculture.

@article{bernacki_biotechnological_2023,
	title = {Biotechnological {Potential} of the {Stress} {Response} and {Plant} {Cell} {Death} {Regulators} {Proteins} in the {Biofuel} {Industry}},
	volume = {12},
	copyright = {http://creativecommons.org/licenses/by/3.0/},
	issn = {2073-4409},
	url = {https://www.mdpi.com/2073-4409/12/16/2018},
	doi = {10.3390/cells12162018},
	abstract = {Production of biofuel from lignocellulosic biomass is relatively low due to the limited knowledge about natural cell wall loosening and cellulolytic processes in plants. Industrial separation of cellulose fiber mass from lignin, its saccharification and alcoholic fermentation is still cost-ineffective and environmentally unfriendly. Assuming that the green transformation is inevitable and that new sources of raw materials for biofuels are needed, we decided to study cell death—a natural process occurring in plants in the context of reducing the recalcitrance of lignocellulose for the production of second-generation bioethanol. “Members of the enzyme families responsible for lysigenous aerenchyma formation were identified during the root hypoxia stress in Arabidopsis thaliana cell death mutants. The cell death regulatory genes, LESION SIMULATING DISEASE 1 (LSD1), PHYTOALEXIN DEFICIENT 4 (PAD4) and ENHANCED DISEASE SUSCEPTIBILITY 1 (EDS1) conditionally regulate the cell wall when suppressed in transgenic aspen. During four years of growth in the field, the following effects were observed: lignin content was reduced, the cellulose fiber polymerization degree increased and the growth itself was unaffected. The wood of transgenic trees was more efficient as a substrate for saccharification, alcoholic fermentation and bioethanol production. The presented results may trigger the development of novel biotechnologies in the biofuel industry.},
	language = {en},
	number = {16},
	urldate = {2023-08-31},
	journal = {Cells},
	author = {Bernacki, Maciej Jerzy and Mielecki, Jakub and Antczak, Andrzej and Drożdżek, Michał and Witoń, Damian and Dąbrowska-Bronk, Joanna and Gawroński, Piotr and Burdiak, Paweł and Marchwicka, Monika and Rusaczonek, Anna and Dąbkowska-Susfał, Katarzyna and Strobel, Wacław Roman and Mellerowicz, Ewa J. and Zawadzki, Janusz and Szechyńska-Hebda, Magdalena and Karpiński, Stanisław},
	month = aug,
	year = {2023},
	note = {Number: 16
Publisher: Multidisciplinary Digital Publishing Institute},
	keywords = {bioethanol, biofuels, cell death, cell wall, lignin, poplar, scarification},
	pages = {2018},
}

Production of biofuel from lignocellulosic biomass is relatively low due to the limited knowledge about natural cell wall loosening and cellulolytic processes in plants. Industrial separation of cellulose fiber mass from lignin, its saccharification and alcoholic fermentation is still cost-ineffective and environmentally unfriendly. Assuming that the green transformation is inevitable and that new sources of raw materials for biofuels are needed, we decided to study cell death—a natural process occurring in plants in the context of reducing the recalcitrance of lignocellulose for the production of second-generation bioethanol. “Members of the enzyme families responsible for lysigenous aerenchyma formation were identified during the root hypoxia stress in Arabidopsis thaliana cell death mutants. The cell death regulatory genes, LESION SIMULATING DISEASE 1 (LSD1), PHYTOALEXIN DEFICIENT 4 (PAD4) and ENHANCED DISEASE SUSCEPTIBILITY 1 (EDS1) conditionally regulate the cell wall when suppressed in transgenic aspen. During four years of growth in the field, the following effects were observed: lignin content was reduced, the cellulose fiber polymerization degree increased and the growth itself was unaffected. The wood of transgenic trees was more efficient as a substrate for saccharification, alcoholic fermentation and bioethanol production. The presented results may trigger the development of novel biotechnologies in the biofuel industry.

@article{jobert_auxin_2023,
	title = {Auxin as an architect of the pectin matrix},
	volume = {74},
	issn = {0022-0957},
	url = {https://doi.org/10.1093/jxb/erad174},
	doi = {10.1093/jxb/erad174},
	abstract = {Auxin is a versatile plant growth regulator that triggers multiple signalling pathways at different spatial and temporal resolutions. A plant cell is surrounded by the cell wall, a complex and dynamic network of polysaccharides. The cell wall needs to be rigid to provide mechanical support and protection and highly flexible to allow cell growth and shape acquisition. The modification of the pectin components, among other processes, is a mechanism by which auxin activity alters the mechanical properties of the cell wall. Auxin signalling precisely controls the transcriptional output of several genes encoding pectin remodelling enzymes, their local activity, pectin deposition, and modulation in different developmental contexts. This review examines the mechanism of auxin activity in regulating pectin chemistry at organ, cellular, and subcellular levels across diverse plant species. Moreover, we ask questions that remain to be addressed to fully understand the interplay between auxin and pectin in plant growth and development.},
	number = {22},
	urldate = {2023-12-08},
	journal = {Journal of Experimental Botany},
	author = {Jobert, François and Yadav, Sandeep and Robert, Stéphanie},
	month = dec,
	year = {2023},
	pages = {6933--6949},
}

Auxin is a versatile plant growth regulator that triggers multiple signalling pathways at different spatial and temporal resolutions. A plant cell is surrounded by the cell wall, a complex and dynamic network of polysaccharides. The cell wall needs to be rigid to provide mechanical support and protection and highly flexible to allow cell growth and shape acquisition. The modification of the pectin components, among other processes, is a mechanism by which auxin activity alters the mechanical properties of the cell wall. Auxin signalling precisely controls the transcriptional output of several genes encoding pectin remodelling enzymes, their local activity, pectin deposition, and modulation in different developmental contexts. This review examines the mechanism of auxin activity in regulating pectin chemistry at organ, cellular, and subcellular levels across diverse plant species. Moreover, we ask questions that remain to be addressed to fully understand the interplay between auxin and pectin in plant growth and development.

@article{davis_toward_2023,
	title = {Toward uncovering an operating system in plant organs},
	issn = {1360-1385},
	url = {https://www.sciencedirect.com/science/article/pii/S1360138523003655},
	doi = {10.1016/j.tplants.2023.11.006},
	abstract = {Molecular motifs can explain information processing within single cells, while how assemblies of cells collectively achieve this remains less well understood. Plant fitness and survival depend upon robust and accurate decision-making in their decentralised multicellular organ systems. Mobile agents, including hormones, metabolites, and RNAs, have a central role in coordinating multicellular collective decision-making, yet mechanisms describing how cell–cell communication scales to organ-level transitions is poorly understood. Here, we explore how unified outputs may emerge in plant organs by distributed information processing across different scales and using different modalities. Mathematical and computational representations of these events are also explored toward understanding how these events take place and are leveraged to manipulate plant development in response to the environment.},
	urldate = {2023-12-08},
	journal = {Trends in Plant Science},
	author = {Davis, Gwendolyn V. and de Souza Moraes, Tatiana and Khanapurkar, Swanand and Dromiack, Hannah and Ahmad, Zaki and Bayer, Emmanuelle M. and Bhalerao, Rishikesh P. and Walker, Sara I. and Bassel, George W.},
	month = nov,
	year = {2023},
	keywords = {Cellular Automata, collective behaviour, decentralised information processing, decision-making, plant development},
}

Molecular motifs can explain information processing within single cells, while how assemblies of cells collectively achieve this remains less well understood. Plant fitness and survival depend upon robust and accurate decision-making in their decentralised multicellular organ systems. Mobile agents, including hormones, metabolites, and RNAs, have a central role in coordinating multicellular collective decision-making, yet mechanisms describing how cell–cell communication scales to organ-level transitions is poorly understood. Here, we explore how unified outputs may emerge in plant organs by distributed information processing across different scales and using different modalities. Mathematical and computational representations of these events are also explored toward understanding how these events take place and are leveraged to manipulate plant development in response to the environment.

@article{haggstrom_environmental_2023,
	title = {Environmental controls on seedling establishment in a boreal forest: implications for {Scots} pine regeneration in continuous cover forestry},
	issn = {1612-4677},
	shorttitle = {Environmental controls on seedling establishment in a boreal forest},
	url = {https://doi.org/10.1007/s10342-023-01609-1},
	doi = {10.1007/s10342-023-01609-1},
	abstract = {In nutrient poor and dry forest sites common to northern Scandinavia, Scots pine (Pinus sylvestris L.) is the most common species both in managed and natural forests. However, Scots pine is sensitive to competition during establishment. Harvesting of all trees within a given area, i.e., clear-cutting, liberates regenerating seedlings from competition with mature trees. However, recently, clear-cut-free or continuous cover forestry has been the subject of substantial debate. When choosing a management method, it is important to recognize how competitive interactions direct the success of Scots pine regeneration. We studied Scots pine regeneration at three environments: beneath the canopy of mature trees, at the canopy edge in full sunlight, and distant from the canopy with no influence of mature trees. We imposed three treatments in each of these environments: root isolation (i.e., trenching), nitrogen (N) fertilization, and control plots. Root isolation enhanced seedling performance under the canopy of mature trees. Nitrogen fertilization enhanced seedling performance to a greater extent in the clear-cut than at the forest edge. However, N fertilization had no effect under the canopy. In the N-fertilized plots, we measured higher N content in the soil under the canopy than in the open environments, indicating that not all excess N was obtained by the mature trees. N-uptake might have been limited by competition for water in the N-fertilized plots. Our results suggest that belowground competition limits the success of regeneration of Scots pine. However, N fertilization presents a tool to compensate for underground competition along canopy edges.},
	language = {en},
	urldate = {2023-12-08},
	journal = {European Journal of Forest Research},
	author = {Häggström, Bodil and Gundale, Michael J. and Nordin, Annika},
	month = oct,
	year = {2023},
	keywords = {Belowground competition, Clear-cutting, Continuous cover forestry, Forest growth, Scots pine, Tree regeneration},
}

In nutrient poor and dry forest sites common to northern Scandinavia, Scots pine (Pinus sylvestris L.) is the most common species both in managed and natural forests. However, Scots pine is sensitive to competition during establishment. Harvesting of all trees within a given area, i.e., clear-cutting, liberates regenerating seedlings from competition with mature trees. However, recently, clear-cut-free or continuous cover forestry has been the subject of substantial debate. When choosing a management method, it is important to recognize how competitive interactions direct the success of Scots pine regeneration. We studied Scots pine regeneration at three environments: beneath the canopy of mature trees, at the canopy edge in full sunlight, and distant from the canopy with no influence of mature trees. We imposed three treatments in each of these environments: root isolation (i.e., trenching), nitrogen (N) fertilization, and control plots. Root isolation enhanced seedling performance under the canopy of mature trees. Nitrogen fertilization enhanced seedling performance to a greater extent in the clear-cut than at the forest edge. However, N fertilization had no effect under the canopy. In the N-fertilized plots, we measured higher N content in the soil under the canopy than in the open environments, indicating that not all excess N was obtained by the mature trees. N-uptake might have been limited by competition for water in the N-fertilized plots. Our results suggest that belowground competition limits the success of regeneration of Scots pine. However, N fertilization presents a tool to compensate for underground competition along canopy edges.

@article{alonso_baez_cell_2023,
	title = {Cell wall dynamics: novel tools and research questions},
	volume = {74},
	issn = {0022-0957},
	shorttitle = {Cell wall dynamics},
	url = {https://doi.org/10.1093/jxb/erad310},
	doi = {10.1093/jxb/erad310},
	abstract = {Years ago, a classic textbook would define plant cell walls based on passive features. For instance, a sort of plant exoskeleton of invariable polysaccharide composition, and probably painted in green. However, currently, this view has been expanded to consider plant cell walls as active, heterogeneous, and dynamic structures with a high degree of complexity. However, what do we mean when we refer to a cell wall as a dynamic structure? How can we investigate the different implications of this dynamism? While the first question has been the subject of several recent publications, defining the ideal strategies and tools needed to address the second question has proven to be challenging due to the myriad of techniques available. In this review, we will describe the capacities of several methodologies to study cell wall composition, structure, and other aspects developed or optimized in recent years. Keeping in mind cell wall dynamism and plasticity, the advantages of performing long-term non-invasive live-imaging methods will be emphasized. We specifically focus on techniques developed for Arabidopsis thaliana primary cell walls, but the techniques could be applied to both secondary cell walls and other plant species. We believe this toolset will help researchers in expanding knowledge of these dynamic/evolving structures.},
	number = {21},
	urldate = {2023-11-24},
	journal = {Journal of Experimental Botany},
	author = {Alonso Baez, Luis and Bacete, Laura},
	month = nov,
	year = {2023},
	pages = {6448--6467},
}

Years ago, a classic textbook would define plant cell walls based on passive features. For instance, a sort of plant exoskeleton of invariable polysaccharide composition, and probably painted in green. However, currently, this view has been expanded to consider plant cell walls as active, heterogeneous, and dynamic structures with a high degree of complexity. However, what do we mean when we refer to a cell wall as a dynamic structure? How can we investigate the different implications of this dynamism? While the first question has been the subject of several recent publications, defining the ideal strategies and tools needed to address the second question has proven to be challenging due to the myriad of techniques available. In this review, we will describe the capacities of several methodologies to study cell wall composition, structure, and other aspects developed or optimized in recent years. Keeping in mind cell wall dynamism and plasticity, the advantages of performing long-term non-invasive live-imaging methods will be emphasized. We specifically focus on techniques developed for Arabidopsis thaliana primary cell walls, but the techniques could be applied to both secondary cell walls and other plant species. We believe this toolset will help researchers in expanding knowledge of these dynamic/evolving structures.

@article{dash_changes_2023,
	title = {Changes in cell wall composition due to a pectin biosynthesis enzyme {GAUT10} impact root growth},
	volume = {193},
	issn = {0032-0889},
	url = {https://doi.org/10.1093/plphys/kiad465},
	doi = {10.1093/plphys/kiad465},
	abstract = {Arabidopsis (Arabidopsis thaliana) root development is regulated by multiple dynamic growth cues that require central metabolism pathways such as β-oxidation and auxin. Loss of the pectin biosynthesizing enzyme GALACTURONOSYLTRANSFERASE 10 (GAUT10) leads to a short-root phenotype under sucrose-limited conditions. The present study focused on determining the specific contributions of GAUT10 to pectin composition in primary roots and the underlying defects associated with gaut10 roots. Using live-cell microscopy, we determined reduced root growth in gaut10 is due to a reduction in both root apical meristem size and epidermal cell elongation. In addition, GAUT10 was required for normal pectin and hemicellulose composition in primary Arabidopsis roots. Specifically, loss of GAUT10 led to a reduction in galacturonic acid and xylose in root cell walls and altered the presence of rhamnogalacturonan-I (RG-I) and homogalacturonan (HG) polymers in the root. Transcriptomic analysis of gaut10 roots compared to wild type uncovered hundreds of genes differentially expressed in the mutant, including genes related to auxin metabolism and peroxisome function. Consistent with these results, both auxin signaling and metabolism were modified in gaut10 roots. The sucrose-dependent short-root phenotype in gaut10 was linked to β-oxidation based on hypersensitivity to indole-3-butyric acid (IBA) and an epistatic interaction with TRANSPORTER OF IBA1 (TOB1). Altogether, these data support a growing body of evidence suggesting that pectin composition may influence auxin pathways and peroxisome activity.},
	number = {4},
	urldate = {2023-11-24},
	journal = {Plant Physiology},
	author = {Dash, Linkan and Swaminathan, Sivakumar and Šimura, Jan and Gonzales, Caitlin Leigh P and Montes, Christian and Solanki, Neel and Mejia, Ludvin and Ljung, Karin and Zabotina, Olga A and Kelley, Dior R},
	month = dec,
	year = {2023},
	pages = {2480--2497},
}

Arabidopsis (Arabidopsis thaliana) root development is regulated by multiple dynamic growth cues that require central metabolism pathways such as β-oxidation and auxin. Loss of the pectin biosynthesizing enzyme GALACTURONOSYLTRANSFERASE 10 (GAUT10) leads to a short-root phenotype under sucrose-limited conditions. The present study focused on determining the specific contributions of GAUT10 to pectin composition in primary roots and the underlying defects associated with gaut10 roots. Using live-cell microscopy, we determined reduced root growth in gaut10 is due to a reduction in both root apical meristem size and epidermal cell elongation. In addition, GAUT10 was required for normal pectin and hemicellulose composition in primary Arabidopsis roots. Specifically, loss of GAUT10 led to a reduction in galacturonic acid and xylose in root cell walls and altered the presence of rhamnogalacturonan-I (RG-I) and homogalacturonan (HG) polymers in the root. Transcriptomic analysis of gaut10 roots compared to wild type uncovered hundreds of genes differentially expressed in the mutant, including genes related to auxin metabolism and peroxisome function. Consistent with these results, both auxin signaling and metabolism were modified in gaut10 roots. The sucrose-dependent short-root phenotype in gaut10 was linked to β-oxidation based on hypersensitivity to indole-3-butyric acid (IBA) and an epistatic interaction with TRANSPORTER OF IBA1 (TOB1). Altogether, these data support a growing body of evidence suggesting that pectin composition may influence auxin pathways and peroxisome activity.

@article{liao_age-dependent_2023,
	title = {Age-dependent seasonal growth cessation in {Populus}},
	volume = {120},
	url = {https://www.pnas.org/doi/10.1073/pnas.2311226120},
	doi = {10.1073/pnas.2311226120},
	abstract = {In temperate and boreal regions, perennial plants adapt their annual growth cycle to the change of seasons. In natural forests, juvenile seedlings usually display longer growth seasons compared to adult trees to ensure their establishment and survival under canopy shade. However, how trees adjust their annual growth according to their age is not known. In this study, we show that age-dependent seasonal growth cessation is genetically controlled and found that the miR156-SPL3/5 module, a key regulon of vegetative phase change (VPC), also triggers age-dependent growth cessation in Populus trees. We show that miR156 promotes shoot elongation during vegetative growth, and its targets SPL3/5s function in the same pathway but as repressors. We find that the miR156-SPL3/5s regulon controls growth cessation in both leaves and shoot apices and through multiple pathways, but with a different mechanism compared to how the miR156-SPL regulon controls VPC in annual plants. Taken together, our results reveal an age-dependent genetic network in mediating seasonal growth cessation, a key phenological process in the climate adaptation of perennial trees.},
	number = {48},
	urldate = {2023-11-24},
	journal = {Proceedings of the National Academy of Sciences},
	author = {Liao, Xiaoli and Su, Yunjie and Klintenäs, Maria and Li, Yue and Sane, Shashank and Wu, Zhihao and Chen, Qihui and Zhang, Bo and Nilsson, Ove and Ding, Jihua},
	month = nov,
	year = {2023},
	note = {Publisher: Proceedings of the National Academy of Sciences},
	pages = {e2311226120},
}

In temperate and boreal regions, perennial plants adapt their annual growth cycle to the change of seasons. In natural forests, juvenile seedlings usually display longer growth seasons compared to adult trees to ensure their establishment and survival under canopy shade. However, how trees adjust their annual growth according to their age is not known. In this study, we show that age-dependent seasonal growth cessation is genetically controlled and found that the miR156-SPL3/5 module, a key regulon of vegetative phase change (VPC), also triggers age-dependent growth cessation in Populus trees. We show that miR156 promotes shoot elongation during vegetative growth, and its targets SPL3/5s function in the same pathway but as repressors. We find that the miR156-SPL3/5s regulon controls growth cessation in both leaves and shoot apices and through multiple pathways, but with a different mechanism compared to how the miR156-SPL regulon controls VPC in annual plants. Taken together, our results reveal an age-dependent genetic network in mediating seasonal growth cessation, a key phenological process in the climate adaptation of perennial trees.

@article{su_tree_2023,
	title = {Tree architecture: {A} strigolactone-deficient mutant reveals a connection between branching order and auxin gradient along the tree stem},
	volume = {120},
	shorttitle = {Tree architecture},
	url = {https://www.pnas.org/doi/10.1073/pnas.2308587120},
	doi = {10.1073/pnas.2308587120},
	abstract = {Due to their long lifespan, trees and bushes develop higher order of branches in a perennial manner. In contrast to a tall tree, with a clearly defined main stem and branching order, a bush is shorter and has a less apparent main stem and branching pattern. To address the developmental basis of these two forms, we studied several naturally occurring architectural variants in silver birch (Betula pendula). Using a candidate gene approach, we identified a bushy kanttarelli variant with a loss-of-function mutation in the BpMAX1 gene required for strigolactone (SL) biosynthesis. While kanttarelli is shorter than the wild type (WT), it has the same number of primary branches, whereas the number of secondary branches is increased, contributing to its bush-like phenotype. To confirm that the identified mutation was responsible for the phenotype, we phenocopied kanttarelli in transgenic BpMAX1::RNAi birch lines. SL profiling confirmed that both kanttarelli and the transgenic lines produced very limited amounts of SL. Interestingly, the auxin (IAA) distribution along the main stem differed between WT and BpMAX1::RNAi. In the WT, the auxin concentration formed a gradient, being higher in the uppermost internodes and decreasing toward the basal part of the stem, whereas in the transgenic line, this gradient was not observed. Through modeling, we showed that the different IAA distribution patterns may result from the difference in the number of higher-order branches and plant height. Future studies will determine whether the IAA gradient itself regulates aspects of plant architecture.},
	number = {48},
	urldate = {2023-11-24},
	journal = {Proceedings of the National Academy of Sciences},
	author = {Su, Chang and Kokosza, Andrzej and Xie, Xiaonan and Pěnčík, Aleš and Zhang, Youjun and Raumonen, Pasi and Shi, Xueping and Muranen, Sampo and Topcu, Melis Kucukoglu and Immanen, Juha and Hagqvist, Risto and Safronov, Omid and Alonso-Serra, Juan and Eswaran, Gugan and Venegas, Mirko Pavicic and Ljung, Karin and Ward, Sally and Mähönen, Ari Pekka and Himanen, Kristiina and Salojärvi, Jarkko and Fernie, Alisdair R. and Novák, Ondřej and Leyser, Ottoline and Pałubicki, Wojtek and Helariutta, Ykä and Nieminen, Kaisa},
	month = nov,
	year = {2023},
	note = {Publisher: Proceedings of the National Academy of Sciences},
	pages = {e2308587120},
}

Due to their long lifespan, trees and bushes develop higher order of branches in a perennial manner. In contrast to a tall tree, with a clearly defined main stem and branching order, a bush is shorter and has a less apparent main stem and branching pattern. To address the developmental basis of these two forms, we studied several naturally occurring architectural variants in silver birch (Betula pendula). Using a candidate gene approach, we identified a bushy kanttarelli variant with a loss-of-function mutation in the BpMAX1 gene required for strigolactone (SL) biosynthesis. While kanttarelli is shorter than the wild type (WT), it has the same number of primary branches, whereas the number of secondary branches is increased, contributing to its bush-like phenotype. To confirm that the identified mutation was responsible for the phenotype, we phenocopied kanttarelli in transgenic BpMAX1::RNAi birch lines. SL profiling confirmed that both kanttarelli and the transgenic lines produced very limited amounts of SL. Interestingly, the auxin (IAA) distribution along the main stem differed between WT and BpMAX1::RNAi. In the WT, the auxin concentration formed a gradient, being higher in the uppermost internodes and decreasing toward the basal part of the stem, whereas in the transgenic line, this gradient was not observed. Through modeling, we showed that the different IAA distribution patterns may result from the difference in the number of higher-order branches and plant height. Future studies will determine whether the IAA gradient itself regulates aspects of plant architecture.

@article{sasaki_confined-microtubule_2023,
	title = {Confined-microtubule assembly shapes three-dimensional cell wall structures in xylem vessels},
	volume = {14},
	copyright = {2023 The Author(s)},
	issn = {2041-1723},
	url = {https://www.nature.com/articles/s41467-023-42487-w},
	doi = {10.1038/s41467-023-42487-w},
	abstract = {Properly patterned deposition of cell wall polymers is prerequisite for the morphogenesis of plant cells. A cortical microtubule array guides the two-dimensional pattern of cell wall deposition. Yet, the mechanism underlying the three-dimensional patterning of cell wall deposition is poorly understood. In metaxylem vessels, cell wall arches are formed over numerous pit membranes, forming highly organized three-dimensional cell wall structures. Here, we show that the microtubule-associated proteins, MAP70-5 and MAP70-1, regulate arch development. The map70-1 map70-5 plants formed oblique arches in an abnormal orientation in pits. Microtubules fit the aperture of developing arches in wild-type cells, whereas microtubules in map70-1 map70-5 cells extended over the boundaries of pit arches. MAP70 caused the bending and bundling of microtubules. These results suggest that MAP70 confines microtubules within the pit apertures by altering the physical properties of microtubules, thereby directing the growth of pit arches in the proper orientation. This study provides clues to understanding how plants develop three-dimensional structure of cell walls.},
	language = {en},
	number = {1},
	urldate = {2023-11-24},
	journal = {Nature Communications},
	author = {Sasaki, Takema and Saito, Kei and Inoue, Daisuke and Serk, Henrik and Sugiyama, Yuki and Pesquet, Edouard and Shimamoto, Yuta and Oda, Yoshihisa},
	month = nov,
	year = {2023},
	note = {Number: 1
Publisher: Nature Publishing Group},
	keywords = {Cell wall, Microtubules, Plant cytoskeleton},
	pages = {6987},
}

Properly patterned deposition of cell wall polymers is prerequisite for the morphogenesis of plant cells. A cortical microtubule array guides the two-dimensional pattern of cell wall deposition. Yet, the mechanism underlying the three-dimensional patterning of cell wall deposition is poorly understood. In metaxylem vessels, cell wall arches are formed over numerous pit membranes, forming highly organized three-dimensional cell wall structures. Here, we show that the microtubule-associated proteins, MAP70-5 and MAP70-1, regulate arch development. The map70-1 map70-5 plants formed oblique arches in an abnormal orientation in pits. Microtubules fit the aperture of developing arches in wild-type cells, whereas microtubules in map70-1 map70-5 cells extended over the boundaries of pit arches. MAP70 caused the bending and bundling of microtubules. These results suggest that MAP70 confines microtubules within the pit apertures by altering the physical properties of microtubules, thereby directing the growth of pit arches in the proper orientation. This study provides clues to understanding how plants develop three-dimensional structure of cell walls.

@article{capovilla_chitin_2023,
	title = {Chitin degradation by {Synechococcus} {WH7803}},
	volume = {13},
	copyright = {2023 The Author(s)},
	issn = {2045-2322},
	url = {https://www.nature.com/articles/s41598-023-47332-0},
	doi = {10.1038/s41598-023-47332-0},
	abstract = {Chitin is an abundant, carbon-rich polymer in the marine environment. Chitinase activity has been detected in spent media of Synechococcus WH7803 cultures—yet it was unclear which specific enzymes were involved. Here we delivered a CRISPR tool into the cells via electroporation to generate loss-of-function mutants of putative candidates and identified ChiA as the enzyme required for the activity detected in the wild type.},
	language = {en},
	number = {1},
	urldate = {2023-11-17},
	journal = {Scientific Reports},
	author = {Capovilla, Giovanna and Castro, Kurt G. and Collani, Silvio and Kearney, Sean M. and Kehoe, David M. and Chisholm, Sallie W.},
	month = nov,
	year = {2023},
	note = {Number: 1
Publisher: Nature Publishing Group},
	keywords = {Ecology, Microbiology, Molecular biology},
	pages = {19944},
}

Chitin is an abundant, carbon-rich polymer in the marine environment. Chitinase activity has been detected in spent media of Synechococcus WH7803 cultures—yet it was unclear which specific enzymes were involved. Here we delivered a CRISPR tool into the cells via electroporation to generate loss-of-function mutants of putative candidates and identified ChiA as the enzyme required for the activity detected in the wild type.

@article{yan_unraveling_2023,
	title = {Unraveling the evolutionary dynamics of the {TPS} gene family in land plants},
	volume = {14},
	issn = {1664-462X},
	url = {https://www.frontiersin.org/articles/10.3389/fpls.2023.1273648},
	doi = {10.3389/fpls.2023.1273648},
	abstract = {Terpenes and terpenoids are key natural compounds for plant defense, development, and composition of plant oil. The synthesis and accumulation of a myriad of volatile terpenoid compounds in these plants may dramatically alter the quality and flavor of the oils, which provide great commercial utilization value for oil-producing plants. Terpene synthases (TPSs) are important enzymes responsible for terpenic diversity. Investigating the differentiation of the TPS gene family could provide valuable theoretical support for the genetic improvement of oil-producing plants. While the origin and function of TPS genes have been extensively studied, the exact origin of the initial gene fusion event - it occurred in plants or microbes - remains uncertain. Furthermore, a comprehensive exploration of the TPS gene differentiation is still pending. Here, phylogenetic analysis revealed that the fusion of the TPS gene likely occurred in the ancestor of land plants, following the acquisition of individual C- and N- terminal domains. Potential mutual transfer of TPS genes was observed among microbes and plants. Gene synteny analysis disclosed a differential divergence pattern between TPS-c and TPS-e/f subfamilies involved in primary metabolism and those (TPS-a/b/d/g/h subfamilies) crucial for secondary metabolites. Biosynthetic gene clusters (BGCs) analysis suggested a correlation between lineage divergence and potential natural selection in structuring terpene diversities. This study provides fresh perspectives on the origin and evolution of the TPS gene family.},
	urldate = {2023-11-03},
	journal = {Frontiers in Plant Science},
	author = {Yan, Xue-Mei and Zhou, Shan-Shan and Liu, Hui and Zhao, Shi-Wei and Tian, Xue-Chan and Shi, Tian-Le and Bao, Yu-Tao and Li, Zhi-Chao and Jia, Kai-Hua and Nie, Shuai and Guo, Jing-Fang and Kong, Lei and Porth, Ilga M. and Mao, Jian-Feng},
	month = oct,
	year = {2023},
	keywords = {⛔ No DOI found},
}

Terpenes and terpenoids are key natural compounds for plant defense, development, and composition of plant oil. The synthesis and accumulation of a myriad of volatile terpenoid compounds in these plants may dramatically alter the quality and flavor of the oils, which provide great commercial utilization value for oil-producing plants. Terpene synthases (TPSs) are important enzymes responsible for terpenic diversity. Investigating the differentiation of the TPS gene family could provide valuable theoretical support for the genetic improvement of oil-producing plants. While the origin and function of TPS genes have been extensively studied, the exact origin of the initial gene fusion event - it occurred in plants or microbes - remains uncertain. Furthermore, a comprehensive exploration of the TPS gene differentiation is still pending. Here, phylogenetic analysis revealed that the fusion of the TPS gene likely occurred in the ancestor of land plants, following the acquisition of individual C- and N- terminal domains. Potential mutual transfer of TPS genes was observed among microbes and plants. Gene synteny analysis disclosed a differential divergence pattern between TPS-c and TPS-e/f subfamilies involved in primary metabolism and those (TPS-a/b/d/g/h subfamilies) crucial for secondary metabolites. Biosynthetic gene clusters (BGCs) analysis suggested a correlation between lineage divergence and potential natural selection in structuring terpene diversities. This study provides fresh perspectives on the origin and evolution of the TPS gene family.

@article{nguyen_lbd18_2023,
	title = {{LBD18} and {IAA14} antagonistically interact with {ARF7} via the invariant {Lys} and acidic residues of the {OPCA} motif in the {PB1} domain},
	volume = {258},
	issn = {1432-2048},
	url = {https://doi.org/10.1007/s00425-023-04183-3},
	doi = {10.1007/s00425-023-04183-3},
	abstract = {LBD18 and IAA14 antagonistically interact with ARF7 through the electrostatic faces in the ARF7PB1 domain, modulating ARF7 transcriptional activity.},
	language = {en},
	number = {2},
	urldate = {2023-11-14},
	journal = {Planta},
	author = {Nguyen, Uyen Thu and Pandey, Shashank K. and Kim, Jungmook},
	month = jun,
	year = {2023},
	keywords = {ARF19, ARF7, Aux/IAA, Auxin response factor, LBD, Lateral organ boundaries domain, PB1 domain},
	pages = {26},
}

LBD18 and IAA14 antagonistically interact with ARF7 through the electrostatic faces in the ARF7PB1 domain, modulating ARF7 transcriptional activity.

@article{haggstrom_effect_2023,
	title = {Effect of arginine-phosphate addition on early survival and growth of {Scots} pine, {Norway} spruce and silver birch},
	volume = {57},
	url = {https://www.silvafennica.fi/article/22013},
	doi = {10.14214/sf.22013},
	language = {en},
	number = {2},
	urldate = {2023-09-29},
	journal = {Silva Fennica},
	author = {Häggström, Bodil and Lutter, Reimo and Lundmark, Tomas and Sjödin, Fredrik and Nordin, Annika},
	month = sep,
	year = {2023},
}

@article{xiao_natural_2023,
	title = {Natural variation in the prolyl 4-hydroxylase gene {PtoP4H9} contributes to perennial stem growth in {Populus}},
	volume = {35},
	issn = {1040-4651},
	url = {https://doi.org/10.1093/plcell/koad212},
	doi = {10.1093/plcell/koad212},
	abstract = {Perennial trees must maintain stem growth throughout their entire lifespan to progressively increase in size as they age. The overarching question of the molecular mechanisms that govern stem perennial growth in trees remains largely unanswered. Here we deciphered the genetic architecture that underlies perennial growth trajectories using genome-wide association studies (GWAS) for measures of growth traits across years in a natural population of Populus tomentosa. By analyzing the stem growth trajectory, we identified PtoP4H9, encoding prolyl 4-hydroxylase 9, which is responsible for the natural variation in the growth rate of diameter at breast height (DBH) across years. Quantifying the dynamic genetic contribution of PtoP4H9 loci to stem growth showed that PtoP4H9 played a pivotal role in stem growth regulation. Spatiotemporal expression analysis showed that PtoP4H9 was highly expressed in cambium tissues of poplars of various ages. Overexpression and knockdown of PtoP4H9 revealed that it altered cell expansion to regulate cell wall modification and mechanical characteristics, thereby promoting stem growth in Populus. We showed that natural variation in PtoP4H9 occurred in a BASIC PENTACYSTEINE transcription factor PtoBPC1-binding promoter element controlling PtoP4H9 expression. The geographic distribution of PtoP4H9 allelic variation was consistent with the modes of selection among populations. Altogether, our study provides important genetic insights into dynamic stem growth in Populus, and we confirmed PtoP4H9 as a potential useful marker for breeding or genetic engineering of poplars.},
	number = {11},
	urldate = {2023-11-10},
	journal = {The Plant Cell},
	author = {Xiao, Liang and Fang, Yuanyuan and Zhang, He and Quan, Mingyang and Zhou, Jiaxuan and Li, Peng and Wang, Dan and Ji, Li and Ingvarsson, Pär K and Wu, Harry X and El-Kassaby, Yousry A and Du, Qingzhang and Zhang, Deqiang},
	month = nov,
	year = {2023},
	pages = {4046--4065},
}

Perennial trees must maintain stem growth throughout their entire lifespan to progressively increase in size as they age. The overarching question of the molecular mechanisms that govern stem perennial growth in trees remains largely unanswered. Here we deciphered the genetic architecture that underlies perennial growth trajectories using genome-wide association studies (GWAS) for measures of growth traits across years in a natural population of Populus tomentosa. By analyzing the stem growth trajectory, we identified PtoP4H9, encoding prolyl 4-hydroxylase 9, which is responsible for the natural variation in the growth rate of diameter at breast height (DBH) across years. Quantifying the dynamic genetic contribution of PtoP4H9 loci to stem growth showed that PtoP4H9 played a pivotal role in stem growth regulation. Spatiotemporal expression analysis showed that PtoP4H9 was highly expressed in cambium tissues of poplars of various ages. Overexpression and knockdown of PtoP4H9 revealed that it altered cell expansion to regulate cell wall modification and mechanical characteristics, thereby promoting stem growth in Populus. We showed that natural variation in PtoP4H9 occurred in a BASIC PENTACYSTEINE transcription factor PtoBPC1-binding promoter element controlling PtoP4H9 expression. The geographic distribution of PtoP4H9 allelic variation was consistent with the modes of selection among populations. Altogether, our study provides important genetic insights into dynamic stem growth in Populus, and we confirmed PtoP4H9 as a potential useful marker for breeding or genetic engineering of poplars.

@article{zeng_chemical_2023,
	title = {Chemical induction of hypocotyl rooting reveals extensive conservation of auxin signalling controlling lateral and adventitious root formation},
	volume = {240},
	copyright = {© 2023 The Authors. New Phytologist © 2023 New Phytologist Foundation},
	issn = {1469-8137},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/nph.19292},
	doi = {10.1111/nph.19292},
	abstract = {Upon exposure to light, etiolated Arabidopsis seedlings form adventitious roots (AR) along the hypocotyl. While processes underlying lateral root formation are studied intensively, comparatively little is known about the molecular processes involved in the initiation of hypocotyl AR. AR and LR formation were studied using a small molecule named Hypocotyl Specific Adventitious Root INducer (HYSPARIN) that strongly induces AR but not LR formation. HYSPARIN does not trigger rapid DR5-reporter activation, DII-Venus degradation or Ca2+ signalling. Transcriptome analysis, auxin signalling reporter lines and mutants show that HYSPARIN AR induction involves nuclear TIR1/AFB and plasma membrane TMK auxin signalling, as well as multiple downstream LR development genes (SHY2/IAA3, PUCHI, MAKR4 and GATA23). Comparison of the AR and LR induction transcriptome identified SAURs, AGC kinases and OFP transcription factors as specifically upregulated by HYSPARIN. Members of the SAUR19 subfamily, OFP4 and AGC2 suppress HYS-induced AR formation. While SAUR19 and OFP subfamily members also mildly modulate LR formation, AGC2 regulates only AR induction. Analysis of HYSPARIN-induced AR formation uncovers an evolutionary conservation of auxin signalling controlling LR and AR induction in Arabidopsis seedlings and identifies SAUR19, OFP4 and AGC2 kinase as novel regulators of AR formation.},
	language = {en},
	number = {5},
	urldate = {2023-11-10},
	journal = {New Phytologist},
	author = {Zeng, Yinwei and Verstraeten, Inge and Trinh, Hoang Khai and Lardon, Robin and Schotte, Sebastien and Olatunji, Damilola and Heugebaert, Thomas and Stevens, Christian and Quareshy, Mussa and Napier, Richard and Nastasi, Sara Paola and Costa, Alex and De Rybel, Bert and Bellini, Catherine and Beeckman, Tom and Vanneste, Steffen and Geelen, Danny},
	month = oct,
	year = {2023},
	note = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1111/nph.19292},
	keywords = {adventitious root, auxin signalling, root branching, root development, synthetic auxin},
	pages = {1883--1899},
}

Upon exposure to light, etiolated Arabidopsis seedlings form adventitious roots (AR) along the hypocotyl. While processes underlying lateral root formation are studied intensively, comparatively little is known about the molecular processes involved in the initiation of hypocotyl AR. AR and LR formation were studied using a small molecule named Hypocotyl Specific Adventitious Root INducer (HYSPARIN) that strongly induces AR but not LR formation. HYSPARIN does not trigger rapid DR5-reporter activation, DII-Venus degradation or Ca2+ signalling. Transcriptome analysis, auxin signalling reporter lines and mutants show that HYSPARIN AR induction involves nuclear TIR1/AFB and plasma membrane TMK auxin signalling, as well as multiple downstream LR development genes (SHY2/IAA3, PUCHI, MAKR4 and GATA23). Comparison of the AR and LR induction transcriptome identified SAURs, AGC kinases and OFP transcription factors as specifically upregulated by HYSPARIN. Members of the SAUR19 subfamily, OFP4 and AGC2 suppress HYS-induced AR formation. While SAUR19 and OFP subfamily members also mildly modulate LR formation, AGC2 regulates only AR induction. Analysis of HYSPARIN-induced AR formation uncovers an evolutionary conservation of auxin signalling controlling LR and AR induction in Arabidopsis seedlings and identifies SAUR19, OFP4 and AGC2 kinase as novel regulators of AR formation.

@incollection{alonso_histochemical_2023,
	address = {New York, NY},
	series = {Methods in {Molecular} {Biology}},
	title = {Histochemical {Detection} of {Peroxidase} and {Laccase} {Activities} in {Populus} {Secondary} {Xylem}},
	isbn = {978-1-07-163477-6},
	url = {https://doi.org/10.1007/978-1-0716-3477-6_11},
	abstract = {Peroxidases (PRXs) and laccases (LACs) are enzymes involved in catalyzing the oxidation of the lignin monomers to facilitate lignin polymerization. However, due to the large number of genes composing these two families of enzymes, many details regarding their specific localization are only partially understood. Here, we present a fast and easy histochemical method that makes use of the artificial substrate 3,3′,5,5′-tetramethylbenzidine (TMB) to visualize PRX and LAC activities in the hybrid aspen (Populus tremula x P. tremuloides) xylem tissue. In addition, we describe a protocol that allows the detection of the PRX substrate, H2O2, using the nonfluorescent dye 2′,7′-dichlorodihydrofluorescein diacetate (H2DCFDA) in woody tissues.},
	language = {en},
	urldate = {2023-11-06},
	booktitle = {Xylem: {Methods} and {Protocols}},
	publisher = {Springer US},
	author = {Alonso, Marta-Marina Pérez and Carrió-Seguí, Àngela and Tuominen, Hannele},
	editor = {Agusti, Javier},
	month = nov,
	year = {2023},
	doi = {10.1007/978-1-0716-3477-6_11},
	keywords = {Cell wall, H2DCFDA, H2O2, Laccase, Lignin, Peroxidase, Populus, TMB, Woody tissues, Xylem},
	pages = {139--148},
}

Peroxidases (PRXs) and laccases (LACs) are enzymes involved in catalyzing the oxidation of the lignin monomers to facilitate lignin polymerization. However, due to the large number of genes composing these two families of enzymes, many details regarding their specific localization are only partially understood. Here, we present a fast and easy histochemical method that makes use of the artificial substrate 3,3′,5,5′-tetramethylbenzidine (TMB) to visualize PRX and LAC activities in the hybrid aspen (Populus tremula x P. tremuloides) xylem tissue. In addition, we describe a protocol that allows the detection of the PRX substrate, H2O2, using the nonfluorescent dye 2′,7′-dichlorodihydrofluorescein diacetate (H2DCFDA) in woody tissues.

@article{svensson_early_2023,
	title = {Early and repeated nutrient additions support far greater stemwood production in {Norway} spruce than traditional late-rotation fertilisation},
	volume = {549},
	issn = {0378-1127},
	url = {https://www.sciencedirect.com/science/article/pii/S037811272300659X},
	doi = {10.1016/j.foreco.2023.121425},
	abstract = {Silvicultural techniques aimed at promoting forest biomass production can help meet the growing demand for renewable materials and mitigate climate change. One-time nitrogen (N) addition late in the rotation is a well-established method to stimulate growth in coniferous forests in northern Europe, but the potential gains from earlier and repeated fertiliser application remain uncertain. Here, we tested the impact of repeated fertilisation in juvenile Norway spruce stands across 9 sites covering a wide range of growing conditions over a 700 km stretch from central to southern Sweden. We tested the fertilisation effects using two separate studies: i) an interval trial with a fertilisation frequency of one (F1), two (F2), or three years (F3) performed at plot-level across five sites (2002–2014), and ii) a practice-oriented trial with a two-year fertilisation interval (F2) applied at stand-level and replicated at four sites (2003–2013). The composition of the nutrient mix in each plot was optimised based on foliar nutrient analyses. In the interval trial, all three fertilisation schedules strongly increased periodic annual increment (PAI) (F1: 105 \%, F2: 93 \%, F3: 79 \%) relative to the unfertilised control, resulting in more than a doubling of stem volume yield in the F1 and F2 treatments (110 \% and 120 \%, respectively) and a significantly smaller but still sizeable yield stimulation of 82 \% in the F3 treatment. Nitrogen use efficiency (NUE, stemwood volume increase per unit mass of N added) was similar among fertilisation intervals (on average 130 m3 ha−1 1000 kg N−1), indicating that the extra N provided through yearly fertilisation (F1) is redundant given the similar stemwood yields in the F2 treatment. In the practice-oriented trial, the sole F2 treatment increased PAI by 95 \% over the control, translating into a yield stimulation of 114 \% and an almost identical NUE to that of the interval trial. NUE greatly exceeded the figures typically observed with traditional late-rotation fertilisation and correlated inversely with baseline site productivity (using site index as a proxy) in the F1 and F2 treatments (the latter pooled across the two trials). Our results clearly indicate that nutrient limitation restricts growth and carbon (C) capture in young Norway spruce plantations in northern Europe to less than half of their potential, highlighting repeated fertilisation at nutrient-poor sites as an effective management tool to support a growing bioeconomy and enhance C sequestration.},
	urldate = {2023-11-03},
	journal = {Forest Ecology and Management},
	author = {Svensson, Carl and Bader, Martin Karl-Friedrich and Forsmark, Benjamin and Nilsson, Urban and Lundmark, Tomas and Nordin, Annika and Bergh, Johan},
	month = dec,
	year = {2023},
	keywords = {Carbon sequestration, Forest fertilisation, Nutrient-limitation, Operational forestry, Stem biomass yield},
	pages = {121425},
}

Silvicultural techniques aimed at promoting forest biomass production can help meet the growing demand for renewable materials and mitigate climate change. One-time nitrogen (N) addition late in the rotation is a well-established method to stimulate growth in coniferous forests in northern Europe, but the potential gains from earlier and repeated fertiliser application remain uncertain. Here, we tested the impact of repeated fertilisation in juvenile Norway spruce stands across 9 sites covering a wide range of growing conditions over a 700 km stretch from central to southern Sweden. We tested the fertilisation effects using two separate studies: i) an interval trial with a fertilisation frequency of one (F1), two (F2), or three years (F3) performed at plot-level across five sites (2002–2014), and ii) a practice-oriented trial with a two-year fertilisation interval (F2) applied at stand-level and replicated at four sites (2003–2013). The composition of the nutrient mix in each plot was optimised based on foliar nutrient analyses. In the interval trial, all three fertilisation schedules strongly increased periodic annual increment (PAI) (F1: 105 %, F2: 93 %, F3: 79 %) relative to the unfertilised control, resulting in more than a doubling of stem volume yield in the F1 and F2 treatments (110 % and 120 %, respectively) and a significantly smaller but still sizeable yield stimulation of 82 % in the F3 treatment. Nitrogen use efficiency (NUE, stemwood volume increase per unit mass of N added) was similar among fertilisation intervals (on average 130 m3 ha−1 1000 kg N−1), indicating that the extra N provided through yearly fertilisation (F1) is redundant given the similar stemwood yields in the F2 treatment. In the practice-oriented trial, the sole F2 treatment increased PAI by 95 % over the control, translating into a yield stimulation of 114 % and an almost identical NUE to that of the interval trial. NUE greatly exceeded the figures typically observed with traditional late-rotation fertilisation and correlated inversely with baseline site productivity (using site index as a proxy) in the F1 and F2 treatments (the latter pooled across the two trials). Our results clearly indicate that nutrient limitation restricts growth and carbon (C) capture in young Norway spruce plantations in northern Europe to less than half of their potential, highlighting repeated fertilisation at nutrient-poor sites as an effective management tool to support a growing bioeconomy and enhance C sequestration.

@article{lstiburek_rolling_2023,
	title = {Rolling front landscape breeding},
	volume = {80},
	issn = {1297-966X},
	url = {https://doi.org/10.1186/s13595-023-01203-w},
	doi = {10.1186/s13595-023-01203-w},
	abstract = {Forest tree breeding must undergo significant revisions to adapt to the evolving challenges posed by climate change. Addressing the shifts in environmental conditions requires a comprehensive multidisciplinary approach that includes theoretical work and practical application. Specifically, there is a need to focus on developing new breeding strategies that are theoretically sound and practically feasible, considering the economic constraints of actual tree breeding programs. We present a novel concept utilizing genetic evaluation of multiple traits in forest stands of successive ages across wide ecological ranges. Incorporating genomics allows for detailed genetic evaluation, making use of high-density SNP markers and sophisticated algorithms like GBLUP for genetic parameter estimates. High-throughput phenotyping is conducted using drone-borne lidar technology to capture tree height and survival data across various forest stands. Assisted migration is considered to strategically position genotypes across predicted environmental climatic gradients, thereby accommodating the dynamic nature of ecological shifts. Mathematical optimization acts as an essential component for logistics, guiding the spatial allocation and timely substitution of genotypes to ensure a continually adaptive breeding program. The concept replaces distinct breeding cycles with continuous evaluation and selection, enhancing the rate of genetic response over time.},
	number = {1},
	urldate = {2023-10-27},
	journal = {Annals of Forest Science},
	author = {Lstibůrek, Milan and García‐Gil, María Rosario and Steffenrem, Arne},
	month = oct,
	year = {2023},
	keywords = {Adaptation, Climate change, Gene diversity, Genetic evaluation, In situ selection, Tree improvement},
	pages = {36},
}

Forest tree breeding must undergo significant revisions to adapt to the evolving challenges posed by climate change. Addressing the shifts in environmental conditions requires a comprehensive multidisciplinary approach that includes theoretical work and practical application. Specifically, there is a need to focus on developing new breeding strategies that are theoretically sound and practically feasible, considering the economic constraints of actual tree breeding programs. We present a novel concept utilizing genetic evaluation of multiple traits in forest stands of successive ages across wide ecological ranges. Incorporating genomics allows for detailed genetic evaluation, making use of high-density SNP markers and sophisticated algorithms like GBLUP for genetic parameter estimates. High-throughput phenotyping is conducted using drone-borne lidar technology to capture tree height and survival data across various forest stands. Assisted migration is considered to strategically position genotypes across predicted environmental climatic gradients, thereby accommodating the dynamic nature of ecological shifts. Mathematical optimization acts as an essential component for logistics, guiding the spatial allocation and timely substitution of genotypes to ensure a continually adaptive breeding program. The concept replaces distinct breeding cycles with continuous evaluation and selection, enhancing the rate of genetic response over time.

@article{urbancsok_flexure_2023,
	title = {Flexure wood formation via growth reprogramming in hybrid aspen involves jasmonates and polyamines and transcriptional changes resembling tension wood development},
	copyright = {New Phytologist© 2023 The Authors New Phytologist © 2023 New Phytologist Foundation},
	issn = {1469-8137},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/nph.19307},
	doi = {10.1111/nph.19307},
	abstract = {Stem bending in trees induces flexure wood but its properties and development are poorly understood. Here, we investigated the effects of low-intensity multidirectional stem flexing on growth and wood properties of hybrid aspen, and on its transcriptomic and hormonal responses. Glasshouse-grown trees were either kept stationary or subjected to several daily shakes for 5 wk, after which the transcriptomes and hormones were analyzed in the cambial region and developing wood tissues, and the wood properties were analyzed by physical, chemical and microscopy techniques. Shaking increased primary and secondary growth and altered wood differentiation by stimulating gelatinous-fiber formation, reducing secondary wall thickness, changing matrix polysaccharides and increasing cellulose, G- and H-lignin contents, cell wall porosity and saccharification yields. Wood-forming tissues exhibited elevated jasmonate, polyamine, ethylene and brassinosteroids and reduced abscisic acid and gibberellin signaling. Transcriptional responses resembled those during tension wood formation but not opposite wood formation and revealed several thigmomorphogenesis-related genes as well as novel gene networks including FLA and XTH genes encoding plasma membrane-bound proteins. Low-intensity stem flexing stimulates growth and induces wood having improved biorefinery properties through molecular and hormonal pathways similar to thigmomorphogenesis in herbaceous plants and largely overlapping with the tension wood program of hardwoods.},
	language = {en},
	urldate = {2023-10-20},
	journal = {New Phytologist},
	author = {Urbancsok, János and Donev, Evgeniy N. and Sivan, Pramod and van Zalen, Elena and Barbut, Félix R. and Derba-Maceluch, Marta and Šimura, Jan and Yassin, Zakiya and Gandla, Madhavi L. and Karady, Michal and Ljung, Karin and Winestrand, Sandra and Jönsson, Leif J. and Scheepers, Gerhard and Delhomme, Nicolas and Street, Nathaniel R. and Mellerowicz, Ewa J.},
	month = oct,
	year = {2023},
	note = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1111/nph.19307},
	keywords = {Populus tremula × tremuloides, flexure wood, jasmonic acid signaling, mechanostimulation, polyamines, saccharification, thigmomorphogenesis, wood development},
}

Stem bending in trees induces flexure wood but its properties and development are poorly understood. Here, we investigated the effects of low-intensity multidirectional stem flexing on growth and wood properties of hybrid aspen, and on its transcriptomic and hormonal responses. Glasshouse-grown trees were either kept stationary or subjected to several daily shakes for 5 wk, after which the transcriptomes and hormones were analyzed in the cambial region and developing wood tissues, and the wood properties were analyzed by physical, chemical and microscopy techniques. Shaking increased primary and secondary growth and altered wood differentiation by stimulating gelatinous-fiber formation, reducing secondary wall thickness, changing matrix polysaccharides and increasing cellulose, G- and H-lignin contents, cell wall porosity and saccharification yields. Wood-forming tissues exhibited elevated jasmonate, polyamine, ethylene and brassinosteroids and reduced abscisic acid and gibberellin signaling. Transcriptional responses resembled those during tension wood formation but not opposite wood formation and revealed several thigmomorphogenesis-related genes as well as novel gene networks including FLA and XTH genes encoding plasma membrane-bound proteins. Low-intensity stem flexing stimulates growth and induces wood having improved biorefinery properties through molecular and hormonal pathways similar to thigmomorphogenesis in herbaceous plants and largely overlapping with the tension wood program of hardwoods.

@article{nair_aswin_opening_2023,
	title = {Opening the gates},
	volume = {9},
	url = {https://www.nature.com/articles/s41477-023-01493-y},
	doi = {10.1038/s41477-023-01493-y},
	urldate = {2023-09-26},
	journal = {Nature Plants},
	author = {{Nair, Aswin} and {Bhalerao, Rishikesh P.}},
	month = sep,
	year = {2023},
	pages = {1375--1376},
}

@article{lee_regulation_2023,
	title = {Regulation of {Flowering} {Time} and {Other} {Developmental} {Plasticities} by 3’ {Splicing} {Factor}-{Mediated} {Alternative} {Splicing} in {Arabidopsis} thaliana},
	volume = {12},
	copyright = {http://creativecommons.org/licenses/by/3.0/},
	issn = {2223-7747},
	url = {https://www.mdpi.com/2223-7747/12/19/3508},
	doi = {10.3390/plants12193508},
	abstract = {Plants, as sessile organisms, show a high degree of plasticity in their growth and development and have various strategies to cope with these alterations under continuously changing environments and unfavorable stress conditions. In particular, the floral transition from the vegetative and reproductive phases in the shoot apical meristem (SAM) is one of the most important developmental changes in plants. In addition, meristem regions, such as the SAM and root apical meristem (RAM), which continually generate new lateral organs throughout the plant life cycle, are important sites for developmental plasticity. Recent findings have shown that the prevailing type of alternative splicing (AS) in plants is intron retention (IR) unlike in animals; thus, AS is an important regulatory mechanism conferring plasticity for plant growth and development under various environmental conditions. Although eukaryotes exhibit some similarities in the composition and dynamics of their splicing machinery, plants have differences in the 3’ splicing characteristics governing AS. Here, we summarize recent findings on the roles of 3’ splicing factors and their interacting partners in regulating the flowering time and other developmental plasticities in Arabidopsis thaliana.},
	language = {en},
	number = {19},
	urldate = {2023-10-20},
	journal = {Plants},
	author = {Lee, Keh Chien and Kim, Young-Cheon and Kim, Jeong-Kook and Lee, Horim and Lee, Jeong Hwan},
	month = oct,
	year = {2023},
	note = {Number: 19
Publisher: Multidisciplinary Digital Publishing Institute},
	keywords = {3’ splicing factors, alternative splicing, developmental plasticity, flowering time, root apical meristem, shoot apical meristem},
	pages = {3508},
}

Plants, as sessile organisms, show a high degree of plasticity in their growth and development and have various strategies to cope with these alterations under continuously changing environments and unfavorable stress conditions. In particular, the floral transition from the vegetative and reproductive phases in the shoot apical meristem (SAM) is one of the most important developmental changes in plants. In addition, meristem regions, such as the SAM and root apical meristem (RAM), which continually generate new lateral organs throughout the plant life cycle, are important sites for developmental plasticity. Recent findings have shown that the prevailing type of alternative splicing (AS) in plants is intron retention (IR) unlike in animals; thus, AS is an important regulatory mechanism conferring plasticity for plant growth and development under various environmental conditions. Although eukaryotes exhibit some similarities in the composition and dynamics of their splicing machinery, plants have differences in the 3’ splicing characteristics governing AS. Here, we summarize recent findings on the roles of 3’ splicing factors and their interacting partners in regulating the flowering time and other developmental plasticities in Arabidopsis thaliana.

@article{noren_lindback_interplay_2023,
	title = {An interplay between {bZIP16}, {bZIP68}, and {GBF1} regulates nuclear photosynthetic genes during photomorphogenesis in {Arabidopsis}},
	volume = {240},
	copyright = {© 2023 The Authors. New Phytologist © 2023 New Phytologist Foundation},
	issn = {1469-8137},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/nph.19219},
	doi = {10.1111/nph.19219},
	abstract = {The development of a seedling into a photosynthetically active plant is a crucial process. Despite its importance, we do not fully understand the regulatory mechanisms behind the establishment of functional chloroplasts. We herein provide new insight into the early light response by identifying the function of three basic region/leucine zipper (bZIP) transcription factors: bZIP16, bZIP68, and GBF1. These proteins are involved in the regulation of key components required for the establishment of photosynthetically active chloroplasts. The activity of these bZIPs is dependent on the redox status of a conserved cysteine residue, which provides a mechanism to finetune light-responsive gene expression. The blue light cryptochrome (CRY) photoreceptors provide one of the major light-signaling pathways, and bZIP target genes overlap with one-third of CRY-regulated genes with an enrichment for photosynthesis/chloroplast-associated genes. bZIP16, bZIP68, and GBF1 were demonstrated as novel interaction partners of CRY1. The interaction between CRY1 and bZIP16 was stimulated by blue light. Furthermore, we demonstrate a genetic link between the bZIP proteins and cryptochromes as the cry1cry2 mutant is epistatic to the cry1cry2bzip16bzip68gbf1 mutant. bZIP16, bZIP68, and GBF1 regulate a subset of photosynthesis associated genes in response to blue light critical for a proper greening process in Arabidopsis.},
	language = {en},
	number = {3},
	urldate = {2023-10-13},
	journal = {New Phytologist},
	author = {Norén Lindbäck, Louise and Ji, Yan and Cervela-Cardona, Luis and Jin, Xu and Pedmale, Ullas V. and Strand, Åsa},
	year = {2023},
	note = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1111/nph.19219},
	keywords = {Arabidopsis thaliana, bZIP, chloroplast development, cryptochrome, light signaling, photomorphogenesis},
	pages = {1082--1096},
}

The development of a seedling into a photosynthetically active plant is a crucial process. Despite its importance, we do not fully understand the regulatory mechanisms behind the establishment of functional chloroplasts. We herein provide new insight into the early light response by identifying the function of three basic region/leucine zipper (bZIP) transcription factors: bZIP16, bZIP68, and GBF1. These proteins are involved in the regulation of key components required for the establishment of photosynthetically active chloroplasts. The activity of these bZIPs is dependent on the redox status of a conserved cysteine residue, which provides a mechanism to finetune light-responsive gene expression. The blue light cryptochrome (CRY) photoreceptors provide one of the major light-signaling pathways, and bZIP target genes overlap with one-third of CRY-regulated genes with an enrichment for photosynthesis/chloroplast-associated genes. bZIP16, bZIP68, and GBF1 were demonstrated as novel interaction partners of CRY1. The interaction between CRY1 and bZIP16 was stimulated by blue light. Furthermore, we demonstrate a genetic link between the bZIP proteins and cryptochromes as the cry1cry2 mutant is epistatic to the cry1cry2bzip16bzip68gbf1 mutant. bZIP16, bZIP68, and GBF1 regulate a subset of photosynthesis associated genes in response to blue light critical for a proper greening process in Arabidopsis.

@article{choudhary_poplar_2023,
	series = {Special {Issue} on {Climate} {Change} and {Food} {Security}: {Plant} {Science} {Roles}},
	title = {Poplar wood - inside out: {High}-resolution spatial, cellular, and pseudotime projections from cambial transcriptomes},
	volume = {16},
	issn = {1674-2052},
	shorttitle = {Poplar wood - inside out},
	url = {https://www.sciencedirect.com/science/article/pii/S1674205223002794},
	doi = {10.1016/j.molp.2023.09.008},
	number = {10},
	urldate = {2023-10-06},
	journal = {Molecular Plant},
	author = {Choudhary, Shruti and Tuominen, Hannele},
	month = oct,
	year = {2023},
	pages = {1490--1492},
}

@article{wang_quantifying_2023,
	title = {Quantifying adaptive evolution and the effects of natural selection across the {Norway} spruce genome},
	volume = {32},
	copyright = {© 2023 The Authors. Molecular Ecology published by John Wiley \& Sons Ltd.},
	issn = {1365-294X},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/mec.17106},
	doi = {10.1111/mec.17106},
	abstract = {Detecting natural selection is one of the major goals of evolutionary genomics. Here, we sequenced the whole genome of 25 Picea abies individuals and quantified the amount of selection across the genome. Using an estimate of the distribution of fitness effects, we showed that both negative selection and the rate of positively selected substitutions are very limited in coding regions. We found a positive correlation between the rate of adaptive substitutions and recombination rate and a negative correlation between the rate of adaptive substitutions and gene density, suggesting a widespread influence from Hill–Robertson interference on the efficiency of protein adaptation in P. abies. Finally, the distinct population statistics between genomic regions under either positive or balancing selection with that under neutral regions indicated the impact of natural selection on the genomic architecture of Norway spruce. Further gene ontology enrichment analysis for genes located in regions identified as undergoing either positive or long-term balancing selection also highlighted the specific molecular functions and biological processes that appear to be targets of selection in Norway spruce.},
	language = {en},
	number = {19},
	urldate = {2023-09-29},
	journal = {Molecular Ecology},
	author = {Wang, Xi and Ingvarsson, Pär K.},
	month = sep,
	year = {2023},
	note = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1111/mec.17106},
	keywords = {Picea abies, balancing selection, negative selection, positive selection, whole-genome resequencing},
	pages = {5288--5304},
}

Detecting natural selection is one of the major goals of evolutionary genomics. Here, we sequenced the whole genome of 25 Picea abies individuals and quantified the amount of selection across the genome. Using an estimate of the distribution of fitness effects, we showed that both negative selection and the rate of positively selected substitutions are very limited in coding regions. We found a positive correlation between the rate of adaptive substitutions and recombination rate and a negative correlation between the rate of adaptive substitutions and gene density, suggesting a widespread influence from Hill–Robertson interference on the efficiency of protein adaptation in P. abies. Finally, the distinct population statistics between genomic regions under either positive or balancing selection with that under neutral regions indicated the impact of natural selection on the genomic architecture of Norway spruce. Further gene ontology enrichment analysis for genes located in regions identified as undergoing either positive or long-term balancing selection also highlighted the specific molecular functions and biological processes that appear to be targets of selection in Norway spruce.

@article{roychoudhry_antigravitropic_2023,
	title = {Antigravitropic {PIN} polarization maintains non-vertical growth in lateral roots},
	volume = {9},
	copyright = {2023 The Author(s)},
	issn = {2055-0278},
	url = {https://www.nature.com/articles/s41477-023-01478-x},
	doi = {10.1038/s41477-023-01478-x},
	abstract = {Lateral roots are typically maintained at non-vertical angles with respect to gravity. These gravitropic setpoint angles are intriguing because their maintenance requires that roots are able to effect growth response both with and against the gravity vector, a phenomenon previously attributed to gravitropism acting against an antigravitropic offset mechanism. Here we show how the components mediating gravitropism in the vertical primary root—PINs and phosphatases acting upon them—are reconfigured in their regulation such that lateral root growth at a range of angles can be maintained. We show that the ability of Arabidopsis lateral roots to bend both downward and upward requires the generation of auxin asymmetries and is driven by angle-dependent variation in downward gravitropic auxin flux acting against angle-independent upward, antigravitropic flux. Further, we demonstrate a symmetry in auxin distribution in lateral roots at gravitropic setpoint angle that can be traced back to a net, balanced polarization of PIN3 and PIN7 auxin transporters in the columella. These auxin fluxes are shifted by altering PIN protein phosphoregulation in the columella, either by introducing PIN3 phosphovariant versions or via manipulation of levels of the phosphatase subunit PP2A/RCN1. Finally, we show that auxin, in addition to driving lateral root directional growth, acts within the lateral root columella to induce more vertical growth by increasing RCN1 levels, causing a downward shift in PIN3 localization, thereby diminishing the magnitude of the upward, antigravitropic auxin flux.},
	language = {en},
	number = {9},
	urldate = {2023-09-29},
	journal = {Nature Plants},
	author = {Roychoudhry, Suruchi and Sageman-Furnas, Katelyn and Wolverton, Chris and Grones, Peter and Tan, Shutang and Molnár, Gergely and De Angelis, Martina and Goodman, Heather L. and Capstaff, Nicola and Lloyd, James P. B. and Mullen, Jack and Hangarter, Roger and Friml, Jiří and Kepinski, Stefan},
	month = sep,
	year = {2023},
	note = {Number: 9
Publisher: Nature Publishing Group},
	keywords = {Auxin, Plant morphogenesis},
	pages = {1500--1513},
}

Lateral roots are typically maintained at non-vertical angles with respect to gravity. These gravitropic setpoint angles are intriguing because their maintenance requires that roots are able to effect growth response both with and against the gravity vector, a phenomenon previously attributed to gravitropism acting against an antigravitropic offset mechanism. Here we show how the components mediating gravitropism in the vertical primary root—PINs and phosphatases acting upon them—are reconfigured in their regulation such that lateral root growth at a range of angles can be maintained. We show that the ability of Arabidopsis lateral roots to bend both downward and upward requires the generation of auxin asymmetries and is driven by angle-dependent variation in downward gravitropic auxin flux acting against angle-independent upward, antigravitropic flux. Further, we demonstrate a symmetry in auxin distribution in lateral roots at gravitropic setpoint angle that can be traced back to a net, balanced polarization of PIN3 and PIN7 auxin transporters in the columella. These auxin fluxes are shifted by altering PIN protein phosphoregulation in the columella, either by introducing PIN3 phosphovariant versions or via manipulation of levels of the phosphatase subunit PP2A/RCN1. Finally, we show that auxin, in addition to driving lateral root directional growth, acts within the lateral root columella to induce more vertical growth by increasing RCN1 levels, causing a downward shift in PIN3 localization, thereby diminishing the magnitude of the upward, antigravitropic auxin flux.

@article{bourdon_ectopic_2023,
	title = {Ectopic callose deposition into woody biomass modulates the nano-architecture of macrofibrils},
	volume = {9},
	copyright = {2023 The Author(s)},
	issn = {2055-0278},
	url = {https://www.nature.com/articles/s41477-023-01459-0},
	doi = {10.1038/s41477-023-01459-0},
	abstract = {Plant biomass plays an increasingly important role in the circular bioeconomy, replacing non-renewable fossil resources. Genetic engineering of this lignocellulosic biomass could benefit biorefinery transformation chains by lowering economic and technological barriers to industrial processing. However, previous efforts have mostly targeted the major constituents of woody biomass: cellulose, hemicellulose and lignin. Here we report the engineering of wood structure through the introduction of callose, a polysaccharide novel to most secondary cell walls. Our multiscale analysis of genetically engineered poplar trees shows that callose deposition modulates cell wall porosity, water and lignin contents and increases the lignin–cellulose distance, ultimately resulting in substantially decreased biomass recalcitrance. We provide a model of the wood cell wall nano-architecture engineered to accommodate the hydrated callose inclusions. Ectopic polymer introduction into biomass manifests in new physico-chemical properties and offers new avenues when considering lignocellulose engineering.},
	language = {en},
	number = {9},
	urldate = {2023-09-22},
	journal = {Nature Plants},
	author = {Bourdon, Matthieu and Lyczakowski, Jan J. and Cresswell, Rosalie and Amsbury, Sam and Vilaplana, Francisco and Le Guen, Marie-Joo and Follain, Nadège and Wightman, Raymond and Su, Chang and Alatorre-Cobos, Fulgencio and Ritter, Maximilian and Liszka, Aleksandra and Terrett, Oliver M. and Yadav, Shri Ram and Vatén, Anne and Nieminen, Kaisa and Eswaran, Gugan and Alonso-Serra, Juan and Müller, Karin H. and Iuga, Dinu and Miskolczi, Pal Csaba and Kalmbach, Lothar and Otero, Sofia and Mähönen, Ari Pekka and Bhalerao, Rishikesh and Bulone, Vincent and Mansfield, Shawn D. and Hill, Stefan and Burgert, Ingo and Beaugrand, Johnny and Benitez-Alfonso, Yoselin and Dupree, Ray and Dupree, Paul and Helariutta, Ykä},
	month = sep,
	year = {2023},
	note = {Number: 9
Publisher: Nature Publishing Group},
	keywords = {Biofuels, Molecular engineering in plants},
	pages = {1530--1546},
}

Plant biomass plays an increasingly important role in the circular bioeconomy, replacing non-renewable fossil resources. Genetic engineering of this lignocellulosic biomass could benefit biorefinery transformation chains by lowering economic and technological barriers to industrial processing. However, previous efforts have mostly targeted the major constituents of woody biomass: cellulose, hemicellulose and lignin. Here we report the engineering of wood structure through the introduction of callose, a polysaccharide novel to most secondary cell walls. Our multiscale analysis of genetically engineered poplar trees shows that callose deposition modulates cell wall porosity, water and lignin contents and increases the lignin–cellulose distance, ultimately resulting in substantially decreased biomass recalcitrance. We provide a model of the wood cell wall nano-architecture engineered to accommodate the hydrated callose inclusions. Ectopic polymer introduction into biomass manifests in new physico-chemical properties and offers new avenues when considering lignocellulose engineering.

@article{nagahage_nac_2023,
	title = {{NAC} domain transcription factors {VNI2} and {ATAF2} form protein complexes and regulate leaf senescence},
	volume = {7},
	copyright = {© 2023 The Authors. Plant Direct published by American Society of Plant Biologists and the Society for Experimental Biology and John Wiley \& Sons Ltd.},
	issn = {2475-4455},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1002/pld3.529},
	doi = {10.1002/pld3.529},
	abstract = {The NAM, ATAF1/2, and CUC2 (NAC) domain transcription factor VND-INTERACTING2 (VNI2) negatively regulates xylem vessel formation by interacting with another NAC domain transcription factor, VASCULAR-RELATED NAC-DOMAIN7 (VND7), a master regulator of xylem vessel formation. Here, we screened interacting proteins with VNI2 using yeast two-hybrid assay and isolated two NAC domain transcription factors, Arabidopsis thaliana ACTIVATION FACTOR 2 (ATAF2) and NAC DOMAIN CONTAINING PROTEIN 102 (ANAC102). A transient gene expression assay showed that ATAF2 upregulates the expression of genes involved in leaf senescence, and VNI2 effectively inhibits the transcriptional activation activity of ATAF2. vni2 mutants accelerate leaf senescence, whereas ataf2 mutants delay leaf senescence. In addition, the accelerated leaf senescence phenotype of the vni2 mutant is recovered by simultaneous mutation of ATAF2. Our findings strongly suggest that VNI2 interacts with and inhibits ATAF2, resulting in negatively regulating leaf senescence.},
	language = {en},
	number = {9},
	urldate = {2023-09-22},
	journal = {Plant Direct},
	author = {Nagahage, Isura Sumeda Priyadarshana and Matsuda, Kohei and Miyashita, Kyoko and Fujiwara, Sumire and Mannapperuma, Chanaka and Yamada, Takuya and Sakamoto, Shingo and Ishikawa, Toshiki and Nagano, Minoru and Ohtani, Misato and Kato, Ko and Uchimiya, Hirofumi and Mitsuda, Nobutaka and Kawai-Yamada, Maki and Demura, Taku and Yamaguchi, Masatoshi},
	month = sep,
	year = {2023},
	note = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1002/pld3.529},
	keywords = {Arabidopsis thaliana, NAC domain protein, leaf senescence, protein–protein interaction, transcription factor},
	pages = {e529},
}

The NAM, ATAF1/2, and CUC2 (NAC) domain transcription factor VND-INTERACTING2 (VNI2) negatively regulates xylem vessel formation by interacting with another NAC domain transcription factor, VASCULAR-RELATED NAC-DOMAIN7 (VND7), a master regulator of xylem vessel formation. Here, we screened interacting proteins with VNI2 using yeast two-hybrid assay and isolated two NAC domain transcription factors, Arabidopsis thaliana ACTIVATION FACTOR 2 (ATAF2) and NAC DOMAIN CONTAINING PROTEIN 102 (ANAC102). A transient gene expression assay showed that ATAF2 upregulates the expression of genes involved in leaf senescence, and VNI2 effectively inhibits the transcriptional activation activity of ATAF2. vni2 mutants accelerate leaf senescence, whereas ataf2 mutants delay leaf senescence. In addition, the accelerated leaf senescence phenotype of the vni2 mutant is recovered by simultaneous mutation of ATAF2. Our findings strongly suggest that VNI2 interacts with and inhibits ATAF2, resulting in negatively regulating leaf senescence.

@article{hoffmann_cauliflower_2023,
	title = {Cauliflower mosaic virus protein {P6} is a multivalent node for {RNA} granule proteins and interferes with stress granule responses during plant infection},
	volume = {35},
	issn = {1040-4651},
	url = {https://doi.org/10.1093/plcell/koad101},
	doi = {10.1093/plcell/koad101},
	abstract = {Biomolecular condensation is a multipurpose cellular process that viruses use ubiquitously during their multiplication. Cauliflower mosaic virus replication complexes are condensates that differ from those of most viruses, as they are nonmembranous assemblies that consist of RNA and protein, mainly the viral protein P6. Although these viral factories (VFs) were described half a century ago, with many observations that followed since, functional details of the condensation process and the properties and relevance of VFs have remained enigmatic. Here, we studied these issues in Arabidopsis thaliana and Nicotiana benthamiana. We observed a large dynamic mobility range of host proteins within VFs, while the viral matrix protein P6 is immobile, as it represents the central node of these condensates. We identified the stress granule (SG) nucleating factors G3BP7 and UBP1 family members as components of VFs. Similarly, as SG components localize to VFs during infection, ectopic P6 localizes to SGs and reduces their assembly after stress. Intriguingly, it appears that soluble rather than condensed P6 suppresses SG formation and mediates other essential P6 functions, suggesting that the increased condensation over the infection time-course may accompany a progressive shift in selected P6 functions. Together, this study highlights VFs as dynamic condensates and P6 as a complex modulator of SG responses.},
	number = {9},
	urldate = {2023-09-07},
	journal = {The Plant Cell},
	author = {Hoffmann, Gesa and López-González, Silvia and Mahboubi, Amir and Hanson, Johannes and Hafrén, Anders},
	month = sep,
	year = {2023},
	pages = {3363--3382},
}

Biomolecular condensation is a multipurpose cellular process that viruses use ubiquitously during their multiplication. Cauliflower mosaic virus replication complexes are condensates that differ from those of most viruses, as they are nonmembranous assemblies that consist of RNA and protein, mainly the viral protein P6. Although these viral factories (VFs) were described half a century ago, with many observations that followed since, functional details of the condensation process and the properties and relevance of VFs have remained enigmatic. Here, we studied these issues in Arabidopsis thaliana and Nicotiana benthamiana. We observed a large dynamic mobility range of host proteins within VFs, while the viral matrix protein P6 is immobile, as it represents the central node of these condensates. We identified the stress granule (SG) nucleating factors G3BP7 and UBP1 family members as components of VFs. Similarly, as SG components localize to VFs during infection, ectopic P6 localizes to SGs and reduces their assembly after stress. Intriguingly, it appears that soluble rather than condensed P6 suppresses SG formation and mediates other essential P6 functions, suggesting that the increased condensation over the infection time-course may accompany a progressive shift in selected P6 functions. Together, this study highlights VFs as dynamic condensates and P6 as a complex modulator of SG responses.

@article{zhao_development_2023,
	title = {Development of an {Advanced}-{Generation} {Multi}-{Objective} {Breeding} {Population} for the 4th {Cycle} of {Chinese} {Fir} ({Cunninghamia} lanceolata ({Lamb}.) {Hook}.)},
	volume = {14},
	copyright = {http://creativecommons.org/licenses/by/3.0/},
	issn = {1999-4907},
	url = {https://www.mdpi.com/1999-4907/14/8/1658},
	doi = {10.3390/f14081658},
	abstract = {Chinese fir (Cunninghamia lanceolata (Lamb.) Hook.) is an important timber species native to southern China. While the single, unstructured breeding strategy was employed in the past three cycles of breeding, it is no longer adequate for managing a more advanced breeding population. In this study, we utilized restriction-site-associated DNA-sequencing (RAD-seq) to estimate the genetic diversity of breeding populations and phenotypic values or breeding values to estimate the genetic gain of hundred-grain weight, diameter at breast height, and wood basic density. To achieve a balance between genetic gain and genetic diversity, we combined the multiple populations and core-main populations methods to construct the fourth cycle breeding population. Finally, the fourth cycle breeding population was made up of a core population of 50 individuals with an inbreeding coefficient of {\textasciitilde}0, and an additional main population of 183 individuals, with an effective population size of 108. Crossings made within and/or between different trait-targeted subpopulations could facilitate bidirectional gene flow between the core and main populations, depending on the breeding objectives. This structured breeding population of Chinese fir could aim for both short- and long-term genetic gains and has the potential to support the preservation of germplasm resources for future climate change.},
	language = {en},
	number = {8},
	urldate = {2023-09-06},
	journal = {Forests},
	author = {Zhao, Benwen and Bian, Liming and Feng, Qihang and Wu, Jinzhang and Zhang, Xuefeng and Zheng, Renhua and Zheng, Xueyan and Yang, Zhiyuan and Chen, Zhiqiang and Wu, Harry X. and Shi, Jisen},
	month = aug,
	year = {2023},
	note = {Number: 8
Publisher: Multidisciplinary Digital Publishing Institute},
	keywords = {Chinese fir, SNP, breeding population, genetic diversity, genetic gain},
	pages = {1658},
}

Chinese fir (Cunninghamia lanceolata (Lamb.) Hook.) is an important timber species native to southern China. While the single, unstructured breeding strategy was employed in the past three cycles of breeding, it is no longer adequate for managing a more advanced breeding population. In this study, we utilized restriction-site-associated DNA-sequencing (RAD-seq) to estimate the genetic diversity of breeding populations and phenotypic values or breeding values to estimate the genetic gain of hundred-grain weight, diameter at breast height, and wood basic density. To achieve a balance between genetic gain and genetic diversity, we combined the multiple populations and core-main populations methods to construct the fourth cycle breeding population. Finally, the fourth cycle breeding population was made up of a core population of 50 individuals with an inbreeding coefficient of ~0, and an additional main population of 183 individuals, with an effective population size of 108. Crossings made within and/or between different trait-targeted subpopulations could facilitate bidirectional gene flow between the core and main populations, depending on the breeding objectives. This structured breeding population of Chinese fir could aim for both short- and long-term genetic gains and has the potential to support the preservation of germplasm resources for future climate change.

@article{sagi-kazar_iron_2023,
	title = {Iron uptake of etioplasts is independent from photosynthesis but applies the reduction-based strategy},
	volume = {14},
	issn = {1664-462X},
	url = {https://www.frontiersin.org/articles/10.3389/fpls.2023.1227811},
	doi = {10.3389/fpls.2023.1227811},
	abstract = {IntroductionIron (Fe) is one of themost important cofactors in the photosynthetic apparatus, and its uptake by chloroplasts has also been associated with the operation of the photosynthetic electron transport chain during reduction-based plastidial Fe uptake. Therefore, plastidial Fe uptake was considered not to be operational in the absence of the photosynthetic activity. Nevertheless, Fe is also required for enzymatic functions unrelated to photosynthesis, highlighting the importance of Fe acquisition by non-photosynthetic plastids. Yet, it remains unclear how these plastids acquire Fe in the absence of photosynthetic function. Furthermore, plastids of etiolated tissues should already possess the ability to acquire Fe, since the biosynthesis of thylakoid membrane complexes requires a massive amount of readily available Fe. Thus, we aimed to investigate whether the reduction-based plastidial Fe uptake solely relies on the functioning photosynthetic apparatus.MethodsIn our combined structure, iron content and transcript amount analysis studies, we used Savoy cabbage plant as a model, which develops natural etiolation in the inner leaves of the heads due to the shading of the outer leaf layers.ResultsFoliar and plastidial Fe content of Savoy cabbage leaves decreased towards the inner leaf layers. The leaves of the innermost leaf layers proved to be etiolated, containing etioplasts that lacked the photosynthetic machinery and thus were photosynthetically inactive. However, we discovered that these etioplasts contained, and were able to take up, Fe. Although the relative transcript abundance of genes associated with plastidial Fe uptake and homeostasis decreased towards the inner leaf layers, both ferric chelate reductase FRO7 transcripts and activity were detected in the innermost leaf layer. Additionally, a significant NADP(H) pool and NAD(P)H dehydrogenase activity was detected in the etioplasts of the innermost leaf layer, indicating the presence of the reducing capacity that likely supports the reduction-based Fe uptake of etioplasts.DiscussionBased on these findings, the reduction-based plastidial Fe acquisition should not be considered exclusively dependent on the photosynthetic functions.},
	urldate = {2023-08-31},
	journal = {Frontiers in Plant Science},
	author = {Sági-Kazár, Máté and Sárvári, Éva and Cseh, Barnabás and Illés, Levente and May, Zoltán and Hegedűs, Csaba and Barócsi, Attila and Lenk, Sándor and Solymosi, Katalin and Solti, Ádám},
	month = aug,
	year = {2023},
}

IntroductionIron (Fe) is one of themost important cofactors in the photosynthetic apparatus, and its uptake by chloroplasts has also been associated with the operation of the photosynthetic electron transport chain during reduction-based plastidial Fe uptake. Therefore, plastidial Fe uptake was considered not to be operational in the absence of the photosynthetic activity. Nevertheless, Fe is also required for enzymatic functions unrelated to photosynthesis, highlighting the importance of Fe acquisition by non-photosynthetic plastids. Yet, it remains unclear how these plastids acquire Fe in the absence of photosynthetic function. Furthermore, plastids of etiolated tissues should already possess the ability to acquire Fe, since the biosynthesis of thylakoid membrane complexes requires a massive amount of readily available Fe. Thus, we aimed to investigate whether the reduction-based plastidial Fe uptake solely relies on the functioning photosynthetic apparatus.MethodsIn our combined structure, iron content and transcript amount analysis studies, we used Savoy cabbage plant as a model, which develops natural etiolation in the inner leaves of the heads due to the shading of the outer leaf layers.ResultsFoliar and plastidial Fe content of Savoy cabbage leaves decreased towards the inner leaf layers. The leaves of the innermost leaf layers proved to be etiolated, containing etioplasts that lacked the photosynthetic machinery and thus were photosynthetically inactive. However, we discovered that these etioplasts contained, and were able to take up, Fe. Although the relative transcript abundance of genes associated with plastidial Fe uptake and homeostasis decreased towards the inner leaf layers, both ferric chelate reductase FRO7 transcripts and activity were detected in the innermost leaf layer. Additionally, a significant NADP(H) pool and NAD(P)H dehydrogenase activity was detected in the etioplasts of the innermost leaf layer, indicating the presence of the reducing capacity that likely supports the reduction-based Fe uptake of etioplasts.DiscussionBased on these findings, the reduction-based plastidial Fe acquisition should not be considered exclusively dependent on the photosynthetic functions.

@article{boussardon_comparison_2023,
	title = {Comparison of plastid proteomes points towards a higher plastidial redox turnover in vascular tissues than in mesophyll cells},
	volume = {74},
	issn = {0022-0957},
	url = {https://doi.org/10.1093/jxb/erad133},
	doi = {10.1093/jxb/erad133},
	abstract = {Plastids are complex organelles that vary in size and function depending on the cell type. Accordingly, they can be referred to as amyloplasts, chloroplasts, chromoplasts, etioplasts, or proplasts, to only cite a few. Over the past decades, methods based on density gradients and differential centrifugation have been extensively used for the purification of plastids. However, these methods need large amounts of starting material, and hardly provide a tissue-specific resolution. Here, we applied our IPTACT (Isolation of Plastids TAgged in specific Cell Types) method, which involves the biotinylation of plastids in vivo using one-shot transgenic lines expressing the Translocon of the Outer Membrane 64 (TOC64) gene coupled with a biotin ligase receptor particle and the BirA biotin ligase, to isolate plastids from mesophyll and companion cells of Arabidopsis using tissue specific pCAB3 and pSUC2 promoters, respectively. Subsequently, a proteome profiling was performed, which allowed the identification of 1672 proteins, among which 1342 were predicted to be plastidial, and 705 were fully confirmed according to the SUBA5 database. Interestingly, although 92\% of plastidial proteins were equally distributed between the two tissues, we observed an accumulation of proteins associated with jasmonic acid biosynthesis, plastoglobuli (e.g. NAD(P)H dehydrogenase C1, vitamin E deficient 1, plastoglobulin of 34 kDa, ABC1-like kinase 1) and cyclic electron flow in plastids originating from vascular tissue. Besides demonstrating the technical feasibility of isolating plastids in a tissue-specific manner, our work provides strong evidence that plastids from vascular tissue have a higher redox turnover to ensure optimal functioning, notably under high solute strength as encountered in vascular cells.},
	number = {14},
	urldate = {2023-08-31},
	journal = {Journal of Experimental Botany},
	author = {Boussardon, Clément and Carrie, Chris and Keech, Olivier},
	month = aug,
	year = {2023},
	pages = {4110--4124},
}

Plastids are complex organelles that vary in size and function depending on the cell type. Accordingly, they can be referred to as amyloplasts, chloroplasts, chromoplasts, etioplasts, or proplasts, to only cite a few. Over the past decades, methods based on density gradients and differential centrifugation have been extensively used for the purification of plastids. However, these methods need large amounts of starting material, and hardly provide a tissue-specific resolution. Here, we applied our IPTACT (Isolation of Plastids TAgged in specific Cell Types) method, which involves the biotinylation of plastids in vivo using one-shot transgenic lines expressing the Translocon of the Outer Membrane 64 (TOC64) gene coupled with a biotin ligase receptor particle and the BirA biotin ligase, to isolate plastids from mesophyll and companion cells of Arabidopsis using tissue specific pCAB3 and pSUC2 promoters, respectively. Subsequently, a proteome profiling was performed, which allowed the identification of 1672 proteins, among which 1342 were predicted to be plastidial, and 705 were fully confirmed according to the SUBA5 database. Interestingly, although 92% of plastidial proteins were equally distributed between the two tissues, we observed an accumulation of proteins associated with jasmonic acid biosynthesis, plastoglobuli (e.g. NAD(P)H dehydrogenase C1, vitamin E deficient 1, plastoglobulin of 34 kDa, ABC1-like kinase 1) and cyclic electron flow in plastids originating from vascular tissue. Besides demonstrating the technical feasibility of isolating plastids in a tissue-specific manner, our work provides strong evidence that plastids from vascular tissue have a higher redox turnover to ensure optimal functioning, notably under high solute strength as encountered in vascular cells.

@article{jourquin_golven_2023,
	title = {{GOLVEN} peptides regulate lateral root spacing as part of a negative feedback loop on the establishment of auxin maxima},
	volume = {74},
	issn = {0022-0957},
	url = {https://doi.org/10.1093/jxb/erad123},
	doi = {10.1093/jxb/erad123},
	abstract = {Lateral root initiation requires the accumulation of auxin in lateral root founder cells, yielding a local auxin maximum. The positioning of auxin maxima along the primary root determines the density and spacing of lateral roots. The GOLVEN6 (GLV6) and GLV10 signaling peptides and their receptors have been established as regulators of lateral root spacing via their inhibitory effect on lateral root initiation in Arabidopsis. However, it was unclear how these GLV peptides interfere with auxin signaling or homeostasis. Here, we show that GLV6/10 signaling regulates the expression of a subset of auxin response genes, downstream of the canonical auxin signaling pathway, while simultaneously inhibiting the establishment of auxin maxima within xylem-pole pericycle cells that neighbor lateral root initiation sites. We present genetic evidence that this inhibitory effect relies on the activity of the PIN3 and PIN7 auxin export proteins. Furthermore, GLV6/10 peptide signaling was found to enhance PIN7 abundance in the plasma membranes of xylem-pole pericycle cells, which likely stimulates auxin efflux from these cells. Based on these findings, we propose a model in which the GLV6/10 signaling pathway serves as a negative feedback mechanism that contributes to the robust patterning of auxin maxima along the primary root.},
	number = {14},
	urldate = {2023-08-31},
	journal = {Journal of Experimental Botany},
	author = {Jourquin, Joris and Fernandez, Ana Ibis and Wang, Qing and Xu, Ke and Chen, Jian and Šimura, Jan and Ljung, Karin and Vanneste, Steffen and Beeckman, Tom},
	month = aug,
	year = {2023},
	pages = {4031--4049},
}

Lateral root initiation requires the accumulation of auxin in lateral root founder cells, yielding a local auxin maximum. The positioning of auxin maxima along the primary root determines the density and spacing of lateral roots. The GOLVEN6 (GLV6) and GLV10 signaling peptides and their receptors have been established as regulators of lateral root spacing via their inhibitory effect on lateral root initiation in Arabidopsis. However, it was unclear how these GLV peptides interfere with auxin signaling or homeostasis. Here, we show that GLV6/10 signaling regulates the expression of a subset of auxin response genes, downstream of the canonical auxin signaling pathway, while simultaneously inhibiting the establishment of auxin maxima within xylem-pole pericycle cells that neighbor lateral root initiation sites. We present genetic evidence that this inhibitory effect relies on the activity of the PIN3 and PIN7 auxin export proteins. Furthermore, GLV6/10 peptide signaling was found to enhance PIN7 abundance in the plasma membranes of xylem-pole pericycle cells, which likely stimulates auxin efflux from these cells. Based on these findings, we propose a model in which the GLV6/10 signaling pathway serves as a negative feedback mechanism that contributes to the robust patterning of auxin maxima along the primary root.

@article{farag_macrophage_2023,
	title = {Macrophage innate immune responses delineate between defective translocon assemblies produced by {Yersinia} pseudotuberculosis {YopD} mutants},
	volume = {14},
	issn = {2150-5594},
	url = {https://doi.org/10.1080/21505594.2023.2249790},
	doi = {10.1080/21505594.2023.2249790},
	abstract = {Translocon pores formed in the eukaryotic cell membrane by a type III secretion system facilitate the translocation of immune-modulatory effector proteins into the host cell interior. The YopB and YopD proteins produced and secreted by pathogenic Yersinia spp. harboring a virulence plasmid-encoded type III secretion system perform this pore-forming translocator function. We had previously characterized in vitro T3SS function and in vivo pathogenicity of a number of strains encoding sited-directed point mutations in yopD. This resulted in the classification of mutants into three different classes based upon the severity of the phenotypic defects. To investigate the molecular and functional basis for these defects, we explored the effectiveness of RAW 264.7 cell line to respond to infection by representative YopD mutants of all three classes. Signature cytokine profiles could separate the different YopD mutants into distinct categories. The activation and suppression of certain cytokines that function as central innate immune response modulators correlated well with the ability of mutant bacteria to alter anti-phagocytosis and programmed cell death pathways. These analyses demonstrated that sub-optimal translocon pores impact the extent and magnitude of host cell responsiveness, and this limits the capacity of pathogenic Yersinia spp. to fortify against attack by both early and late arms of the host innate immune response.},
	number = {1},
	urldate = {2023-08-31},
	journal = {Virulence},
	author = {Farag, Salah I. and Francis, Monika K. and Gurung, Jyoti M. and Wai, Sun Nyunt and Stenlund, Hans and Francis, Matthew S. and Nadeem, Aftab},
	month = aug,
	year = {2023},
	pmid = {37621095},
	note = {Publisher: Taylor \& Francis
\_eprint: https://doi.org/10.1080/21505594.2023.2249790},
	keywords = {Cytokine profiling, anti-phagocytosis, bacteria-eukaryotic cell contact, inflammasome, programmed cell death, translocon complexes},
	pages = {2249790},
}

Translocon pores formed in the eukaryotic cell membrane by a type III secretion system facilitate the translocation of immune-modulatory effector proteins into the host cell interior. The YopB and YopD proteins produced and secreted by pathogenic Yersinia spp. harboring a virulence plasmid-encoded type III secretion system perform this pore-forming translocator function. We had previously characterized in vitro T3SS function and in vivo pathogenicity of a number of strains encoding sited-directed point mutations in yopD. This resulted in the classification of mutants into three different classes based upon the severity of the phenotypic defects. To investigate the molecular and functional basis for these defects, we explored the effectiveness of RAW 264.7 cell line to respond to infection by representative YopD mutants of all three classes. Signature cytokine profiles could separate the different YopD mutants into distinct categories. The activation and suppression of certain cytokines that function as central innate immune response modulators correlated well with the ability of mutant bacteria to alter anti-phagocytosis and programmed cell death pathways. These analyses demonstrated that sub-optimal translocon pores impact the extent and magnitude of host cell responsiveness, and this limits the capacity of pathogenic Yersinia spp. to fortify against attack by both early and late arms of the host innate immune response.

@article{topcu_growths_2023,
	title = {Growth’s secret maestros: {LBD11}–{ROS} harmony drives vascular cambium activity in {Arabidopsis}},
	volume = {16},
	issn = {1674-2052},
	shorttitle = {Growth’s secret maestros},
	url = {https://www.cell.com/molecular-plant/abstract/S1674-2052(23)00214-9},
	doi = {10.1016/j.molp.2023.07.012},
	abstract = {Integration of metabolic products such as reactive oxygen species (ROS) into vital
processes play essential roles in plants. ROS refers to oxygen-derived free radicals,
which exhibit a higher reactivity compared to the diatomic oxygen molecule (O2) (Waszczak
et al., 2018). Numerous forms of ROS have been identified in plants with various degrees
of stability: singlet oxygen (1O2), superoxide anion (O2·−), hydrogen peroxide (H2O2),
and hydroxyl radical (HO·) are the major forms. ROS are generated during normal plant
growth as products of aerobic metabolism in almost all cellular compartments, including
chloroplasts, mitochondria, and peroxisomes as well as in apoplast.},
	language = {English},
	number = {8},
	urldate = {2023-08-28},
	journal = {Molecular Plant},
	author = {Topcu, Melis Kucukoglu and Bhalerao, Rishikesh P.},
	month = aug,
	year = {2023},
	pmid = {37528579},
	note = {Publisher: Elsevier},
	pages = {1246--1248},
}

Integration of metabolic products such as reactive oxygen species (ROS) into vital processes play essential roles in plants. ROS refers to oxygen-derived free radicals, which exhibit a higher reactivity compared to the diatomic oxygen molecule (O2) (Waszczak et al., 2018). Numerous forms of ROS have been identified in plants with various degrees of stability: singlet oxygen (1O2), superoxide anion (O2·−), hydrogen peroxide (H2O2), and hydroxyl radical (HO·) are the major forms. ROS are generated during normal plant growth as products of aerobic metabolism in almost all cellular compartments, including chloroplasts, mitochondria, and peroxisomes as well as in apoplast.

@article{le_vitro_2023,
	title = {In {Vitro} {Propagation} of the {Blueberry} ‘{Blue} {Suede}™’ ({Vaccinium} hybrid) in {Semi}-{Solid} {Medium} and {Temporary} {Immersion} {Bioreactors}},
	volume = {12},
	copyright = {http://creativecommons.org/licenses/by/3.0/},
	issn = {2223-7747},
	url = {https://www.mdpi.com/2223-7747/12/15/2752},
	doi = {10.3390/plants12152752},
	abstract = {The production of blueberries for fresh and processed consumption is increasing globally and has more than doubled in the last decade. Blueberry is grown commercially across a variety of climates in over 30 countries. The major classes of plants utilized for the planting and breeding of new cultivars are highbush, lowbush, half-high, Rabbiteye, and Southern highbush. Plants can be propagated by cuttings or in vitro micropropagation techniques. In vitro propagation offers advantages for faster generation of a large number of disease-free plants independent of season. Labor costs for in vitro propagation can be reduced using new cultivation technology and automation. Here, we test and demonstrate successful culture conditions and medium compositions for in vitro initiation, multiplication, and rooting of the Southern highbush cultivar ‘Blue Suede™’ (Vaccinium hybrid).},
	language = {en},
	number = {15},
	urldate = {2023-08-21},
	journal = {Plants},
	author = {Le, Kim-Cuong and Johnson, Shannon and Aidun, Cyrus K. and Egertsdotter, Ulrika},
	month = jul,
	year = {2023},
	note = {Number: 15
Publisher: Multidisciplinary Digital Publishing Institute},
	keywords = {blueberry, micropropagation, temporary immersion bioreactor, ‘Blue Suede™’ (\textit{Vaccinium} hybrid)},
	pages = {2752},
}

The production of blueberries for fresh and processed consumption is increasing globally and has more than doubled in the last decade. Blueberry is grown commercially across a variety of climates in over 30 countries. The major classes of plants utilized for the planting and breeding of new cultivars are highbush, lowbush, half-high, Rabbiteye, and Southern highbush. Plants can be propagated by cuttings or in vitro micropropagation techniques. In vitro propagation offers advantages for faster generation of a large number of disease-free plants independent of season. Labor costs for in vitro propagation can be reduced using new cultivation technology and automation. Here, we test and demonstrate successful culture conditions and medium compositions for in vitro initiation, multiplication, and rooting of the Southern highbush cultivar ‘Blue Suede™’ (Vaccinium hybrid).

@article{guo_genomic_2023,
	title = {Genomic clines across the species boundary between a hybrid pine and its progenitor in the eastern {Tibetan} {Plateau}},
	volume = {4},
	issn = {2590-3462},
	url = {https://www.sciencedirect.com/science/article/pii/S259034622300072X},
	doi = {10.1016/j.xplc.2023.100574},
	abstract = {Most species have clearly defined distribution ranges and ecological niches. The genetic and ecological causes of species differentiation and the mechanisms that maintain species boundaries between newly evolved taxa and their progenitors are, however, less clearly defined. This study investigated the genetic structure and clines in Pinus densata, a pine of hybrid origin on the southeastern Tibetan Plateau, to gain an understanding of the contemporary dynamics of species barriers. We analyzed genetic diversity in a range-wide collection of P. densata and representative populations of its progenitors, Pinus tabuliformis and Pinus yunnanensis, using exome capture sequencing. We detected four distinct genetic groups within P. densata that reflect its migration history and major gene-flow barriers across the landscape. The demographies of these genetic groups in the Pleistocene were associated with regional glaciation histories. Interestingly, population sizes rebounded rapidly during interglacial periods, suggesting persistence and resilience of the species during the Quaternary ice age. In the contact zone between P. densata and P. yunnanensis, 3.36\% of the analyzed loci (57 849) showed exceptional patterns of introgression, suggesting their potential roles in either adaptive introgression or reproductive isolation. These outliers showed strong clines along critical climate gradients and enrichment in a number of biological processes relevant to high-altitude adaptation. This indicates that ecological selection played an important role in generating genomic heterogeneity and a genetic barrier across a zone of species transition. Our study highlights the forces that operate to maintain species boundaries and promote speciation in the Qinghai-Tibetan Plateau and other mountain systems.},
	number = {4},
	urldate = {2023-08-24},
	journal = {Plant Communications},
	author = {Guo, Jing-Fang and Zhao, Wei and Andersson, Bea and Mao, Jian-Feng and Wang, Xiao-Ru},
	month = jul,
	year = {2023},
	keywords = {demographic history, ecological selection, genomic cline, introgression outliers, reproductive isolation, species boundary},
	pages = {100574},
}

Most species have clearly defined distribution ranges and ecological niches. The genetic and ecological causes of species differentiation and the mechanisms that maintain species boundaries between newly evolved taxa and their progenitors are, however, less clearly defined. This study investigated the genetic structure and clines in Pinus densata, a pine of hybrid origin on the southeastern Tibetan Plateau, to gain an understanding of the contemporary dynamics of species barriers. We analyzed genetic diversity in a range-wide collection of P. densata and representative populations of its progenitors, Pinus tabuliformis and Pinus yunnanensis, using exome capture sequencing. We detected four distinct genetic groups within P. densata that reflect its migration history and major gene-flow barriers across the landscape. The demographies of these genetic groups in the Pleistocene were associated with regional glaciation histories. Interestingly, population sizes rebounded rapidly during interglacial periods, suggesting persistence and resilience of the species during the Quaternary ice age. In the contact zone between P. densata and P. yunnanensis, 3.36% of the analyzed loci (57 849) showed exceptional patterns of introgression, suggesting their potential roles in either adaptive introgression or reproductive isolation. These outliers showed strong clines along critical climate gradients and enrichment in a number of biological processes relevant to high-altitude adaptation. This indicates that ecological selection played an important role in generating genomic heterogeneity and a genetic barrier across a zone of species transition. Our study highlights the forces that operate to maintain species boundaries and promote speciation in the Qinghai-Tibetan Plateau and other mountain systems.

@article{hao_simple_2023,
	title = {A {Simple} {Sonication} {Method} to {Isolate} the {Chloroplast} {Lumen} in {Arabidopsis} thaliana},
	volume = {13},
	url = {https://bio-protocol.org/en/bpdetail?id=4756&type=0},
	doi = {10.21769/BioProtoc.4756},
	abstract = {The chloroplast lumen contains at least 80 proteins whose function and regulation are not yet fully understood. Isolating the chloroplast lumen enables the characterization of the lumenal proteins. The lumen can be isolated in several ways through thylakoid disruption using a Yeda press or sonication, or through thylakoid solubilization using a detergent. Here, we present a simple procedure to isolate thylakoid lumen by sonication using leaves of the plant Arabidopsis thaliana. The step-by-step procedure is as follows: thylakoids are isolated from chloroplasts, loosely associated thylakoid surface proteins from the stroma are removed, and the lumen fraction is collected in the supernatant following sonication and centrifugation. Compared to other procedures, this method is easy to implement and saves time, plant material, and cost. Lumenal proteins are obtained in high quantity and purity; however, some stromal membrane–associated proteins are released to the lumen fraction, so this method could be further adapted if needed by decreasing sonication power and/or time.},
	language = {en},
	number = {15},
	urldate = {2023-08-21},
	journal = {Bio-protocol},
	author = {Hao, Jingfang and Malnoë, Alizée},
	month = aug,
	year = {2023},
	pages = {4756},
}

The chloroplast lumen contains at least 80 proteins whose function and regulation are not yet fully understood. Isolating the chloroplast lumen enables the characterization of the lumenal proteins. The lumen can be isolated in several ways through thylakoid disruption using a Yeda press or sonication, or through thylakoid solubilization using a detergent. Here, we present a simple procedure to isolate thylakoid lumen by sonication using leaves of the plant Arabidopsis thaliana. The step-by-step procedure is as follows: thylakoids are isolated from chloroplasts, loosely associated thylakoid surface proteins from the stroma are removed, and the lumen fraction is collected in the supernatant following sonication and centrifugation. Compared to other procedures, this method is easy to implement and saves time, plant material, and cost. Lumenal proteins are obtained in high quantity and purity; however, some stromal membrane–associated proteins are released to the lumen fraction, so this method could be further adapted if needed by decreasing sonication power and/or time.

@incollection{riechmann_isolation_2023,
	address = {New York, NY},
	title = {Isolation of {Nuclei} {Tagged} in {Specific} {Cell} {Types} ({INTACT}) in {Arabidopsis}},
	volume = {2686},
	isbn = {978-1-07-163298-7 978-1-07-163299-4},
	url = {https://link.springer.com/10.1007/978-1-0716-3299-4_16},
	abstract = {Many functionally distinct plant tissues have relatively low numbers of cells that are embedded within complex tissues. For example, the shoot apical meristem (SAM) consists of a small population of pluripotent stem cells surrounded by developing leaves and/or flowers at the growing tip of the plant. It is technically challenging to collect enough high-quality SAM samples for molecular analyses. Isolation of Nuclei Tagged in specific Cell Types (INTACT) is an easily reproducible method that allows the enrichment of biotin-tagged cell-type-specific nuclei from the total nuclei pool using biotin-streptavidin affinity purification. Here, we provide a detailed INTACT protocol for isolating nuclei from the Arabidopsis SAM. One can also adapt this protocol to isolate nuclei from other tissues and cell types for investigating tissue/cell-type-specific transcriptome and epigenome and their changes during developmental programs at a high spatiotemporal resolution. Furthermore, due to its low cost and simple procedures, INTACT can be conducted in any standard molecular laboratory.},
	language = {en},
	urldate = {2023-08-14},
	booktitle = {Flower {Development}},
	author = {Benstein, Ruben M. and Schmid, Markus and You, Yuan},
	editor = {Riechmann, José Luis and Ferrándiz, Cristina},
	month = jan,
	year = {2023},
	doi = {10.1007/978-1-0716-3299-4_16},
	note = {Series Title: Methods in Molecular Biology},
	pages = {313--328},
}

Many functionally distinct plant tissues have relatively low numbers of cells that are embedded within complex tissues. For example, the shoot apical meristem (SAM) consists of a small population of pluripotent stem cells surrounded by developing leaves and/or flowers at the growing tip of the plant. It is technically challenging to collect enough high-quality SAM samples for molecular analyses. Isolation of Nuclei Tagged in specific Cell Types (INTACT) is an easily reproducible method that allows the enrichment of biotin-tagged cell-type-specific nuclei from the total nuclei pool using biotin-streptavidin affinity purification. Here, we provide a detailed INTACT protocol for isolating nuclei from the Arabidopsis SAM. One can also adapt this protocol to isolate nuclei from other tissues and cell types for investigating tissue/cell-type-specific transcriptome and epigenome and their changes during developmental programs at a high spatiotemporal resolution. Furthermore, due to its low cost and simple procedures, INTACT can be conducted in any standard molecular laboratory.

@article{bizjak_presence_2023,
	title = {Presence and activity of nitrogen-fixing bacteria in {Scots} pine needles in a boreal forest: a nitrogen-addition experiment},
	volume = {43},
	issn = {1758-4469},
	shorttitle = {Presence and activity of nitrogen-fixing bacteria in {Scots} pine needles in a boreal forest},
	url = {https://doi.org/10.1093/treephys/tpad048},
	doi = {10.1093/treephys/tpad048},
	abstract = {Endophytic nitrogen-fixing bacteria have been detected and isolated from the needles of conifer trees growing in North American boreal forests. Because boreal forests are nutrient-limited, these bacteria could provide an important source of nitrogen for tree species. This study aimed to determine their presence and activity in a Scandinavian boreal forest, using immunodetection of nitrogenase enzyme subunits and acetylene-reduction assays of native Scots pine (Pinus sylvestris L.) needles. The presence and rate of nitrogen fixation by endophytic bacteria were compared between control plots and fertilized plots in a nitrogen-addition experiment. In contrast to the expectation that nitrogen-fixation rates would decline in fertilized plots, as seen, for instance, with nitrogen-fixing bacteria associated with bryophytes, there was no difference in the presence or activity of nitrogen-fixing bacteria between the two treatments. The extrapolated calculated rate of nitrogen fixation relevant for the forest stand was 20 g N ha−1 year−1, which is rather low compared with Scots pine annual nitrogen use but could be important for the nitrogen-poor forest in the long term. In addition, of 13 colonies of potential nitrogen-fixing bacteria isolated from the needles on nitrogen-free media, 10 showed in vitro nitrogen fixation. In summary, 16S rRNA sequencing identified the species as belonging to the genera Bacillus, Variovorax, Novosphingobium, Sphingomonas, Microbacterium and Priestia, which was confirmed by Illumina whole-genome sequencing. Our results confirm the presence of endophytic nitrogen-fixing bacteria in Scots pine needles and suggest that they could be important for the long-term nitrogen budget of the Scandinavian boreal forest.},
	number = {8},
	urldate = {2023-08-21},
	journal = {Tree Physiology},
	author = {Bizjak, Tinkara and Sellstedt, Anita and Gratz, Regina and Nordin, Annika},
	month = aug,
	year = {2023},
	pages = {1354--1364},
}

Endophytic nitrogen-fixing bacteria have been detected and isolated from the needles of conifer trees growing in North American boreal forests. Because boreal forests are nutrient-limited, these bacteria could provide an important source of nitrogen for tree species. This study aimed to determine their presence and activity in a Scandinavian boreal forest, using immunodetection of nitrogenase enzyme subunits and acetylene-reduction assays of native Scots pine (Pinus sylvestris L.) needles. The presence and rate of nitrogen fixation by endophytic bacteria were compared between control plots and fertilized plots in a nitrogen-addition experiment. In contrast to the expectation that nitrogen-fixation rates would decline in fertilized plots, as seen, for instance, with nitrogen-fixing bacteria associated with bryophytes, there was no difference in the presence or activity of nitrogen-fixing bacteria between the two treatments. The extrapolated calculated rate of nitrogen fixation relevant for the forest stand was 20 g N ha−1 year−1, which is rather low compared with Scots pine annual nitrogen use but could be important for the nitrogen-poor forest in the long term. In addition, of 13 colonies of potential nitrogen-fixing bacteria isolated from the needles on nitrogen-free media, 10 showed in vitro nitrogen fixation. In summary, 16S rRNA sequencing identified the species as belonging to the genera Bacillus, Variovorax, Novosphingobium, Sphingomonas, Microbacterium and Priestia, which was confirmed by Illumina whole-genome sequencing. Our results confirm the presence of endophytic nitrogen-fixing bacteria in Scots pine needles and suggest that they could be important for the long-term nitrogen budget of the Scandinavian boreal forest.

@article{hall_effect_2023,
	title = {The effect of gene flow on frost tolerance in {Scots} pine – {Latitudinal} translocation of genetic material},
	volume = {544},
	issn = {0378-1127},
	url = {https://www.sciencedirect.com/science/article/pii/S0378112723004498},
	doi = {10.1016/j.foreco.2023.121215},
	abstract = {Extensive gene flow can be detrimental to local adaptation and similarly, forestry seed sources such as seed orchards can be heavily influenced by external pollination, especially if the orchard material has been translocated a great distance. Here we conducted a coordinated genotyping-phenotyping study to examine how external pollination events and fecundity variation in a Pinus sylvestris seed orchard influence the genetic composition and the seed-lots’ autumn frost hardiness when genetic material had been translocated 630 km south. The results were then compared to those of a in situ established seed orchard. We genotyped and phenotype {\textgreater}1000 seedlings from these orchards, and constructed their pedigrees and scored their autumn frost tolerance in a controlled climate chamber environment. The hardiness scores were compared with a reference of nine natural stands along a latitudinal cline. We find substantial variation in fecundity and external pollination over crop years, thus unpredictable genetic composition because the contribution of some orchard clones is high in one crop but low in another. We observed that seedlings produced by mating among orchard genotypes were less hardy than expected (corresponding to an origin of −0.6°N) but the opposite in externally pollinated seedlings (+0.3 to +0.7°N). The freeze damage levels reflect the origin of parental genotypes, but to a smaller degree than expected (13\% lower than expected damage levels for externally pollinate seedlings and 21\% greater damage levels for internally pollinates seedlings). These results suggest that orchard parents’ origins, mating composition and orchard local environment could all affect the seed crops’ quality and their climate adaptation. Seed orchard crops are the key to realize the gain in forestry from breeding efforts. However, genetic monitoring of seed crops is necessary to improve the performance of seed orchards further and adjust deployment areas of seed crops in a timely manner for a more dynamic forestry, considering climate change and biodiversity demands.},
	urldate = {2023-08-21},
	journal = {Forest Ecology and Management},
	author = {Hall, David and Zhao, Wei and Heuchel, Alisa and Gao, Jie and Wennström, Ulfstand and Wang, Xiao-Ru},
	month = sep,
	year = {2023},
	keywords = {Cold hardiness, External pollination, Genetic composition, Pollen contamination, Scots pine, Seed orchard crops},
	pages = {121215},
}

Extensive gene flow can be detrimental to local adaptation and similarly, forestry seed sources such as seed orchards can be heavily influenced by external pollination, especially if the orchard material has been translocated a great distance. Here we conducted a coordinated genotyping-phenotyping study to examine how external pollination events and fecundity variation in a Pinus sylvestris seed orchard influence the genetic composition and the seed-lots’ autumn frost hardiness when genetic material had been translocated 630 km south. The results were then compared to those of a in situ established seed orchard. We genotyped and phenotype \textgreater1000 seedlings from these orchards, and constructed their pedigrees and scored their autumn frost tolerance in a controlled climate chamber environment. The hardiness scores were compared with a reference of nine natural stands along a latitudinal cline. We find substantial variation in fecundity and external pollination over crop years, thus unpredictable genetic composition because the contribution of some orchard clones is high in one crop but low in another. We observed that seedlings produced by mating among orchard genotypes were less hardy than expected (corresponding to an origin of −0.6°N) but the opposite in externally pollinated seedlings (+0.3 to +0.7°N). The freeze damage levels reflect the origin of parental genotypes, but to a smaller degree than expected (13% lower than expected damage levels for externally pollinate seedlings and 21% greater damage levels for internally pollinates seedlings). These results suggest that orchard parents’ origins, mating composition and orchard local environment could all affect the seed crops’ quality and their climate adaptation. Seed orchard crops are the key to realize the gain in forestry from breeding efforts. However, genetic monitoring of seed crops is necessary to improve the performance of seed orchards further and adjust deployment areas of seed crops in a timely manner for a more dynamic forestry, considering climate change and biodiversity demands.

@article{zacharaki_non-coding_2023,
	title = {The non-coding {RNA} {SVALKA} locus produces a cis-natural antisense transcript that negatively regulates the expression of {CBF1} and biomass production at normal temperatures},
	volume = {4},
	issn = {2590-3462},
	url = {https://www.sciencedirect.com/science/article/pii/S2590346223000494},
	doi = {10.1016/j.xplc.2023.100551},
	abstract = {Non-coding transcription is present in all eukaryotic genomes, but we lack fundamental knowledge about its importance for an organism’s ability to develop properly. In plants, emerging evidence highlights the essential biological role of non-coding transcription in the regulation of coding transcription. However, we have few molecular insights into this regulation. Here, we show that a long isoform of the long non-coding RNA SVALKA-L (SVK-L) forms a natural antisense transcript to the host gene CBF1 and negatively regulates CBF1 mRNA levels at normal temperatures in the model plant Arabidopsis thaliana. Furthermore, we show detailed evidence for the specific mode of action of SVK-L. This pathway includes the formation of double-stranded RNA that is recognized by the DICER proteins and subsequent downregulation of CBF1 mRNA levels. Thus, the CBF1-SVK regulatory circuit is not only important for its previously known role in cold temperature acclimation but also for biomass production at normal temperatures. Our study characterizes the developmental role of SVK-L and offers mechanistic insight into how biologically important overlapping natural antisense transcripts can act on and fine-tune the steady-state levels of their host gene’s mRNA.},
	number = {4},
	urldate = {2023-08-21},
	journal = {Plant Communications},
	author = {Zacharaki, Vasiliki and Meena, Shiv Kumar and Kindgren, Peter},
	month = jul,
	year = {2023},
	keywords = {-natural antisense transcript, cis- natural antisense transcript, non-coding transcription},
	pages = {100551},
}

Non-coding transcription is present in all eukaryotic genomes, but we lack fundamental knowledge about its importance for an organism’s ability to develop properly. In plants, emerging evidence highlights the essential biological role of non-coding transcription in the regulation of coding transcription. However, we have few molecular insights into this regulation. Here, we show that a long isoform of the long non-coding RNA SVALKA-L (SVK-L) forms a natural antisense transcript to the host gene CBF1 and negatively regulates CBF1 mRNA levels at normal temperatures in the model plant Arabidopsis thaliana. Furthermore, we show detailed evidence for the specific mode of action of SVK-L. This pathway includes the formation of double-stranded RNA that is recognized by the DICER proteins and subsequent downregulation of CBF1 mRNA levels. Thus, the CBF1-SVK regulatory circuit is not only important for its previously known role in cold temperature acclimation but also for biomass production at normal temperatures. Our study characterizes the developmental role of SVK-L and offers mechanistic insight into how biologically important overlapping natural antisense transcripts can act on and fine-tune the steady-state levels of their host gene’s mRNA.

@article{manoharan_okinawan-based_2023,
	title = {An {Okinawan}-{Based} {Nordic} {Diet} {Leads} to {Profound} {Effects} on {Gut} {Microbiota} and {Plasma} {Metabolites} {Linked} to {Glucose} and {Lipid} {Metabolism}},
	volume = {15},
	issn = {2072-6643},
	url = {https://www.mdpi.com/2072-6643/15/14/3273},
	doi = {10.3390/nu15143273},
	abstract = {Dietary interventions modify gut microbiota and clinical outcomes. Weight reduction and improved glucose and lipid homeostasis were observed after adopting an Okinawan-based Nordic diet (O-BN) in individuals with type 2 diabetes. The aim of the present study was to explore changes in metabolomics and gut microbiota during O-BN and correlate changes with clinical outcomes. A total of 30 patients (17 women), aged 57.5 ± 8.2 years, diabetes duration 10.4 ± 7.6 years, 90\% over-weight, were included. Participants were provided an O-BN for 12 weeks. Before and after intervention, and 16 weeks afterwards, anthropometry and clinical data were estimated and questionnaires were collected, as well as samples of blood and stool. Plasma metabolomics were determined by gas- (GC-MS) or liquid- (LC-MS) chromatography-based mass spectrometry and fecal microbiota determination was based on 16S rRNA amplicons from regions V1–V2. During the intervention, weight (6.8\%), waist circumference (6.1\%), and levels of glucose, HbA1c, insulin, triglycerides, and cholesterol were decreased. Of 602 metabolites, 323 were changed for any or both periods; 199 (101 lipids) metabolites were decreased while 58 (43 lipids) metabolites were increased during the intervention. Changes in glucose homeostasis were linked to changes in, e.g., 1,5-anhydroglucitol, thyroxine, and chiro-inositol. Changes of microbe beta diversity correlated positively with food components and negatively with IL-18 (p = 0.045). Abundance differences at phylum and genus levels were found. Abundances of Actinobacteria, Bacteroidetes, Firmicutes, and Verrucomicrobia correlated with anthropometry, HbA1c, lipids, inflammation, and food. Changes in metabolites and microbiota were reversed after the intervention. The O-BN-induced changes in metabolomics and gut microbiota correspond to clinical outcomes of reduced weight and inflammation and improved glucose and lipid metabolism.},
	language = {en},
	number = {14},
	urldate = {2023-08-04},
	journal = {Nutrients},
	author = {Manoharan, Lokeshwaran and Roth, Bodil and Bang, Corinna and Stenlund, Hans and Ohlsson, Bodil},
	month = jul,
	year = {2023},
	pages = {3273},
}

Dietary interventions modify gut microbiota and clinical outcomes. Weight reduction and improved glucose and lipid homeostasis were observed after adopting an Okinawan-based Nordic diet (O-BN) in individuals with type 2 diabetes. The aim of the present study was to explore changes in metabolomics and gut microbiota during O-BN and correlate changes with clinical outcomes. A total of 30 patients (17 women), aged 57.5 ± 8.2 years, diabetes duration 10.4 ± 7.6 years, 90% over-weight, were included. Participants were provided an O-BN for 12 weeks. Before and after intervention, and 16 weeks afterwards, anthropometry and clinical data were estimated and questionnaires were collected, as well as samples of blood and stool. Plasma metabolomics were determined by gas- (GC-MS) or liquid- (LC-MS) chromatography-based mass spectrometry and fecal microbiota determination was based on 16S rRNA amplicons from regions V1–V2. During the intervention, weight (6.8%), waist circumference (6.1%), and levels of glucose, HbA1c, insulin, triglycerides, and cholesterol were decreased. Of 602 metabolites, 323 were changed for any or both periods; 199 (101 lipids) metabolites were decreased while 58 (43 lipids) metabolites were increased during the intervention. Changes in glucose homeostasis were linked to changes in, e.g., 1,5-anhydroglucitol, thyroxine, and chiro-inositol. Changes of microbe beta diversity correlated positively with food components and negatively with IL-18 (p = 0.045). Abundance differences at phylum and genus levels were found. Abundances of Actinobacteria, Bacteroidetes, Firmicutes, and Verrucomicrobia correlated with anthropometry, HbA1c, lipids, inflammation, and food. Changes in metabolites and microbiota were reversed after the intervention. The O-BN-induced changes in metabolomics and gut microbiota correspond to clinical outcomes of reduced weight and inflammation and improved glucose and lipid metabolism.

@article{armada-moreira_plant_2023,
	title = {Plant electrophysiology with conformable organic electronics: {Deciphering} the propagation of {Venus} flytrap action potentials},
	volume = {9},
	issn = {2375-2548},
	shorttitle = {Plant electrophysiology with conformable organic electronics},
	url = {https://www.science.org/doi/10.1126/sciadv.adh4443},
	doi = {10.1126/sciadv.adh4443},
	abstract = {Electrical signals in plants are mediators of long-distance signaling and correlate with plant movements and responses to stress. These signals are studied with single surface electrodes that cannot resolve signal propagation and integration, thus impeding their decoding and link to function. Here, we developed a conformable multielectrode array based on organic electronics for large-scale and high-resolution plant electrophysiology. We performed precise spatiotemporal mapping of the action potential (AP) in Venus flytrap and found that the AP actively propagates through the tissue with constant speed and without strong directionality. We also found that spontaneously generated APs can originate from unstimulated hairs and that they correlate with trap movement. Last, we demonstrate that the Venus flytrap circuitry can be activated by cells other than the sensory hairs. Our work reveals key properties of the AP and establishes the capacity of organic bioelectronics for resolving electrical signaling in plants contributing to the mechanistic understanding of long-distance responses in plants.
          , 
            Organic bioelectronics enable large-scale and high-resolution plant electrophysiology monitoring of the Venus flytrap signaling.},
	language = {en},
	number = {30},
	urldate = {2023-08-14},
	journal = {Science Advances},
	author = {Armada-Moreira, Adam and Dar, Abdul Manan and Zhao, Zifang and Cea, Claudia and Gelinas, Jennifer and Berggren, Magnus and Costa, Alex and Khodagholy, Dion and Stavrinidou, Eleni},
	month = jul,
	year = {2023},
	pages = {eadh4443},
}

Electrical signals in plants are mediators of long-distance signaling and correlate with plant movements and responses to stress. These signals are studied with single surface electrodes that cannot resolve signal propagation and integration, thus impeding their decoding and link to function. Here, we developed a conformable multielectrode array based on organic electronics for large-scale and high-resolution plant electrophysiology. We performed precise spatiotemporal mapping of the action potential (AP) in Venus flytrap and found that the AP actively propagates through the tissue with constant speed and without strong directionality. We also found that spontaneously generated APs can originate from unstimulated hairs and that they correlate with trap movement. Last, we demonstrate that the Venus flytrap circuitry can be activated by cells other than the sensory hairs. Our work reveals key properties of the AP and establishes the capacity of organic bioelectronics for resolving electrical signaling in plants contributing to the mechanistic understanding of long-distance responses in plants. , Organic bioelectronics enable large-scale and high-resolution plant electrophysiology monitoring of the Venus flytrap signaling.

@article{derba-maceluch_impact_2023,
	title = {Impact of xylan on field productivity and wood saccharification properties in aspen},
	volume = {14},
	issn = {1664-462X},
	url = {https://www.frontiersin.org/articles/10.3389/fpls.2023.1218302},
	doi = {10.3389/fpls.2023.1218302},
	abstract = {Xylan that comprises roughly 25\% of hardwood biomass is undesirable in biorefinery applications involving saccharification and fermentation. Efforts to reduce xylan levels have therefore been made in many species, usually resulting in improved saccharification. However, such modified plants have not yet been tested under field conditions. Here we evaluate the field performance of transgenic hybrid aspen lines with reduced xylan levels and assess their usefulness as short-rotation feedstocks for biorefineries. Three types of transgenic lines were tested in four-year field tests with RNAi constructs targeting either Populus GT43 clades B and C (GT43BC) corresponding to Arabidopsis clades IRX9 and IRX14, respectively, involved in xylan backbone biosynthesis, GATL1.1 corresponding to AtGALT1 involved in xylan reducing end sequence biosynthesis, or ASPR1 encoding an atypical aspartate protease. Their productivity, wood quality traits, and saccharification efficiency were analyzed. The only lines differing significantly from the wild type with respect to growth and biotic stress resistance were the ASPR1 lines, whose stems were roughly 10\% shorter and narrower and leaves showed increased arthropod damage. GT43BC lines exhibited no growth advantage in the field despite their superior growth in greenhouse experiments. Wood from the ASPR1 and GT43BC lines had slightly reduced density due to thinner cell walls and, in the case of ASPR1, larger cell diameters. The xylan was less extractable by alkali but more hydrolysable by acid, had increased glucuronosylation, and its content was reduced in all three types of transgenic lines. The hemicellulose size distribution in the GALT1.1 and ASPR1 lines was skewed towards higher molecular mass compared to the wild type. These results provide experimental evidence that GATL1.1 functions in xylan biosynthesis and suggest that ASPR1 may regulate this process. In saccharification without pretreatment, lines of all three constructs provided 8-11\% higher average glucose yields than wild-type plants. In saccharification with acid pretreatment, the GT43BC construct provided a 10\% yield increase on average. The best transgenic lines of each construct are thus predicted to modestly outperform the wild type in terms of glucose yields per hectare. The field evaluation of transgenic xylan-reduced aspen represents an important step towards more productive feedstocks for biorefineries.},
	urldate = {2023-07-18},
	journal = {Frontiers in Plant Science},
	author = {Derba-Maceluch, Marta and Sivan, Pramod and Donev, Evgeniy N. and Gandla, Madhavi Latha and Yassin, Zakiya and Vaasan, Rakhesh and Heinonen, Emilia and Andersson, Sanna and Amini, Fariba and Scheepers, Gerhard and Johansson, Ulf and Vilaplana, Francisco J. and Albrectsen, Benedicte R. and Hertzberg, Magnus and Jönsson, Leif J. and Mellerowicz, Ewa J.},
	year = {2023},
}

Xylan that comprises roughly 25% of hardwood biomass is undesirable in biorefinery applications involving saccharification and fermentation. Efforts to reduce xylan levels have therefore been made in many species, usually resulting in improved saccharification. However, such modified plants have not yet been tested under field conditions. Here we evaluate the field performance of transgenic hybrid aspen lines with reduced xylan levels and assess their usefulness as short-rotation feedstocks for biorefineries. Three types of transgenic lines were tested in four-year field tests with RNAi constructs targeting either Populus GT43 clades B and C (GT43BC) corresponding to Arabidopsis clades IRX9 and IRX14, respectively, involved in xylan backbone biosynthesis, GATL1.1 corresponding to AtGALT1 involved in xylan reducing end sequence biosynthesis, or ASPR1 encoding an atypical aspartate protease. Their productivity, wood quality traits, and saccharification efficiency were analyzed. The only lines differing significantly from the wild type with respect to growth and biotic stress resistance were the ASPR1 lines, whose stems were roughly 10% shorter and narrower and leaves showed increased arthropod damage. GT43BC lines exhibited no growth advantage in the field despite their superior growth in greenhouse experiments. Wood from the ASPR1 and GT43BC lines had slightly reduced density due to thinner cell walls and, in the case of ASPR1, larger cell diameters. The xylan was less extractable by alkali but more hydrolysable by acid, had increased glucuronosylation, and its content was reduced in all three types of transgenic lines. The hemicellulose size distribution in the GALT1.1 and ASPR1 lines was skewed towards higher molecular mass compared to the wild type. These results provide experimental evidence that GATL1.1 functions in xylan biosynthesis and suggest that ASPR1 may regulate this process. In saccharification without pretreatment, lines of all three constructs provided 8-11% higher average glucose yields than wild-type plants. In saccharification with acid pretreatment, the GT43BC construct provided a 10% yield increase on average. The best transgenic lines of each construct are thus predicted to modestly outperform the wild type in terms of glucose yields per hectare. The field evaluation of transgenic xylan-reduced aspen represents an important step towards more productive feedstocks for biorefineries.

@article{lihavainen_salicylic_2023,
	title = {Salicylic acid metabolism and signalling coordinate senescence initiation in aspen in nature},
	volume = {14},
	copyright = {2023 The Author(s)},
	issn = {2041-1723},
	url = {https://www.nature.com/articles/s41467-023-39564-5},
	doi = {10.1038/s41467-023-39564-5},
	abstract = {Deciduous trees exhibit a spectacular phenomenon of autumn senescence driven by the seasonality of their growth environment, yet there is no consensus which external or internal cues trigger it. Senescence starts at different times in European aspen (Populus tremula L.) genotypes grown in same location. By integrating omics studies, we demonstrate that aspen genotypes utilize similar transcriptional cascades and metabolic cues to initiate senescence, but at different times during autumn. The timing of autumn senescence initiation appeared to be controlled by two consecutive “switches”; 1) first the environmental variation induced the rewiring of the transcriptional network, stress signalling pathways and metabolic perturbations and 2) the start of senescence process was defined by the ability of the genotype to activate and sustain stress tolerance mechanisms mediated by salicylic acid. We propose that salicylic acid represses the onset of leaf senescence in stressful natural conditions, rather than promoting it as often observed in annual plants.},
	language = {en},
	number = {1},
	urldate = {2023-07-21},
	journal = {Nature Communications},
	author = {Lihavainen, Jenna and Šimura, Jan and Bag, Pushan and Fataftah, Nazeer and Robinson, Kathryn Megan and Delhomme, Nicolas and Novák, Ondřej and Ljung, Karin and Jansson, Stefan},
	month = jul,
	year = {2023},
	note = {Number: 1
Publisher: Nature Publishing Group},
	keywords = {Metabolomics, Plant physiology, Regulatory networks, Senescence},
	pages = {4288},
}

Deciduous trees exhibit a spectacular phenomenon of autumn senescence driven by the seasonality of their growth environment, yet there is no consensus which external or internal cues trigger it. Senescence starts at different times in European aspen (Populus tremula L.) genotypes grown in same location. By integrating omics studies, we demonstrate that aspen genotypes utilize similar transcriptional cascades and metabolic cues to initiate senescence, but at different times during autumn. The timing of autumn senescence initiation appeared to be controlled by two consecutive “switches”; 1) first the environmental variation induced the rewiring of the transcriptional network, stress signalling pathways and metabolic perturbations and 2) the start of senescence process was defined by the ability of the genotype to activate and sustain stress tolerance mechanisms mediated by salicylic acid. We propose that salicylic acid represses the onset of leaf senescence in stressful natural conditions, rather than promoting it as often observed in annual plants.

@article{grenzi_long-distance_2023,
	title = {Long-distance turgor pressure changes induce local activation of plant glutamate receptor-like channels},
	issn = {0960-9822},
	url = {https://www.sciencedirect.com/science/article/pii/S0960982223000763},
	doi = {10.1016/j.cub.2023.01.042},
	abstract = {In Arabidopsis thaliana, local wounding and herbivore feeding provoke leaf-to-leaf propagating Ca2+ waves that are dependent on the activity of members of the glutamate receptor-like channels (GLRs). In systemic tissues, GLRs are needed to sustain the synthesis of jasmonic acid (JA) with the subsequent activation of JA-dependent signaling response required for the plant acclimation to the perceived stress. Even though the role of GLRs is well established, the mechanism through which they are activated remains unclear. Here, we report that in vivo, the amino-acid-dependent activation of the AtGLR3.3 channel and systemic responses require a functional ligand-binding domain. By combining imaging and genetics, we show that leaf mechanical injury, such as wounds and burns, as well as hypo-osmotic stress in root cells, induces the systemic apoplastic increase of L-glutamate (L-Glu), which is largely independent of AtGLR3.3 that is instead required for systemic cytosolic Ca2+ elevation. Moreover, by using a bioelectronic approach, we show that the local release of minute concentrations of L-Glu in the leaf lamina fails to induce any long-distance Ca2+ waves.},
	language = {en},
	urldate = {2023-03-23},
	journal = {Current Biology},
	author = {Grenzi, Matteo and Buratti, Stefano and Parmagnani, Ambra Selene and Abdel Aziz, Ilaria and Bernacka-Wojcik, Iwona and Resentini, Francesca and Šimura, Jan and Doccula, Fabrizio Gandolfo and Alfieri, Andrea and Luoni, Laura and Ljung, Karin and Bonza, Maria Cristina and Stavrinidou, Eleni and Costa, Alex},
	month = feb,
	year = {2023},
	keywords = {glutamate receptor-like channels, implantable bioelectronic device, ligand-binding domain, long-distance Ca signaling},
}

In Arabidopsis thaliana, local wounding and herbivore feeding provoke leaf-to-leaf propagating Ca2+ waves that are dependent on the activity of members of the glutamate receptor-like channels (GLRs). In systemic tissues, GLRs are needed to sustain the synthesis of jasmonic acid (JA) with the subsequent activation of JA-dependent signaling response required for the plant acclimation to the perceived stress. Even though the role of GLRs is well established, the mechanism through which they are activated remains unclear. Here, we report that in vivo, the amino-acid-dependent activation of the AtGLR3.3 channel and systemic responses require a functional ligand-binding domain. By combining imaging and genetics, we show that leaf mechanical injury, such as wounds and burns, as well as hypo-osmotic stress in root cells, induces the systemic apoplastic increase of L-glutamate (L-Glu), which is largely independent of AtGLR3.3 that is instead required for systemic cytosolic Ca2+ elevation. Moreover, by using a bioelectronic approach, we show that the local release of minute concentrations of L-Glu in the leaf lamina fails to induce any long-distance Ca2+ waves.

@article{gautam_functional_2023,
	title = {Functional characterization of rice metallothionein {OsMT}-{I}-{Id}: {Insights} into metal binding and heavy metal tolerance mechanisms},
	volume = {458},
	issn = {03043894},
	shorttitle = {Functional characterization of rice metallothionein {OsMT}-{I}-{Id}},
	url = {https://linkinghub.elsevier.com/retrieve/pii/S0304389423010981},
	doi = {10.1016/j.jhazmat.2023.131815},
	language = {en},
	urldate = {2023-08-04},
	journal = {Journal of Hazardous Materials},
	author = {Gautam, Neelam and Tiwari, Madhu and Kidwai, Maria and Dutta, Prasanna and Chakrabarty, Debasis},
	month = sep,
	year = {2023},
	pages = {131815},
}

@article{pitsili_phloem-localized_2023,
	title = {A phloem-localized {Arabidopsis} metacaspase ({AtMC3}) improves drought tolerance},
	volume = {239},
	copyright = {© 2023 The Authors. New Phytologist © 2023 New Phytologist Foundation},
	issn = {1469-8137},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/nph.19022},
	doi = {10.1111/nph.19022},
	abstract = {Increasing drought phenomena pose a serious threat to agricultural productivity. Although plants have multiple ways to respond to the complexity of drought stress, the underlying mechanisms of stress sensing and signaling remain unclear. The role of the vasculature, in particular the phloem, in facilitating inter-organ communication is critical and poorly understood. Combining genetic, proteomic and physiological approaches, we investigated the role of AtMC3, a phloem-specific member of the metacaspase family, in osmotic stress responses in Arabidopsis thaliana. Analyses of the proteome in plants with altered AtMC3 levels revealed differential abundance of proteins related to osmotic stress pointing into a role of the protein in water-stress-related responses. Overexpression of AtMC3 conferred drought tolerance by enhancing the differentiation of specific vascular tissues and maintaining higher levels of vascular-mediated transportation, while plants lacking the protein showed an impaired response to drought and inability to respond effectively to the hormone abscisic acid. Overall, our data highlight the importance of AtMC3 and vascular plasticity in fine-tuning early drought responses at the whole plant level without affecting growth or yield.},
	language = {en},
	number = {4},
	urldate = {2023-07-21},
	journal = {New Phytologist},
	author = {Pitsili, Eugenia and Rodriguez-Trevino, Ricardo and Ruiz-Solani, Nerea and Demir, Fatih and Kastanaki, Elizabeth and Dambire, Charlene and de Pedro-Jové, Roger and Vercammen, Dominique and Salguero-Linares, Jose and Hall, Hardy and Mantz, Melissa and Schuler, Martin and Tuominen, Hannele and Van Breusegem, Frank and Valls, Marc and Munné-Bosch, Sergi and Holdsworth, Michael J. and Huesgen, Pitter F. and Rodriguez-Villalon, Antia and Coll, Nuria S.},
	year = {2023},
	note = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1111/nph.19022},
	keywords = {Arabidopsis thaliana, abscisic acid, drought, hypoxia, metacaspases, osmotic stress, phloem},
	pages = {1281--1299},
}

Increasing drought phenomena pose a serious threat to agricultural productivity. Although plants have multiple ways to respond to the complexity of drought stress, the underlying mechanisms of stress sensing and signaling remain unclear. The role of the vasculature, in particular the phloem, in facilitating inter-organ communication is critical and poorly understood. Combining genetic, proteomic and physiological approaches, we investigated the role of AtMC3, a phloem-specific member of the metacaspase family, in osmotic stress responses in Arabidopsis thaliana. Analyses of the proteome in plants with altered AtMC3 levels revealed differential abundance of proteins related to osmotic stress pointing into a role of the protein in water-stress-related responses. Overexpression of AtMC3 conferred drought tolerance by enhancing the differentiation of specific vascular tissues and maintaining higher levels of vascular-mediated transportation, while plants lacking the protein showed an impaired response to drought and inability to respond effectively to the hormone abscisic acid. Overall, our data highlight the importance of AtMC3 and vascular plasticity in fine-tuning early drought responses at the whole plant level without affecting growth or yield.

@article{israeli_modulating_2023,
	title = {Modulating auxin response stabilizes tomato fruit set},
	volume = {192},
	issn = {0032-0889},
	url = {https://doi.org/10.1093/plphys/kiad205},
	doi = {10.1093/plphys/kiad205},
	abstract = {Fruit formation depends on successful fertilization and is highly sensitive to weather fluctuations that affect pollination. Auxin promotes fruit initiation and growth following fertilization. Class A auxin response factors (Class A ARFs) repress transcription in the absence of auxin and activate transcription in its presence. Here we explore how multiple members of the ARF family regulate fruit set and fruit growth in tomato (Solanum lycopersicum) and Arabidopsis thaliana, and test whether reduction of SlARF activity improves yield stability in fluctuating temperatures. We found that several tomato Slarf mutant combinations produced seedless parthenocarpic fruits, most notably mutants deficient in SlARF8A and SlARF8B genes. Arabidopsis Atarf8 mutants deficient in the orthologous gene had less complete parthenocarpy than did tomato Slarf8a Slarf8b mutants. Conversely, Atarf6 Atarf8 double mutants had reduced fruit growth after fertilization. AtARF6 and AtARF8 likely switch from repression to activation of fruit growth in response to a fertilization-induced auxin increase in gynoecia. Tomato plants with reduced SlARF8A and SlARF8B gene dosage had substantially higher yield than the wild type under controlled or ambient hot and cold growth conditions. In field trials, partial reduction in the SlARF8 dose increased yield under extreme temperature with minimal pleiotropic effects. The stable yield of the mutant plants resulted from a combination of early onset of fruit set, more fruit-bearing branches and more flowers setting fruits. Thus, ARF8 proteins mediate the control of fruit set, and relieving this control with Slarf8 mutations may be utilized in breeding to increase yield stability in tomato and other crops.},
	number = {3},
	urldate = {2023-04-14},
	journal = {Plant Physiology},
	author = {Israeli, Alon and Schubert, Ramona and Man, Nave and Teboul, Naama and Serrani Yarce, Juan Carlos and Rosowski, Emily E and Wu, Miin-Feng and Levy, Matan and Efroni, Idan and Ljung, Karin and Hause, Bettina and Reed, Jason W and Ori, Naomi},
	month = jul,
	year = {2023},
	pages = {2336--2355},
}

Fruit formation depends on successful fertilization and is highly sensitive to weather fluctuations that affect pollination. Auxin promotes fruit initiation and growth following fertilization. Class A auxin response factors (Class A ARFs) repress transcription in the absence of auxin and activate transcription in its presence. Here we explore how multiple members of the ARF family regulate fruit set and fruit growth in tomato (Solanum lycopersicum) and Arabidopsis thaliana, and test whether reduction of SlARF activity improves yield stability in fluctuating temperatures. We found that several tomato Slarf mutant combinations produced seedless parthenocarpic fruits, most notably mutants deficient in SlARF8A and SlARF8B genes. Arabidopsis Atarf8 mutants deficient in the orthologous gene had less complete parthenocarpy than did tomato Slarf8a Slarf8b mutants. Conversely, Atarf6 Atarf8 double mutants had reduced fruit growth after fertilization. AtARF6 and AtARF8 likely switch from repression to activation of fruit growth in response to a fertilization-induced auxin increase in gynoecia. Tomato plants with reduced SlARF8A and SlARF8B gene dosage had substantially higher yield than the wild type under controlled or ambient hot and cold growth conditions. In field trials, partial reduction in the SlARF8 dose increased yield under extreme temperature with minimal pleiotropic effects. The stable yield of the mutant plants resulted from a combination of early onset of fruit set, more fruit-bearing branches and more flowers setting fruits. Thus, ARF8 proteins mediate the control of fruit set, and relieving this control with Slarf8 mutations may be utilized in breeding to increase yield stability in tomato and other crops.

@article{sivan_sequential_2023,
	title = {Sequential extraction of hemicelluloses by subcritical water improves saccharification of hybrid aspen wood grown in greenhouse and field conditions},
	volume = {25},
	issn = {1463-9270},
	url = {https://pubs.rsc.org/en/content/articlelanding/2023/gc/d3gc01020a},
	doi = {10.1039/D3GC01020A},
	abstract = {Fast growing hardwoods are one of the major renewable resources available to produce bio-based materials, platform chemicals and biofuels. However, the industrial processing of lignocellulosic biomass is hindered by the complex molecular structure of the cell wall components and their supramolecular organization. This highlights the necessity of improving green processing strategies to enhance biomass conversion to valuable products from industrial wood production species. In the present study, we implemented a hydrothermal step by sequential subcritical water (SW) in aspen wood prior to saccharification and validated the process for trees grown in greenhouse and field conditions. Subcritical water enables extraction of non-cellulosic cell wall polysaccharides in native polymeric form. A major part of the pectic fraction was easily extracted within the first 10 min, while acetylated xylan was enriched in the subsequent extracts after 20- and 30-min rounds. Prolonged extraction (above 60 min) resulted in partial deacetylation and a reduction of the molar mass of xylan. The analysis of the residues enriched with cellulose and lignin showed several micromorphological changes caused by subcritical water treatment, such as an increased porosity, a loosening of the fibre matrix and a decrease in the macrofibrillar dimensions. These morphological and molecular changes in the organization of cell wall polymers after SW treatment significantly enhanced saccharification yields compared to those of non-treated aspen wood chips from both field and greenhouse conditions. Our study demonstrates that SW can be implemented as pretreatment prior to saccharification reducing the requirements for chemical acid pretreatments. This process enables the extraction of native non-cellulosic cell wall polymers for potential material applications and promotes the subsequent biochemical conversion of the residual biomass into fermentable sugars and platform chemicals in future biorefineries.},
	language = {en},
	number = {14},
	urldate = {2023-07-18},
	journal = {Green Chemistry},
	author = {Sivan, Pramod and Heinonen, Emilia and Gandla, Madhavi Latha and Jiménez-Quero, Amparo and Özeren, Hüsamettin Deniz and Jönsson, Leif J. and Mellerowicz, Ewa J. and Vilaplana, Francisco},
	month = jul,
	year = {2023},
	note = {Publisher: The Royal Society of Chemistry},
	pages = {5634--5646},
}

Fast growing hardwoods are one of the major renewable resources available to produce bio-based materials, platform chemicals and biofuels. However, the industrial processing of lignocellulosic biomass is hindered by the complex molecular structure of the cell wall components and their supramolecular organization. This highlights the necessity of improving green processing strategies to enhance biomass conversion to valuable products from industrial wood production species. In the present study, we implemented a hydrothermal step by sequential subcritical water (SW) in aspen wood prior to saccharification and validated the process for trees grown in greenhouse and field conditions. Subcritical water enables extraction of non-cellulosic cell wall polysaccharides in native polymeric form. A major part of the pectic fraction was easily extracted within the first 10 min, while acetylated xylan was enriched in the subsequent extracts after 20- and 30-min rounds. Prolonged extraction (above 60 min) resulted in partial deacetylation and a reduction of the molar mass of xylan. The analysis of the residues enriched with cellulose and lignin showed several micromorphological changes caused by subcritical water treatment, such as an increased porosity, a loosening of the fibre matrix and a decrease in the macrofibrillar dimensions. These morphological and molecular changes in the organization of cell wall polymers after SW treatment significantly enhanced saccharification yields compared to those of non-treated aspen wood chips from both field and greenhouse conditions. Our study demonstrates that SW can be implemented as pretreatment prior to saccharification reducing the requirements for chemical acid pretreatments. This process enables the extraction of native non-cellulosic cell wall polymers for potential material applications and promotes the subsequent biochemical conversion of the residual biomass into fermentable sugars and platform chemicals in future biorefineries.

@article{demes_high-throughput_2023,
	title = {High-throughput characterization of cortical microtubule arrays response to anisotropic tensile stress},
	volume = {21},
	issn = {1741-7007},
	url = {https://doi.org/10.1186/s12915-023-01654-7},
	doi = {10.1186/s12915-023-01654-7},
	abstract = {Plants can perceive and respond to mechanical signals. For instance, cortical microtubule (CMT) arrays usually reorganize following the predicted maximal tensile stress orientation at the cell and tissue level. While research in the last few years has started to uncover some of the mechanisms mediating these responses, much remains to be discovered, including in most cases the actual nature of the mechanosensors. Such discovery is hampered by the absence of adequate quantification tools that allow the accurate and sensitive detection of phenotypes, along with high throughput and automated handling of large datasets that can be generated with recent imaging devices.},
	number = {1},
	urldate = {2023-07-14},
	journal = {BMC Biology},
	author = {Demes, Elsa and Verger, Stéphane},
	month = jul,
	year = {2023},
	keywords = {Image analysis, Mechanical stress, Microtubules, Plants},
	pages = {154},
}

Plants can perceive and respond to mechanical signals. For instance, cortical microtubule (CMT) arrays usually reorganize following the predicted maximal tensile stress orientation at the cell and tissue level. While research in the last few years has started to uncover some of the mechanisms mediating these responses, much remains to be discovered, including in most cases the actual nature of the mechanosensors. Such discovery is hampered by the absence of adequate quantification tools that allow the accurate and sensitive detection of phenotypes, along with high throughput and automated handling of large datasets that can be generated with recent imaging devices.

@article{ranade_clinal_2023,
	title = {Clinal variation in {PHY} ({PAS} domain) and {CRY} ({CCT} domain)—{Signs} of local adaptation to light quality in {Norway} spruce},
	volume = {n/a},
	copyright = {© 2023 The Authors. Plant, Cell \& Environment published by John Wiley \& Sons Ltd.},
	issn = {1365-3040},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/pce.14638},
	doi = {10.1111/pce.14638},
	abstract = {Detection of the genomic basis of local adaptation to environmental conditions is challenging in forest trees. Phytochromes (PHY) and cryptochromes (CRY) perceive the red (R)/far-red (FR) and blue light respectively, thus playing a fundamental role in regulating plant growth and development. PHYO and PHYP from conifers are the equivalents of PHYA/PHYC and PHYB in angiosperms, respectively. Norway spruce shows an adaptive latitudinal cline for shade (low R:FR or FR-enriched light) tolerance and requirement of FR light for its growth. We analyzed the exome capture data that included a uniquely large data set of 1654 Norway spruce trees sampled across many latitudes in Sweden to capture the natural clines for photoperiod and FR light exposure during the growth season. Statistically significant clinal variation was detected in allele and genotype frequencies of missense mutations in coding regions belonging to well-defined functional domains of PHYO (PAS-B), PHYP2 (PAS fold-2), CRY1 (CCT1) and CRY2 (CCT2) that strongly correlates with the latitudinal gradient in response to variable light quality in Norway spruce. The missense SNP in PHYO resulting in Asn835Ser, displayed the steepest cline among all other polymorphisms. We propose that these variations in the photoreceptors represent signs of local adaptation to light quality.},
	language = {en},
	number = {n/a},
	urldate = {2023-06-09},
	journal = {Plant, Cell \& Environment},
	author = {Ranade, Sonali Sachin and García-Gil, María Rosario},
	month = jun,
	year = {2023},
	note = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1111/pce.14638},
	keywords = {SNP, cline, cryptochrome, missense mutation, photoreceptor, phytochrome, polymorphism},
}

Detection of the genomic basis of local adaptation to environmental conditions is challenging in forest trees. Phytochromes (PHY) and cryptochromes (CRY) perceive the red (R)/far-red (FR) and blue light respectively, thus playing a fundamental role in regulating plant growth and development. PHYO and PHYP from conifers are the equivalents of PHYA/PHYC and PHYB in angiosperms, respectively. Norway spruce shows an adaptive latitudinal cline for shade (low R:FR or FR-enriched light) tolerance and requirement of FR light for its growth. We analyzed the exome capture data that included a uniquely large data set of 1654 Norway spruce trees sampled across many latitudes in Sweden to capture the natural clines for photoperiod and FR light exposure during the growth season. Statistically significant clinal variation was detected in allele and genotype frequencies of missense mutations in coding regions belonging to well-defined functional domains of PHYO (PAS-B), PHYP2 (PAS fold-2), CRY1 (CCT1) and CRY2 (CCT2) that strongly correlates with the latitudinal gradient in response to variable light quality in Norway spruce. The missense SNP in PHYO resulting in Asn835Ser, displayed the steepest cline among all other polymorphisms. We propose that these variations in the photoreceptors represent signs of local adaptation to light quality.

@article{ortiz_inbreeding_2023,
	title = {Inbreeding {Effects} on the {Performance} and {Genomic} {Prediction} for {Polysomic} {Tetraploid} {Potato} {Offspring} {Grown} at {High} {Nordic} {Latitudes}},
	volume = {14},
	copyright = {http://creativecommons.org/licenses/by/3.0/},
	issn = {2073-4425},
	url = {https://www.mdpi.com/2073-4425/14/6/1302},
	doi = {10.3390/genes14061302},
	abstract = {Inbreeding depression (ID) is caused by increased homozygosity in the offspring after selfing. Although the self-compatible, highly heterozygous, tetrasomic polyploid potato (Solanum tuberosum L.) suffers from ID, some argue that the potential genetic gains from using inbred lines in a sexual propagation system of potato are too large to be ignored. The aim of this research was to assess the effects of inbreeding on potato offspring performance under a high latitude and the accuracy of the genomic prediction of breeding values (GEBVs) for further use in selection. Four inbred (S1) and two hybrid (F1) offspring and their parents (S0) were used in the experiment, with a field layout of an augmented design with the four S0 replicated in nine incomplete blocks comprising 100, four-plant plots at Umeå (63°49′30″ N 20°15′50″ E), Sweden. S0 was significantly (p {\textless} 0.01) better than both S1 and F1 offspring for tuber weight (total and according to five grading sizes), tuber shape and size uniformity, tuber eye depth and reducing sugars in the tuber flesh, while F1 was significantly (p {\textless} 0.01) better than S1 for all tuber weight and uniformity traits. Some F1 hybrid offspring (15–19\%) had better total tuber yield than the best-performing parent. The GEBV accuracy ranged from −0.3928 to 0.4436. Overall, tuber shape uniformity had the highest GEBV accuracy, while tuber weight traits exhibited the lowest accuracy. The F1 full sib’s GEBV accuracy was higher, on average, than that of S1. Genomic prediction may facilitate eliminating undesired inbred or hybrid offspring for further use in the genetic betterment of potato.},
	language = {en},
	number = {6},
	urldate = {2023-06-30},
	journal = {Genes},
	author = {Ortiz, Rodomiro and Reslow, Fredrik and Vetukuri, Ramesh and García-Gil, M. Rosario and Pérez-Rodríguez, Paulino and Crossa, José},
	month = jun,
	year = {2023},
	note = {Number: 6
Publisher: Multidisciplinary Digital Publishing Institute},
	keywords = {\textit{Solanum tuberosum} L., Fennoscandia, GEBV, QTL, Scandinavia, accuracy, genetic gains, germplasm enhancement, hybrid, inbred},
	pages = {1302},
}

Inbreeding depression (ID) is caused by increased homozygosity in the offspring after selfing. Although the self-compatible, highly heterozygous, tetrasomic polyploid potato (Solanum tuberosum L.) suffers from ID, some argue that the potential genetic gains from using inbred lines in a sexual propagation system of potato are too large to be ignored. The aim of this research was to assess the effects of inbreeding on potato offspring performance under a high latitude and the accuracy of the genomic prediction of breeding values (GEBVs) for further use in selection. Four inbred (S1) and two hybrid (F1) offspring and their parents (S0) were used in the experiment, with a field layout of an augmented design with the four S0 replicated in nine incomplete blocks comprising 100, four-plant plots at Umeå (63°49′30″ N 20°15′50″ E), Sweden. S0 was significantly (p \textless 0.01) better than both S1 and F1 offspring for tuber weight (total and according to five grading sizes), tuber shape and size uniformity, tuber eye depth and reducing sugars in the tuber flesh, while F1 was significantly (p \textless 0.01) better than S1 for all tuber weight and uniformity traits. Some F1 hybrid offspring (15–19%) had better total tuber yield than the best-performing parent. The GEBV accuracy ranged from −0.3928 to 0.4436. Overall, tuber shape uniformity had the highest GEBV accuracy, while tuber weight traits exhibited the lowest accuracy. The F1 full sib’s GEBV accuracy was higher, on average, than that of S1. Genomic prediction may facilitate eliminating undesired inbred or hybrid offspring for further use in the genetic betterment of potato.

@article{schiffthaler_seir_2023,
	title = {Seiðr: {Efficient} calculation of robust ensemble gene networks},
	volume = {9},
	issn = {2405-8440},
	shorttitle = {Seiðr},
	url = {https://www.sciencedirect.com/science/article/pii/S2405844023040185},
	doi = {10.1016/j.heliyon.2023.e16811},
	abstract = {Gene regulatory and gene co-expression networks are powerful research tools for identifying biological signal within high-dimensional gene expression data. In recent years, research has focused on addressing shortcomings of these techniques with regard to the low signal-to-noise ratio, non-linear interactions and dataset dependent biases of published methods. Furthermore, it has been shown that aggregating networks from multiple methods provides improved results. Despite this, few useable and scalable software tools have been implemented to perform such best-practice analyses. Here, we present Seidr (stylized Seiðr), a software toolkit designed to assist scientists in gene regulatory and gene co-expression network inference. Seidr creates community networks to reduce algorithmic bias and utilizes noise corrected network backboning to prune noisy edges in the networks. Using benchmarks in real-world conditions across three eukaryotic model organisms, Saccharomyces cerevisiae, Drosophila melanogaster, and Arabidopsis thaliana, we show that individual algorithms are biased toward functional evidence for certain gene-gene interactions. We further demonstrate that the community network is less biased, providing robust performance across different standards and comparisons for the model organisms. Finally, we apply Seidr to a network of drought stress in Norway spruce (Picea abies (L.) H. Krast) as an example application in a non-model species. We demonstrate the use of a network inferred using Seidr for identifying key components, communities and suggesting gene function for non-annotated genes.},
	language = {en},
	number = {6},
	urldate = {2023-06-16},
	journal = {Heliyon},
	author = {Schiffthaler, Bastian and van Zalen, Elena and Serrano, Alonso R. and Street, Nathaniel R. and Delhomme, Nicolas},
	month = jun,
	year = {2023},
	keywords = {Functional genomics, Gene co-expression network, Gene network inference, Gene regulatory network, Systems biology},
	pages = {e16811},
}

Gene regulatory and gene co-expression networks are powerful research tools for identifying biological signal within high-dimensional gene expression data. In recent years, research has focused on addressing shortcomings of these techniques with regard to the low signal-to-noise ratio, non-linear interactions and dataset dependent biases of published methods. Furthermore, it has been shown that aggregating networks from multiple methods provides improved results. Despite this, few useable and scalable software tools have been implemented to perform such best-practice analyses. Here, we present Seidr (stylized Seiðr), a software toolkit designed to assist scientists in gene regulatory and gene co-expression network inference. Seidr creates community networks to reduce algorithmic bias and utilizes noise corrected network backboning to prune noisy edges in the networks. Using benchmarks in real-world conditions across three eukaryotic model organisms, Saccharomyces cerevisiae, Drosophila melanogaster, and Arabidopsis thaliana, we show that individual algorithms are biased toward functional evidence for certain gene-gene interactions. We further demonstrate that the community network is less biased, providing robust performance across different standards and comparisons for the model organisms. Finally, we apply Seidr to a network of drought stress in Norway spruce (Picea abies (L.) H. Krast) as an example application in a non-model species. We demonstrate the use of a network inferred using Seidr for identifying key components, communities and suggesting gene function for non-annotated genes.

@article{wieloch_model_2023,
	title = {A model of photosynthetic {CO2} assimilation in {C3} leaves accounting for respiration and energy recycling by the plastidial oxidative pentose phosphate pathway},
	volume = {239},
	copyright = {© 2023 The Authors New Phytologist © 2023 New Phytologist Foundation},
	issn = {1469-8137},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/nph.18965},
	doi = {10.1111/nph.18965},
	abstract = {Recently, we reported estimates of anaplerotic carbon flux through the oxidative pentose phosphate pathway (OPPP) in chloroplasts into the Calvin–Benson cycle. These estimates were based on intramolecular hydrogen isotope analysis of sunflower leaf starch. However, the isotope method is believed to underestimate the actual flux at low atmospheric CO2 concentration (Ca). Since the OPPP releases CO2 and reduces NADP+, it can be expected to affect leaf gas exchange under both rubisco- and RuBP-regeneration-limited conditions. Therefore, we expanded Farquhar-von Caemmerer–Berry models to account for OPPP metabolism. Based on model parameterisation with values from the literature, we estimated OPPP-related effects on leaf carbon and energy metabolism in the sunflowers analysed previously. We found that flux through the plastidial OPPP increases both above and below Ca ≈ 450 ppm (the condition the plants were acclimated to). This is qualitatively consistent with our previous isotope-based estimates, yet gas-exchange-based estimates are larger at low Ca. We discuss our results in relation to regulatory properties of the plastidial and cytosolic OPPP, the proposed variability of CO2 mesophyll conductance, and the contribution of day respiration to the A/Ci curve drop at high Ca. Furthermore, we critically examine the models and parameterisation and derive recommendations for follow-up studies.},
	language = {en},
	number = {2},
	urldate = {2023-06-14},
	journal = {New Phytologist},
	author = {Wieloch, Thomas and Augusti, Angela and Schleucher, Jürgen},
	month = jul,
	year = {2023},
	note = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1111/nph.18965},
	keywords = {ATP : NADPH ratio, CO2 mesophyll conductance, Calvin–Benson cycle, Farquhar-von Caemmerer–Berry photosynthesis model, day respiration, glucose-6-phosphate shunt, net CO2 assimilation, oxidative pentose phosphate pathway},
	pages = {518--532},
}

Recently, we reported estimates of anaplerotic carbon flux through the oxidative pentose phosphate pathway (OPPP) in chloroplasts into the Calvin–Benson cycle. These estimates were based on intramolecular hydrogen isotope analysis of sunflower leaf starch. However, the isotope method is believed to underestimate the actual flux at low atmospheric CO2 concentration (Ca). Since the OPPP releases CO2 and reduces NADP+, it can be expected to affect leaf gas exchange under both rubisco- and RuBP-regeneration-limited conditions. Therefore, we expanded Farquhar-von Caemmerer–Berry models to account for OPPP metabolism. Based on model parameterisation with values from the literature, we estimated OPPP-related effects on leaf carbon and energy metabolism in the sunflowers analysed previously. We found that flux through the plastidial OPPP increases both above and below Ca ≈ 450 ppm (the condition the plants were acclimated to). This is qualitatively consistent with our previous isotope-based estimates, yet gas-exchange-based estimates are larger at low Ca. We discuss our results in relation to regulatory properties of the plastidial and cytosolic OPPP, the proposed variability of CO2 mesophyll conductance, and the contribution of day respiration to the A/Ci curve drop at high Ca. Furthermore, we critically examine the models and parameterisation and derive recommendations for follow-up studies.

@article{decker_exploring_2023,
	title = {Exploring {Redox} {Modulation} of {Plant} {UDP}-{Glucose} {Pyrophosphorylase}},
	volume = {24},
	copyright = {http://creativecommons.org/licenses/by/3.0/},
	issn = {1422-0067},
	url = {https://www.mdpi.com/1422-0067/24/10/8914},
	doi = {10.3390/ijms24108914},
	abstract = {UDP-glucose (UDPG) pyrophosphorylase (UGPase) catalyzes a reversible reaction, producing UDPG, which serves as an essential precursor for hundreds of glycosyltransferases in all organisms. In this study, activities of purified UGPases from sugarcane and barley were found to be reversibly redox modulated in vitro through oxidation by hydrogen peroxide or oxidized glutathione (GSSG) and through reduction by dithiothreitol or glutathione. Generally, while oxidative treatment decreased UGPase activity, a subsequent reduction restored the activity. The oxidized enzyme had increased Km values with substrates, especially pyrophosphate. The increased Km values were also observed, regardless of redox status, for UGPase cysteine mutants (Cys102Ser and Cys99Ser for sugarcane and barley UGPases, respectively). However, activities and substrate affinities (Kms) of sugarcane Cys102Ser mutant, but not barley Cys99Ser, were still prone to redox modulation. The data suggest that plant UGPase is subject to redox control primarily via changes in the redox status of a single cysteine. Other cysteines may also, to some extent, contribute to UGPase redox status, as seen for sugarcane enzymes. The results are discussed with respect to earlier reported details of redox modulation of eukaryotic UGPases and regarding the structure/function properties of these proteins.},
	language = {en},
	number = {10},
	urldate = {2023-06-01},
	journal = {International Journal of Molecular Sciences},
	author = {Decker, Daniel and Aubert, Juliette and Wilczynska, Malgorzata and Kleczkowski, Leszek A.},
	month = jan,
	year = {2023},
	note = {Number: 10
Publisher: Multidisciplinary Digital Publishing Institute},
	keywords = {UDP-glucose pyrophosphorylase, carbohydrate metabolism, glutathione, hydrogen peroxide, protein structure, redox regulation, substrate affinity},
	pages = {8914},
}

UDP-glucose (UDPG) pyrophosphorylase (UGPase) catalyzes a reversible reaction, producing UDPG, which serves as an essential precursor for hundreds of glycosyltransferases in all organisms. In this study, activities of purified UGPases from sugarcane and barley were found to be reversibly redox modulated in vitro through oxidation by hydrogen peroxide or oxidized glutathione (GSSG) and through reduction by dithiothreitol or glutathione. Generally, while oxidative treatment decreased UGPase activity, a subsequent reduction restored the activity. The oxidized enzyme had increased Km values with substrates, especially pyrophosphate. The increased Km values were also observed, regardless of redox status, for UGPase cysteine mutants (Cys102Ser and Cys99Ser for sugarcane and barley UGPases, respectively). However, activities and substrate affinities (Kms) of sugarcane Cys102Ser mutant, but not barley Cys99Ser, were still prone to redox modulation. The data suggest that plant UGPase is subject to redox control primarily via changes in the redox status of a single cysteine. Other cysteines may also, to some extent, contribute to UGPase redox status, as seen for sugarcane enzymes. The results are discussed with respect to earlier reported details of redox modulation of eukaryotic UGPases and regarding the structure/function properties of these proteins.

@article{bag_flavodiiron-mediated_2023,
	title = {Flavodiiron-mediated {O2} photoreduction at photosystem {I} acceptor-side provides photoprotection to conifer thylakoids in early spring},
	volume = {14},
	copyright = {2023 The Author(s)},
	issn = {2041-1723},
	url = {https://www.nature.com/articles/s41467-023-38938-z},
	doi = {10.1038/s41467-023-38938-z},
	abstract = {Green organisms evolve oxygen (O2) via photosynthesis and consume it by respiration. Generally, net O2 consumption only becomes dominant when photosynthesis is suppressed at night. Here, we show that green thylakoid membranes of Scots pine (Pinus sylvestris L) and Norway spruce (Picea abies) needles display strong O2 consumption even in the presence of light when extremely low temperatures coincide with high solar irradiation during early spring (ES). By employing different electron transport chain inhibitors, we show that this unusual light-induced O2 consumption occurs around photosystem (PS) I and correlates with higher abundance of flavodiiron (Flv) A protein in ES thylakoids. With P700 absorption changes, we demonstrate that electron scavenging from the acceptor-side of PSI via O2 photoreduction is a major alternative pathway in ES. This photoprotection mechanism in vascular plants indicates that conifers have developed an adaptative evolution trajectory for growing in harsh environments.},
	language = {en},
	number = {1},
	urldate = {2023-06-09},
	journal = {Nature Communications},
	author = {Bag, Pushan and Shutova, Tatyana and Shevela, Dmitry and Lihavainen, Jenna and Nanda, Sanchali and Ivanov, Alexander G. and Messinger, Johannes and Jansson, Stefan},
	month = jun,
	year = {2023},
	note = {Number: 1
Publisher: Nature Publishing Group},
	keywords = {Abiotic, Light responses, Photosystem I},
	pages = {3210},
}

Green organisms evolve oxygen (O2) via photosynthesis and consume it by respiration. Generally, net O2 consumption only becomes dominant when photosynthesis is suppressed at night. Here, we show that green thylakoid membranes of Scots pine (Pinus sylvestris L) and Norway spruce (Picea abies) needles display strong O2 consumption even in the presence of light when extremely low temperatures coincide with high solar irradiation during early spring (ES). By employing different electron transport chain inhibitors, we show that this unusual light-induced O2 consumption occurs around photosystem (PS) I and correlates with higher abundance of flavodiiron (Flv) A protein in ES thylakoids. With P700 absorption changes, we demonstrate that electron scavenging from the acceptor-side of PSI via O2 photoreduction is a major alternative pathway in ES. This photoprotection mechanism in vascular plants indicates that conifers have developed an adaptative evolution trajectory for growing in harsh environments.

@article{zukauskaite_new_2023,
	title = {New {PEO}-{IAA}-{Inspired} {Anti}-{Auxins}: {Synthesis}, {Biological} {Activity}, and {Possible} {Application} in {Hemp} ({Cannabis} {Sativa} {L}.) {Micropropagation}},
	issn = {1435-8107},
	shorttitle = {New {PEO}-{IAA}-{Inspired} {Anti}-{Auxins}},
	url = {https://doi.org/10.1007/s00344-023-11031-x},
	doi = {10.1007/s00344-023-11031-x},
	abstract = {Auxins play an important role in plant physiology and are involved in numerous aspects of plant development, such as cell division, elongation and differentiation, fruit development, and phototropic response. In addition, through their antagonistic interaction with cytokinins, auxins play a key role in the regulation of root growth and apical dominance. Thanks to this capacity to determine plant architecture, natural and synthetic auxins have been successfully employed to obtain more economically advantageous plants. The crosstalk between auxins and cytokinins determines plant development and thus is of particular importance in the field of plant micropropagation, where the ratios between these two phytohormones need to be tightly controlled to achieve proper rooting and shoot generation. Previously reported anti-auxin PEO-IAA, which blocks auxin signalling through binding to TIR1 receptor and inhibiting the expression of auxin-responsive genes, has been successfully used to facilitate hemp micropropagation. Herein, we report a set of new PEO-IAA-inspired anti-auxins capable of antagonizing auxin responses in vivo. The capacity of these compounds to bind to the TIR1 receptor was confirmed in vitro by SPR analysis. Using DESI-MSI analysis, we evaluated the uptake and distribution of the compounds at the whole plant level. Finally, we characterized the effect of the compounds on the organogenesis of hemp explants, where they showed to be able to improve beneficial morphological traits, such as the balanced growth of all the produced shoots and enhanced bud proliferation.},
	language = {en},
	urldate = {2023-06-09},
	journal = {Journal of Plant Growth Regulation},
	author = {Žukauskaitė, Asta and Saiz-Fernández, Iñigo and Bieleszová, Kristýna and Iškauskienė, Monika and Zhang, Chao and Smýkalová, Iva and Dzedulionytė, Karolina and Kubeš, Martin F. and Sedlářová, Michaela and Pařízková, Barbora and Pavlović, Iva and Vain, Thomas and Petřík, Ivan and Malinauskienė, Vida and Šačkus, Algirdas and Strnad, Miroslav and Robert, Stéphanie and Napier, Richard and Novák, Ondřej and Doležal, Karel},
	month = may,
	year = {2023},
	keywords = {Anti-auxin, Arabidopsis thaliana, DESI-MSI analysis, Indole-3-acetic acid (IAA), Multiple shoot culture, SPR analysis},
}

Auxins play an important role in plant physiology and are involved in numerous aspects of plant development, such as cell division, elongation and differentiation, fruit development, and phototropic response. In addition, through their antagonistic interaction with cytokinins, auxins play a key role in the regulation of root growth and apical dominance. Thanks to this capacity to determine plant architecture, natural and synthetic auxins have been successfully employed to obtain more economically advantageous plants. The crosstalk between auxins and cytokinins determines plant development and thus is of particular importance in the field of plant micropropagation, where the ratios between these two phytohormones need to be tightly controlled to achieve proper rooting and shoot generation. Previously reported anti-auxin PEO-IAA, which blocks auxin signalling through binding to TIR1 receptor and inhibiting the expression of auxin-responsive genes, has been successfully used to facilitate hemp micropropagation. Herein, we report a set of new PEO-IAA-inspired anti-auxins capable of antagonizing auxin responses in vivo. The capacity of these compounds to bind to the TIR1 receptor was confirmed in vitro by SPR analysis. Using DESI-MSI analysis, we evaluated the uptake and distribution of the compounds at the whole plant level. Finally, we characterized the effect of the compounds on the organogenesis of hemp explants, where they showed to be able to improve beneficial morphological traits, such as the balanced growth of all the produced shoots and enhanced bud proliferation.

@article{he_evolutionary_2023,
	title = {Evolutionary origin and establishment of a dioecious diploid-tetraploid complex},
	volume = {32},
	issn = {1365-294X},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/mec.16902},
	doi = {10.1111/mec.16902},
	abstract = {Polyploids recurrently emerge in angiosperms, but most polyploids are likely to go extinct before establishment due to minority cytotype exclusion, which may be specifically a constraint for dioecious plants. Here we test the hypothesis that a stable sex-determination system and spatial/ecological isolation facilitate the establishment of dioecious polyploids. We determined the ploidy levels of 351 individuals from 28 populations of the dioecious species Salix polyclona, and resequenced 190 individuals of S. polyclona and related taxa for genomic diversity analyses. The ploidy survey revealed a frequency 52\% of tetraploids in S. polyclona, and genomic k-mer spectra analyses suggested an autopolyploid origin for them. Comparisons of diploid male and female genomes identified a female heterogametic sex-determining factor on chromosome 15, which probably also acts in the dioecious tetraploids. Phylogenetic analyses revealed two diploid clades and a separate clade/grade of tetraploids with a distinct geographic distribution confined to western and central China, where complex mountain systems create higher levels of environmental heterogeneity. Fossil-calibrated phylogenies showed that the polyploids emerged during 7.6–2.3 million years ago, and population demographic histories largely matched the geological and climatic history of the region. Our results suggest that inheritance of the sex-determining system from the diploid progenitor as intrinsic factor and spatial isolation as extrinsic factor may have facilitated the preservation and establishment of polyploid dioecious populations.},
	language = {en},
	number = {11},
	urldate = {2023-05-26},
	journal = {Molecular Ecology},
	author = {He, Li and Guo, Fei-Yi and Cai, Xin-Jie and Chen, Hong-Pu and Lian, Chun-Lan and Wang, Yuan and Shang, Ce and Zhang, Yue and Wagner, Natascha Dorothea and Zhang, Zhi-Xiang and Hörandl, Elvira and Wang, Xiao-Ru},
	month = jun,
	year = {2023},
	note = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1111/mec.16902},
	keywords = {dioecious plants, mountain biodiversity, polyploidization, population history, sex determination system},
	pages = {2732--2749},
}

Polyploids recurrently emerge in angiosperms, but most polyploids are likely to go extinct before establishment due to minority cytotype exclusion, which may be specifically a constraint for dioecious plants. Here we test the hypothesis that a stable sex-determination system and spatial/ecological isolation facilitate the establishment of dioecious polyploids. We determined the ploidy levels of 351 individuals from 28 populations of the dioecious species Salix polyclona, and resequenced 190 individuals of S. polyclona and related taxa for genomic diversity analyses. The ploidy survey revealed a frequency 52% of tetraploids in S. polyclona, and genomic k-mer spectra analyses suggested an autopolyploid origin for them. Comparisons of diploid male and female genomes identified a female heterogametic sex-determining factor on chromosome 15, which probably also acts in the dioecious tetraploids. Phylogenetic analyses revealed two diploid clades and a separate clade/grade of tetraploids with a distinct geographic distribution confined to western and central China, where complex mountain systems create higher levels of environmental heterogeneity. Fossil-calibrated phylogenies showed that the polyploids emerged during 7.6–2.3 million years ago, and population demographic histories largely matched the geological and climatic history of the region. Our results suggest that inheritance of the sex-determining system from the diploid progenitor as intrinsic factor and spatial isolation as extrinsic factor may have facilitated the preservation and establishment of polyploid dioecious populations.

@article{bernacka-wojcik_flexible_2023,
	title = {Flexible {Organic} {Electronic} {Ion} {Pump} for {Flow}-{Free} {Phytohormone} {Delivery} into {Vasculature} of {Intact} {Plants}},
	volume = {10},
	issn = {2198-3844},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1002/advs.202206409},
	doi = {10.1002/advs.202206409},
	abstract = {Plant vasculature transports molecules that play a crucial role in plant signaling including systemic responses and acclimation to diverse environmental conditions. Targeted controlled delivery of molecules to the vascular tissue can be a biomimetic way to induce long distance responses, providing a new tool for the fundamental studies and engineering of stress-tolerant plants. Here, a flexible organic electronic ion pump, an electrophoretic delivery device, for controlled delivery of phytohormones directly in plant vascular tissue is developed. The c-OEIP is based on polyimide-coated glass capillaries that significantly enhance the mechanical robustness of these microscale devices while being minimally disruptive for the plant. The polyelectrolyte channel is based on low-cost and commercially available precursors that can be photocured with blue light, establishing much cheaper and safer system than the state-of-the-art. To trigger OEIP-induced plant response, the phytohormone abscisic acid (ABA) in the petiole of intact Arabidopsis plants is delivered. ABA is one of the main phytohormones involved in plant stress responses and induces stomata closure under drought conditions to reduce water loss and prevent wilting. The OEIP-mediated ABA delivery triggered fast and long-lasting stomata closure far away from the delivery point demonstrating systemic vascular transport of the delivered ABA, verified delivering deuterium-labeled ABA.},
	language = {en},
	number = {14},
	urldate = {2023-05-26},
	journal = {Advanced Science},
	author = {Bernacka-Wojcik, Iwona and Talide, Loïc and Abdel Aziz, Ilaria and Simura, Jan and Oikonomou, Vasileios K. and Rossi, Stefano and Mohammadi, Mohsen and Dar, Abdul Manan and Seitanidou, Maria and Berggren, Magnus and Simon, Daniel T. and Tybrandt, Klas and Jonsson, Magnus P. and Ljung, Karin and Niittylä, Totte and Stavrinidou, Eleni},
	month = may,
	year = {2023},
	note = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1002/advs.202206409},
	keywords = {bioelectronic devices, drug delivery, photo-crosslinking, plants vasculature, polyelectrolytes},
	pages = {2206409},
}

Plant vasculature transports molecules that play a crucial role in plant signaling including systemic responses and acclimation to diverse environmental conditions. Targeted controlled delivery of molecules to the vascular tissue can be a biomimetic way to induce long distance responses, providing a new tool for the fundamental studies and engineering of stress-tolerant plants. Here, a flexible organic electronic ion pump, an electrophoretic delivery device, for controlled delivery of phytohormones directly in plant vascular tissue is developed. The c-OEIP is based on polyimide-coated glass capillaries that significantly enhance the mechanical robustness of these microscale devices while being minimally disruptive for the plant. The polyelectrolyte channel is based on low-cost and commercially available precursors that can be photocured with blue light, establishing much cheaper and safer system than the state-of-the-art. To trigger OEIP-induced plant response, the phytohormone abscisic acid (ABA) in the petiole of intact Arabidopsis plants is delivered. ABA is one of the main phytohormones involved in plant stress responses and induces stomata closure under drought conditions to reduce water loss and prevent wilting. The OEIP-mediated ABA delivery triggered fast and long-lasting stomata closure far away from the delivery point demonstrating systemic vascular transport of the delivered ABA, verified delivering deuterium-labeled ABA.

@article{brunoni_amino_2023,
	title = {Amino acid conjugation of {oxIAA} is a secondary metabolic regulation involved in auxin homeostasis},
	volume = {238},
	issn = {1469-8137},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/nph.18887},
	doi = {10.1111/nph.18887},
	language = {en},
	number = {6},
	urldate = {2023-05-26},
	journal = {New Phytologist},
	author = {Brunoni, Federica and Pěnčík, Aleš and Žukauskaitė, Asta and Ament, Anita and Kopečná, Martina and Collani, Silvio and Kopečný, David and Novák, Ondřej},
	month = jun,
	year = {2023},
	note = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1111/nph.18887},
	keywords = {Arabidopsis, auxin inactivation, conjugation, moss, oxidation, spruce},
	pages = {2264--2270},
}

@article{yang_chromosome-level_2023,
	title = {The chromosome-level genome assembly and genes involved in biosynthesis of nervonic acid of {Malania} oleifera},
	volume = {10},
	copyright = {2023 The Author(s)},
	issn = {2052-4463},
	url = {https://www.nature.com/articles/s41597-023-02218-8},
	doi = {10.1038/s41597-023-02218-8},
	abstract = {Nervonic acid (C24:1 Δ15, NA) is a very long-chain monounsaturated fatty acid, a clinically indispensable resource in maintaining the brain and nerve cells development and regeneration. Till now, NA has been found in 38 plant species, among which the garlic-fruit tree (Malania oleifera) has been evaluated to be the best candidate for NA production. Here, we generated a high-quality chromosome-scale assembly of M. oleifera employing PacBio long-read, short-read Illumina as well as Hi-C sequencing data. The genome assembly consisted of 1.5 Gb with a contig N50 of {\textasciitilde}4.9 Mb and a scaffold N50 of {\textasciitilde}112.6 Mb. {\textasciitilde}98.2\% of the assembly was anchored into 13 pseudo-chromosomes. It contains {\textasciitilde}1123 Mb repeat sequences, and 27,638 protein-coding genes, 568 tRNAs, 230 rRNAs and 352 other non-coding RNAs. Additionally, we documented candidate genes involved in NA biosynthesis including 20 KCSs, 4 KCRs, 1 HCD and 1 ECR, and profiled the expression patterns of these genes in developing seeds. The high-quality assembly of the genome provides insights into the genome evolution of the M. oleifera genome and candidate genes involved in NA biosynthesis in the seeds of this important woody tree.},
	language = {en},
	number = {1},
	urldate = {2023-05-26},
	journal = {Scientific Data},
	author = {Yang, Tianquan and Zhang, Rengang and Tian, Xiaoling and Yao, Gang and Shen, Yuanting and Wang, Sihai and Mao, Jianfeng and Li, Guangyuan and Liu, Aizhong and Sun, Weibang and Ma, Yongpeng},
	month = may,
	year = {2023},
	note = {Number: 1
Publisher: Nature Publishing Group},
	keywords = {Genome, Genomics},
	pages = {298},
}

Nervonic acid (C24:1 Δ15, NA) is a very long-chain monounsaturated fatty acid, a clinically indispensable resource in maintaining the brain and nerve cells development and regeneration. Till now, NA has been found in 38 plant species, among which the garlic-fruit tree (Malania oleifera) has been evaluated to be the best candidate for NA production. Here, we generated a high-quality chromosome-scale assembly of M. oleifera employing PacBio long-read, short-read Illumina as well as Hi-C sequencing data. The genome assembly consisted of 1.5 Gb with a contig N50 of ~4.9 Mb and a scaffold N50 of ~112.6 Mb. ~98.2% of the assembly was anchored into 13 pseudo-chromosomes. It contains ~1123 Mb repeat sequences, and 27,638 protein-coding genes, 568 tRNAs, 230 rRNAs and 352 other non-coding RNAs. Additionally, we documented candidate genes involved in NA biosynthesis including 20 KCSs, 4 KCRs, 1 HCD and 1 ECR, and profiled the expression patterns of these genes in developing seeds. The high-quality assembly of the genome provides insights into the genome evolution of the M. oleifera genome and candidate genes involved in NA biosynthesis in the seeds of this important woody tree.

@article{qu_functional_2023,
	title = {Functional significance of asymmetrical retention of parental alleles in a hybrid pine species complex},
	issn = {1759-6831},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/jse.12953},
	doi = {10.1111/jse.12953},
	abstract = {Hybrid genomes usually harbor asymmetrical parental contributions. However, it is challenging to infer the functional significance of asymmetrical retention of parental alleles in hybrid populations of conifer trees. Here we investigated the diversity in the glutathione S-transferase (GST) gene family in a hybrid pine Pinus densata and its parents (Pinus tabuliformis and Pinus yunnanensis). Plant GSTs play major roles in protecting plants against biotic and abiotic stresses. In this study, 19 orthologous groups of GST genes were identified and cloned from these three species. We examined their expression in different tissues, and then purified the corresponding proteins to characterize their enzymatic activities and specificities toward different substrates. We found that among the 19 GST orthologous groups, divergence in gene expression and in enzymatic activities toward different substrates was prevalent. P. densata preferentially retained P. yunnanensis-like GSTs for 17 out of the 19 gene loci. We determined the first GST crystal structure from conifer species at a resolution of 2.19 Å. Based on this structure, we performed site-directed mutagenesis to replace amino acid residuals in different wild-types of GSTs to understand their functional impacts. Reciprocal replacement of amino acid residuals in native GSTs of P. densata and P. tabuliformis demonstrated significant changes in enzyme functions and identified key sites controlling GSTs activities. This study illustrates an approach to evaluating the functional significance of sequence variations in conifer genomes. Our study also sheds light on plausible mechanisms for controlling the selective retention of parental alleles in the P. densata genome.},
	language = {en},
	urldate = {2023-04-28},
	journal = {Journal of Systematics and Evolution},
	author = {Qu, Chang and Kao, Hong-Na and Xu, Hui and Wang, Bao-Sheng and Yang, Zhi-Ling and Yang, Qi and Liu, Gui-Feng and Wang, Xiao-Ru and Liu, Yan-Jing and Zeng, Qing-Yin},
	month = mar,
	year = {2023},
	note = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1111/jse.12953},
	keywords = {enzymatic function, functional divergence, gene expression, glutathione S-transferases, homoploid hybrid species},
}

Hybrid genomes usually harbor asymmetrical parental contributions. However, it is challenging to infer the functional significance of asymmetrical retention of parental alleles in hybrid populations of conifer trees. Here we investigated the diversity in the glutathione S-transferase (GST) gene family in a hybrid pine Pinus densata and its parents (Pinus tabuliformis and Pinus yunnanensis). Plant GSTs play major roles in protecting plants against biotic and abiotic stresses. In this study, 19 orthologous groups of GST genes were identified and cloned from these three species. We examined their expression in different tissues, and then purified the corresponding proteins to characterize their enzymatic activities and specificities toward different substrates. We found that among the 19 GST orthologous groups, divergence in gene expression and in enzymatic activities toward different substrates was prevalent. P. densata preferentially retained P. yunnanensis-like GSTs for 17 out of the 19 gene loci. We determined the first GST crystal structure from conifer species at a resolution of 2.19 Å. Based on this structure, we performed site-directed mutagenesis to replace amino acid residuals in different wild-types of GSTs to understand their functional impacts. Reciprocal replacement of amino acid residuals in native GSTs of P. densata and P. tabuliformis demonstrated significant changes in enzyme functions and identified key sites controlling GSTs activities. This study illustrates an approach to evaluating the functional significance of sequence variations in conifer genomes. Our study also sheds light on plausible mechanisms for controlling the selective retention of parental alleles in the P. densata genome.

@article{aryal_lrr_2023,
	title = {An {LRR} receptor kinase controls {ABC} transporter substrate preferences during plant growth-defense decisions},
	volume = {33},
	issn = {0960-9822},
	url = {https://www.cell.com/current-biology/abstract/S0960-9822(23)00477-3},
	doi = {10.1016/j.cub.2023.04.029},
	abstract = {The exporter of the auxin precursor indole-3-butyric acid (IBA), ABCG36/PDR8/PEN3, from the model plant Arabidopsis has recently been proposed to also function in the transport of the phytoalexin camalexin. Based on these bonafide substrates, it has been suggested that ABCG36 functions at the interface between growth and defense.
Here, we provide evidence that ABCG36 catalyzes the direct, ATP-dependent export of camalexin across the plasma membrane. We identify the leucine-rich repeat receptor kinase, QIAN SHOU KINASE1 (QSK1), as a functional kinase that physically interacts with and phosphorylates ABCG36. Phosphorylation of ABCG36 by QSK1 unilaterally represses IBA export, allowing camalexin export by ABCG36 conferring pathogen resistance. As a consequence, phospho-dead mutants of ABCG36, as well as qsk1 and abcg36 alleles, are hypersensitive to infection with the root pathogen Fusarium oxysporum, caused by elevated fungal progression.
Our findings indicate a direct regulatory circuit between a receptor kinase and an ABC transporter that functions to control transporter substrate preference during plant growth and defense balance decisions.},
	language = {English},
	number = {10},
	urldate = {2023-05-24},
	journal = {Current Biology},
	author = {Aryal, Bibek and Xia, Jian and Hu, Zehan and Stumpe, Michael and Tsering, Tashi and Liu, Jie and Huynh, John and Fukao, Yoichiro and Glöckner, Nina and Huang, Hsin-Yao and Sáncho-Andrés, Gloria and Pakula, Konrad and Ziegler, Joerg and Gorzolka, Karin and Zwiewka, Marta and Nodzynski, Tomasz and Harter, Klaus and Sánchez-Rodríguez, Clara and Jasiński, Michał and Rosahl, Sabine and Geisler, Markus M.},
	month = may,
	year = {2023},
	keywords = {ABCG36, Arabidopsis thaliana, Botrytis cinerea, Fusarium oxysporum, IBA, PDR8, PEN3, Phytophtora infestans, QSK1, auxin, camalexin, defense, growth},
	pages = {2008--2023.e8},
}

The exporter of the auxin precursor indole-3-butyric acid (IBA), ABCG36/PDR8/PEN3, from the model plant Arabidopsis has recently been proposed to also function in the transport of the phytoalexin camalexin. Based on these bonafide substrates, it has been suggested that ABCG36 functions at the interface between growth and defense. Here, we provide evidence that ABCG36 catalyzes the direct, ATP-dependent export of camalexin across the plasma membrane. We identify the leucine-rich repeat receptor kinase, QIAN SHOU KINASE1 (QSK1), as a functional kinase that physically interacts with and phosphorylates ABCG36. Phosphorylation of ABCG36 by QSK1 unilaterally represses IBA export, allowing camalexin export by ABCG36 conferring pathogen resistance. As a consequence, phospho-dead mutants of ABCG36, as well as qsk1 and abcg36 alleles, are hypersensitive to infection with the root pathogen Fusarium oxysporum, caused by elevated fungal progression. Our findings indicate a direct regulatory circuit between a receptor kinase and an ABC transporter that functions to control transporter substrate preference during plant growth and defense balance decisions.

@article{wu_threatened_2023,
	title = {Threatened forests},
	volume = {24},
	issn = {1469-221X},
	url = {https://www.embopress.org/doi/full/10.15252/embr.202357106},
	doi = {10.15252/embr.202357106},
	abstract = {Climate change is having dramatic effects on forest health and growth ? tree genomics provides tools for understanding and mitigating these effects.},
	number = {5},
	urldate = {2023-05-12},
	journal = {EMBO reports},
	author = {Wu, Harry and Nilsson, Ove},
	month = may,
	year = {2023},
	note = {Publisher: John Wiley \& Sons, Ltd},
	pages = {e57106},
}

Climate change is having dramatic effects on forest health and growth ? tree genomics provides tools for understanding and mitigating these effects.

@article{dube_transcriptomics_2023,
	title = {Transcriptomics of ivermectin response in {Caenorhabditis} elegans: {Integrating} abamectin quantitative trait loci and comparison to the {Ivermectin}-exposed {DA1316} strain},
	volume = {18},
	issn = {1932-6203},
	shorttitle = {Transcriptomics of ivermectin response in {Caenorhabditis} elegans},
	url = {https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0285262},
	doi = {10.1371/journal.pone.0285262},
	abstract = {Parasitic nematodes pose a significant threat to human and animal health, as well as cause economic losses in the agricultural sector. The use of anthelmintic drugs, such as Ivermectin (IVM), to control these parasites has led to widespread drug resistance. Identifying genetic markers of resistance in parasitic nematodes can be challenging, but the free-living nematode Caenorhabditis elegans provides a suitable model. In this study, we aimed to analyze the transcriptomes of adult C. elegans worms of the N2 strain exposed to the anthelmintic drug Ivermectin (IVM), and compare them to those of the resistant strain DA1316 and the recently identified Abamectin Quantitative Trait Loci (QTL) on chromosome V. We exposed pools of 300 adult N2 worms to IVM (10−7 and 10−8 M) for 4 hours at 20°C, extracted total RNA and sequenced it on the Illumina NovaSeq6000 platform. Differentially expressed genes (DEGs) were determined using an in-house pipeline. The DEGs were compared to genes from a previous microarray study on IVM-resistant C. elegans and Abamectin-QTL. Our results revealed 615 DEGs (183 up-regulated and 432 down-regulated genes) from diverse gene families in the N2 C. elegans strain. Of these DEGs, 31 overlapped with genes from IVM-exposed adult worms of the DA1316 strain. We identified 19 genes, including the folate transporter (folt-2) and the transmembrane transporter (T22F3.11), which exhibited an opposite expression in N2 and the DA1316 strain and were deemed potential candidates. Additionally, we compiled a list of potential candidates for further research including T-type calcium channel (cca-1), potassium chloride cotransporter (kcc-2), as well as other genes such as glutamate-gated channel (glc-1) that mapped to the Abamectin-QTL.},
	language = {en},
	number = {5},
	urldate = {2023-05-12},
	journal = {PLOS ONE},
	author = {Dube, Faruk and Hinas, Andrea and Delhomme, Nicolas and Åbrink, Magnus and Svärd, Staffan and Tydén, Eva},
	year = {2023},
	note = {Publisher: Public Library of Science},
	keywords = {Apoptosis, Caenorhabditis elegans, Gene expression, Quantitative trait loci, Transcription factors, Transcriptional control, Transmembrane receptors, Transmembrane transport proteins},
	pages = {e0285262},
}

Parasitic nematodes pose a significant threat to human and animal health, as well as cause economic losses in the agricultural sector. The use of anthelmintic drugs, such as Ivermectin (IVM), to control these parasites has led to widespread drug resistance. Identifying genetic markers of resistance in parasitic nematodes can be challenging, but the free-living nematode Caenorhabditis elegans provides a suitable model. In this study, we aimed to analyze the transcriptomes of adult C. elegans worms of the N2 strain exposed to the anthelmintic drug Ivermectin (IVM), and compare them to those of the resistant strain DA1316 and the recently identified Abamectin Quantitative Trait Loci (QTL) on chromosome V. We exposed pools of 300 adult N2 worms to IVM (10−7 and 10−8 M) for 4 hours at 20°C, extracted total RNA and sequenced it on the Illumina NovaSeq6000 platform. Differentially expressed genes (DEGs) were determined using an in-house pipeline. The DEGs were compared to genes from a previous microarray study on IVM-resistant C. elegans and Abamectin-QTL. Our results revealed 615 DEGs (183 up-regulated and 432 down-regulated genes) from diverse gene families in the N2 C. elegans strain. Of these DEGs, 31 overlapped with genes from IVM-exposed adult worms of the DA1316 strain. We identified 19 genes, including the folate transporter (folt-2) and the transmembrane transporter (T22F3.11), which exhibited an opposite expression in N2 and the DA1316 strain and were deemed potential candidates. Additionally, we compiled a list of potential candidates for further research including T-type calcium channel (cca-1), potassium chloride cotransporter (kcc-2), as well as other genes such as glutamate-gated channel (glc-1) that mapped to the Abamectin-QTL.

@article{zhao_haplotype-resolved_2023,
	title = {Haplotype-resolved genome assembly of {Coriaria} nepalensis a non-legume nitrogen-fixing shrub},
	volume = {10},
	copyright = {2023 The Author(s)},
	issn = {2052-4463},
	url = {https://www.nature.com/articles/s41597-023-02171-6},
	doi = {10.1038/s41597-023-02171-6},
	abstract = {Coriaria nepalensis Wall. (Coriariaceae) is a nitrogen-fixing shrub which forms root nodules with the actinomycete Frankia. Oils and extracts of C. nepalensis have been reported to be bacteriostatic and insecticidal, and C. nepalensis bark provides a valuable tannin resource. Here, by combining PacBio HiFi sequencing and Hi-C scaffolding techniques, we generated a haplotype-resolved chromosome-scale genome assembly for C. nepalensis. This genome assembly is approximately 620 Mb in size with a contig N50 of 11 Mb, with 99.9\% of the total assembled sequences anchored to 40 pseudochromosomes. We predicted 60,862 protein-coding genes of which 99.5\% were annotated from databases. We further identified 939 tRNAs, 7,297 rRNAs, and 982 ncRNAs. The chromosome-scale genome of C. nepalensis is expected to be a significant resource for understanding the genetic basis of root nodulation with Frankia, toxicity, and tannin biosynthesis.},
	language = {en},
	number = {1},
	urldate = {2023-05-12},
	journal = {Scientific Data},
	author = {Zhao, Shi-Wei and Guo, Jing-Fang and Kong, Lei and Nie, Shuai and Yan, Xue-Mei and Shi, Tian-Le and Tian, Xue-Chan and Ma, Hai-Yao and Bao, Yu-Tao and Li, Zhi-Chao and Chen, Zhao-Yang and Zhang, Ren-Gang and Ma, Yong-Peng and El-Kassaby, Yousry A. and Porth, Ilga and Zhao, Wei and Mao, Jian-Feng},
	month = may,
	year = {2023},
	note = {Number: 1
Publisher: Nature Publishing Group},
	keywords = {Computational biology and bioinformatics, Plant sciences},
	pages = {259},
}

Coriaria nepalensis Wall. (Coriariaceae) is a nitrogen-fixing shrub which forms root nodules with the actinomycete Frankia. Oils and extracts of C. nepalensis have been reported to be bacteriostatic and insecticidal, and C. nepalensis bark provides a valuable tannin resource. Here, by combining PacBio HiFi sequencing and Hi-C scaffolding techniques, we generated a haplotype-resolved chromosome-scale genome assembly for C. nepalensis. This genome assembly is approximately 620 Mb in size with a contig N50 of 11 Mb, with 99.9% of the total assembled sequences anchored to 40 pseudochromosomes. We predicted 60,862 protein-coding genes of which 99.5% were annotated from databases. We further identified 939 tRNAs, 7,297 rRNAs, and 982 ncRNAs. The chromosome-scale genome of C. nepalensis is expected to be a significant resource for understanding the genetic basis of root nodulation with Frankia, toxicity, and tannin biosynthesis.

@article{gil-munoz_qtl_2023,
	title = {{QTL} mapping of the narrow-branch “{Pendula}” phenotype in {Norway} spruce ({Picea} abies {L}. {Karst}.)},
	volume = {19},
	issn = {1614-2950},
	url = {https://doi.org/10.1007/s11295-023-01599-6},
	doi = {10.1007/s11295-023-01599-6},
	abstract = {Pendula-phenotyped Norway spruce has a potential forestry interest for high-density plantations. This phenotype is believed to be caused by a dominant single mutation. Despite the availability of RAPD markers linked to the trait, the nature of the mutation is yet unknown. We performed a quantitative trait loci (QTL) mapping based on two different progenies of F1 crosses between pendula and normal crowned trees using NGS technologies. Approximately 25\% of all gene bearing scaffolds of Picea abies genome assembly v1.0 were mapped to 12 linkage groups and a single QTL, positioned near the center of LG VI, was found in both crosses. The closest probe markers placed on the maps were positioned 0.82 cm and 0.48 cm away from the Pendula marker in two independent pendula-crowned × normal-crowned wild-type crosses, respectively. We have identified genes close to the QTL region with differential mutations on coding regions and discussed their potential role in changing branch architecture.},
	language = {en},
	number = {3},
	urldate = {2023-05-08},
	journal = {Tree Genetics \& Genomes},
	author = {Gil-Muñoz, Francisco and Bernhardsson, Carolina and Ranade, Sonali Sachin and Scofield, Douglas G. and Pulkkinen, Pertti O. and Ingvarsson, Pär K. and García-Gil, M. Rosario},
	month = may,
	year = {2023},
	keywords = {Forest breeding, Genetic map, Pendula, Picea, QTL, Spruce},
	pages = {28},
}

Pendula-phenotyped Norway spruce has a potential forestry interest for high-density plantations. This phenotype is believed to be caused by a dominant single mutation. Despite the availability of RAPD markers linked to the trait, the nature of the mutation is yet unknown. We performed a quantitative trait loci (QTL) mapping based on two different progenies of F1 crosses between pendula and normal crowned trees using NGS technologies. Approximately 25% of all gene bearing scaffolds of Picea abies genome assembly v1.0 were mapped to 12 linkage groups and a single QTL, positioned near the center of LG VI, was found in both crosses. The closest probe markers placed on the maps were positioned 0.82 cm and 0.48 cm away from the Pendula marker in two independent pendula-crowned × normal-crowned wild-type crosses, respectively. We have identified genes close to the QTL region with differential mutations on coding regions and discussed their potential role in changing branch architecture.

@article{wang_chromosome-scale_2023,
	title = {Chromosome-scale genome assembly and insights into the metabolome and gene regulation of leaf color transition in an important oak species, {Quercus} dentata},
	volume = {238},
	issn = {1469-8137},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/nph.18814},
	doi = {10.1111/nph.18814},
	abstract = {Quercus dentata Thunb., a dominant forest tree species in northern China, has significant ecological and ornamental value due to its adaptability and beautiful autumn coloration, with color changes from green to yellow into red resulting from the autumnal shifts in leaf pigmentation. However, the key genes and molecular regulatory mechanisms for leaf color transition remain to be investigated. First, we presented a high-quality chromosome-scale assembly for Q. dentata. This 893.54 Mb sized genome (contig N50 = 4.21 Mb, scaffold N50 = 75.55 Mb; 2n = 24) harbors 31 584 protein-coding genes. Second, our metabolome analyses uncovered pelargonidin-3-O-glucoside, cyanidin-3-O-arabinoside, and cyanidin-3-O-glucoside as the main pigments involved in leaf color transition. Third, gene co-expression further identified the MYB-bHLH-WD40 (MBW) transcription activation complex as central to anthocyanin biosynthesis regulation. Notably, transcription factor (TF) QdNAC (QD08G038820) was highly co-expressed with this MBW complex and may regulate anthocyanin accumulation and chlorophyll degradation during leaf senescence through direct interaction with another TF, QdMYB (QD01G020890), as revealed by our further protein–protein and DNA–protein interaction assays. Our high-quality genome assembly, metabolome, and transcriptome resources further enrich Quercus genomics and will facilitate upcoming exploration of ornamental values and environmental adaptability in this important genus.},
	language = {en},
	number = {5},
	urldate = {2023-05-05},
	journal = {New Phytologist},
	author = {Wang, Wen-Bo and He, Xiang-Feng and Yan, Xue-Mei and Ma, Bo and Lu, Cun-Fu and Wu, Jing and Zheng, Yi and Wang, Wen-He and Xue, Wen-Bo and Tian, Xue-Chan and Guo, Jing-Fang and El-Kassaby, Yousry A. and Porth, Ilga and Leng, Ping-Sheng and Hu, Zeng-Hui and Mao, Jian-Feng},
	year = {2023},
	note = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1111/nph.18814},
	keywords = {Quercus, co-expression network, flavonoids, gene regulation, leaf color transition},
	pages = {2016--2032},
}

Quercus dentata Thunb., a dominant forest tree species in northern China, has significant ecological and ornamental value due to its adaptability and beautiful autumn coloration, with color changes from green to yellow into red resulting from the autumnal shifts in leaf pigmentation. However, the key genes and molecular regulatory mechanisms for leaf color transition remain to be investigated. First, we presented a high-quality chromosome-scale assembly for Q. dentata. This 893.54 Mb sized genome (contig N50 = 4.21 Mb, scaffold N50 = 75.55 Mb; 2n = 24) harbors 31 584 protein-coding genes. Second, our metabolome analyses uncovered pelargonidin-3-O-glucoside, cyanidin-3-O-arabinoside, and cyanidin-3-O-glucoside as the main pigments involved in leaf color transition. Third, gene co-expression further identified the MYB-bHLH-WD40 (MBW) transcription activation complex as central to anthocyanin biosynthesis regulation. Notably, transcription factor (TF) QdNAC (QD08G038820) was highly co-expressed with this MBW complex and may regulate anthocyanin accumulation and chlorophyll degradation during leaf senescence through direct interaction with another TF, QdMYB (QD01G020890), as revealed by our further protein–protein and DNA–protein interaction assays. Our high-quality genome assembly, metabolome, and transcriptome resources further enrich Quercus genomics and will facilitate upcoming exploration of ornamental values and environmental adaptability in this important genus.

@article{green_formate_2023,
	title = {Formate overflow drives toxic folate trapping in {MTHFD1} inhibited cancer cells},
	volume = {5},
	copyright = {2023 The Author(s)},
	issn = {2522-5812},
	url = {https://www.nature.com/articles/s42255-023-00771-5},
	doi = {10.1038/s42255-023-00771-5},
	abstract = {Cancer cells fuel their increased need for nucleotide supply by upregulating one-carbon (1C) metabolism, including the enzymes methylenetetrahydrofolate dehydrogenase–cyclohydrolase 1 and 2 (MTHFD1 and MTHFD2). TH9619 is a potent inhibitor of dehydrogenase and cyclohydrolase activities in both MTHFD1 and MTHFD2, and selectively kills cancer cells. Here, we reveal that, in cells, TH9619 targets nuclear MTHFD2 but does not inhibit mitochondrial MTHFD2. Hence, overflow of formate from mitochondria continues in the presence of TH9619. TH9619 inhibits the activity of MTHFD1 occurring downstream of mitochondrial formate release, leading to the accumulation of 10-formyl-tetrahydrofolate, which we term a ‘folate trap’. This results in thymidylate depletion and death of MTHFD2-expressing cancer cells. This previously uncharacterized folate trapping mechanism is exacerbated by physiological hypoxanthine levels that block the de novo purine synthesis pathway, and additionally prevent 10-formyl-tetrahydrofolate consumption for purine synthesis. The folate trapping mechanism described here for TH9619 differs from other MTHFD1/2 inhibitors and antifolates. Thus, our findings uncover an approach to attack cancer and reveal a regulatory mechanism in 1C metabolism.},
	language = {en},
	number = {4},
	urldate = {2023-05-05},
	journal = {Nature Metabolism},
	author = {Green, Alanna C. and Marttila, Petra and Kiweler, Nicole and Chalkiadaki, Christina and Wiita, Elisée and Cookson, Victoria and Lesur, Antoine and Eiden, Kim and Bernardin, François and Vallin, Karl S. A. and Borhade, Sanjay and Long, Maeve and Ghahe, Elahe Kamali and Jiménez-Alonso, Julio J. and Jemth, Ann-Sofie and Loseva, Olga and Mortusewicz, Oliver and Meyers, Marianne and Viry, Elodie and Johansson, Annika I. and Hodek, Ondřej and Homan, Evert and Bonagas, Nadilly and Ramos, Louise and Sandberg, Lars and Frödin, Morten and Moussay, Etienne and Slipicevic, Ana and Letellier, Elisabeth and Paggetti, Jérôme and Sørensen, Claus Storgaard and Helleday, Thomas and Henriksson, Martin and Meiser, Johannes},
	month = apr,
	year = {2023},
	note = {Number: 4
Publisher: Nature Publishing Group},
	keywords = {Cancer metabolism, Cell death, Metabolism},
	pages = {642--659},
}

Cancer cells fuel their increased need for nucleotide supply by upregulating one-carbon (1C) metabolism, including the enzymes methylenetetrahydrofolate dehydrogenase–cyclohydrolase 1 and 2 (MTHFD1 and MTHFD2). TH9619 is a potent inhibitor of dehydrogenase and cyclohydrolase activities in both MTHFD1 and MTHFD2, and selectively kills cancer cells. Here, we reveal that, in cells, TH9619 targets nuclear MTHFD2 but does not inhibit mitochondrial MTHFD2. Hence, overflow of formate from mitochondria continues in the presence of TH9619. TH9619 inhibits the activity of MTHFD1 occurring downstream of mitochondrial formate release, leading to the accumulation of 10-formyl-tetrahydrofolate, which we term a ‘folate trap’. This results in thymidylate depletion and death of MTHFD2-expressing cancer cells. This previously uncharacterized folate trapping mechanism is exacerbated by physiological hypoxanthine levels that block the de novo purine synthesis pathway, and additionally prevent 10-formyl-tetrahydrofolate consumption for purine synthesis. The folate trapping mechanism described here for TH9619 differs from other MTHFD1/2 inhibitors and antifolates. Thus, our findings uncover an approach to attack cancer and reveal a regulatory mechanism in 1C metabolism.

@article{giaume_two_2023,
	title = {Two florigens and a florigen-like protein form a triple regulatory module at the shoot apical meristem to promote reproductive transitions in rice},
	volume = {9},
	copyright = {2023 The Author(s), under exclusive licence to Springer Nature Limited},
	issn = {2055-0278},
	url = {https://www.nature.com/articles/s41477-023-01383-3},
	doi = {10.1038/s41477-023-01383-3},
	abstract = {Many plant species monitor and respond to changes in day length (photoperiod) for aligning reproduction with a favourable season. Day length is measured in leaves and, when appropriate, leads to the production of floral stimuli called florigens that are transmitted to the shoot apical meristem to initiate inflorescence development1. Rice possesses two florigens encoded by HEADING DATE 3a (Hd3a) and RICE FLOWERING LOCUS T 1 (RFT1)2. Here we show that the arrival of Hd3a and RFT1 at the shoot apical meristem activates FLOWERING LOCUS T-LIKE 1 (FT-L1), encoding a florigen-like protein that shows features partially differentiating it from typical florigens. FT-L1 potentiates the effects of Hd3a and RFT1 during the conversion of the vegetative meristem into an inflorescence meristem and organizes panicle branching by imposing increasing determinacy to distal meristems. A module comprising Hd3a, RFT1 and FT-L1 thus enables the initiation and balanced progression of panicle development towards determinacy.},
	language = {en},
	number = {4},
	urldate = {2023-04-28},
	journal = {Nature Plants},
	author = {Giaume, Francesca and Bono, Giulia Ave and Martignago, Damiano and Miao, Yiling and Vicentini, Giulio and Toriba, Taiyo and Wang, Rui and Kong, Dali and Cerise, Martina and Chirivì, Daniele and Biancucci, Marco and Khahani, Bahman and Morandini, Piero and Tameling, Wladimir and Martinotti, Michela and Goretti, Daniela and Coupland, George and Kater, Martin and Brambilla, Vittoria and Miki, Daisuke and Kyozuka, Junko and Fornara, Fabio},
	month = apr,
	year = {2023},
	note = {Number: 4
Publisher: Nature Publishing Group},
	keywords = {Flowering, Light responses, Plant signalling},
	pages = {525--534},
}

Many plant species monitor and respond to changes in day length (photoperiod) for aligning reproduction with a favourable season. Day length is measured in leaves and, when appropriate, leads to the production of floral stimuli called florigens that are transmitted to the shoot apical meristem to initiate inflorescence development1. Rice possesses two florigens encoded by HEADING DATE 3a (Hd3a) and RICE FLOWERING LOCUS T 1 (RFT1)2. Here we show that the arrival of Hd3a and RFT1 at the shoot apical meristem activates FLOWERING LOCUS T-LIKE 1 (FT-L1), encoding a florigen-like protein that shows features partially differentiating it from typical florigens. FT-L1 potentiates the effects of Hd3a and RFT1 during the conversion of the vegetative meristem into an inflorescence meristem and organizes panicle branching by imposing increasing determinacy to distal meristems. A module comprising Hd3a, RFT1 and FT-L1 thus enables the initiation and balanced progression of panicle development towards determinacy.

@article{li_methylation_2023,
	title = {The methylation landscape of giga-genome and the epigenetic timer of age in {Chinese} pine},
	volume = {14},
	copyright = {2023 The Author(s)},
	issn = {2041-1723},
	url = {https://www.nature.com/articles/s41467-023-37684-6},
	doi = {10.1038/s41467-023-37684-6},
	abstract = {DNA methylation level declines during aging of mammals. Here, the authors report single-base resolution landscape of cytosine DNA methylation at different ages of Chinese pine and show that the global cytosine DNA methylation gradually increases as age progresses.},
	language = {en},
	number = {1},
	urldate = {2023-04-21},
	journal = {Nature Communications},
	author = {Li, Jiang and Han, Fangxu and Yuan, Tongqi and Li, Wei and Li, Yue and Wu, Harry X. and Wei, Hairong and Niu, Shihui},
	month = apr,
	year = {2023},
	note = {Number: 1
Publisher: Nature Publishing Group},
	keywords = {Agricultural genetics, DNA methylation, Plant development, Plant genetics},
	pages = {1--11},
}

DNA methylation level declines during aging of mammals. Here, the authors report single-base resolution landscape of cytosine DNA methylation at different ages of Chinese pine and show that the global cytosine DNA methylation gradually increases as age progresses.

@article{donev_field_2023,
	title = ,
	volume = {21},
	issn = {1467-7652},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/pbi.14012},
	doi = {10.1111/pbi.14012},
	abstract = {Trees constitute promising renewable feedstocks for biorefinery using biochemical conversion, but their recalcitrance restricts their attractiveness for the industry. To obtain trees with reduced recalcitrance, large-scale genetic engineering experiments were performed in hybrid aspen blindly targeting genes expressed during wood formation and 32 lines representing seven constructs were selected for characterization in the field. Here we report phenotypes of five-year old trees considering 49 traits related to growth and wood properties. The best performing construct considering growth and glucose yield in saccharification with acid pretreatment had suppressed expression of the gene encoding an uncharacterized 2-oxoglutarate-dependent dioxygenase (2OGD). It showed minor changes in wood chemistry but increased nanoporosity and glucose conversion. Suppressed levels of SUCROSE SYNTHASE, (SuSy), CINNAMATE 4-HYDROXYLASE (C4H) and increased levels of GTPase activating protein for ADP-ribosylation factor ZAC led to significant growth reductions and anatomical abnormalities. However, C4H and SuSy constructs greatly improved glucose yields in saccharification without and with pretreatment, respectively. Traits associated with high glucose yields were different for saccharification with and without pretreatment. While carbohydrates, phenolics and tension wood contents positively impacted the yields without pretreatment and growth, lignin content and S/G ratio were negative factors, the yields with pretreatment positively correlated with S lignin and negatively with carbohydrate contents. The genotypes with high glucose yields had increased nanoporosity and mGlcA/Xyl ratio, and some had shorter polymers extractable with subcritical water compared to wild-type. The pilot-scale industrial-like pretreatment of best-performing 2OGD construct confirmed its superior sugar yields, supporting our strategy.},
	language = {en},
	number = {5},
	urldate = {2023-04-21},
	journal = {Plant Biotechnology Journal},
	author = {Donev, Evgeniy N. and Derba-Maceluch, Marta and Yassin, Zakiya and Gandla, Madhavi Latha and Pramod, Sivan and Heinonen, Emilia and Kumar, Vikash and Scheepers, Gerhard and Vilaplana, Francisco and Johansson, Ulf and Hertzberg, Magnus and Sundberg, Björn and Winestrand, Sandra and Hörnberg, Andreas and Alriksson, Björn and Jönsson, Leif J. and Mellerowicz, Ewa J.},
	year = {2023},
	note = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1111/pbi.14012},
	keywords = {BET analysis, Populus, SilviScan, enzymatic saccharification, field trial, secondary cell wall, subcritical water extraction, transgenic Populus, transgenic trees, wood quality},
	pages = {1005--1021},
}

Trees constitute promising renewable feedstocks for biorefinery using biochemical conversion, but their recalcitrance restricts their attractiveness for the industry. To obtain trees with reduced recalcitrance, large-scale genetic engineering experiments were performed in hybrid aspen blindly targeting genes expressed during wood formation and 32 lines representing seven constructs were selected for characterization in the field. Here we report phenotypes of five-year old trees considering 49 traits related to growth and wood properties. The best performing construct considering growth and glucose yield in saccharification with acid pretreatment had suppressed expression of the gene encoding an uncharacterized 2-oxoglutarate-dependent dioxygenase (2OGD). It showed minor changes in wood chemistry but increased nanoporosity and glucose conversion. Suppressed levels of SUCROSE SYNTHASE, (SuSy), CINNAMATE 4-HYDROXYLASE (C4H) and increased levels of GTPase activating protein for ADP-ribosylation factor ZAC led to significant growth reductions and anatomical abnormalities. However, C4H and SuSy constructs greatly improved glucose yields in saccharification without and with pretreatment, respectively. Traits associated with high glucose yields were different for saccharification with and without pretreatment. While carbohydrates, phenolics and tension wood contents positively impacted the yields without pretreatment and growth, lignin content and S/G ratio were negative factors, the yields with pretreatment positively correlated with S lignin and negatively with carbohydrate contents. The genotypes with high glucose yields had increased nanoporosity and mGlcA/Xyl ratio, and some had shorter polymers extractable with subcritical water compared to wild-type. The pilot-scale industrial-like pretreatment of best-performing 2OGD construct confirmed its superior sugar yields, supporting our strategy.

@article{hodek_structural_2023,
	title = {Structural elucidation of 3-nitrophenylhydrazine derivatives of tricarboxylic acid cycle acids and optimization of their fragmentation to boost sensitivity in liquid chromatography-mass spectrometry},
	volume = {1222},
	issn = {1570-0232},
	url = {https://www.sciencedirect.com/science/article/pii/S1570023223001290},
	doi = {10.1016/j.jchromb.2023.123719},
	abstract = {Carboxylic acids participate in many metabolic pathways including tricarboxylic acid (TCA) cycle. Therefore, there have been ongoing attempts to develop sensitive liquid chromatography-mass spectrometry methods over the last decades. Derivatization of the carboxylic acids with 3-nitrophenylhydrazine presents a well-established methodology, and yet the derivatized species of polycarboxylic acids and their fragmentation in collision-induced dissociation have not been fully studied before. In our study, we elucidated how annotation of most abundant 3-nitrophenylhydrazine derivatives and optimization of their fragmentation in multiple reaction monitoring can boost the sensitivity, especially for polycarboxylic acids. Finally, the optimized liquid chromatography-tandem mass spectrometry method allowed for low detection limits ranging from 10 pM for 2-oxoglutaric acid to 800 pM for pyruvic acid. All TCA carboxylates were quantified in 20 µL of human plasma and the targeted method was validated in the same matrix. The same methodology with a modified gradient elution was also applied to untargeted screening of fatty acids by using high-resolution mass spectrometry enabling identification of 29 medium- to long-chain fatty acids in human plasma. The TCA carboxylates were also quantified in 105 of C2C12 mouse myuotube cells grown under different treatments to proof applicability of the methodology to biological studies in a wider sense. However, unfortunately all the TCA carboxylates were also found in the derivatized blanks in substantial amounts, which prevents from using the methodology for quantification of the carboxylates in less than 105 cells.},
	language = {en},
	urldate = {2023-04-21},
	journal = {Journal of Chromatography B},
	author = {Hodek, Ondřej and Henderson, John and Argemi-Muntadas, Lidia and Khan, Adnan and Moritz, Thomas},
	month = apr,
	year = {2023},
	keywords = {3-nitrophenylhydrazine, Carboxylic acid, Derivatization, Liquid chromatography-mass spectrometry},
	pages = {123719},
}

Carboxylic acids participate in many metabolic pathways including tricarboxylic acid (TCA) cycle. Therefore, there have been ongoing attempts to develop sensitive liquid chromatography-mass spectrometry methods over the last decades. Derivatization of the carboxylic acids with 3-nitrophenylhydrazine presents a well-established methodology, and yet the derivatized species of polycarboxylic acids and their fragmentation in collision-induced dissociation have not been fully studied before. In our study, we elucidated how annotation of most abundant 3-nitrophenylhydrazine derivatives and optimization of their fragmentation in multiple reaction monitoring can boost the sensitivity, especially for polycarboxylic acids. Finally, the optimized liquid chromatography-tandem mass spectrometry method allowed for low detection limits ranging from 10 pM for 2-oxoglutaric acid to 800 pM for pyruvic acid. All TCA carboxylates were quantified in 20 µL of human plasma and the targeted method was validated in the same matrix. The same methodology with a modified gradient elution was also applied to untargeted screening of fatty acids by using high-resolution mass spectrometry enabling identification of 29 medium- to long-chain fatty acids in human plasma. The TCA carboxylates were also quantified in 105 of C2C12 mouse myuotube cells grown under different treatments to proof applicability of the methodology to biological studies in a wider sense. However, unfortunately all the TCA carboxylates were also found in the derivatized blanks in substantial amounts, which prevents from using the methodology for quantification of the carboxylates in less than 105 cells.

@article{priebe_spectrum_2023,
	title = {The spectrum of knowledge: integrating knowledge dimensions in the context of forests and climate change},
	issn = {1862-4057},
	shorttitle = {The spectrum of knowledge},
	url = {https://doi.org/10.1007/s11625-023-01309-0},
	doi = {10.1007/s11625-023-01309-0},
	abstract = {Integrated approaches to knowledge that recognize meaning, behavior, culture, and systems as domains of knowledge are increasingly employed in holistic views on sustainability transformation but often remain conceptually driven. In this study, we analyze empirical data from a collaborative process with local forest stakeholders in Sweden through the lens of individual, collective, interior, and exterior knowledge dimensions. We show that the participants’ understanding of knowledge about forests and climate change presents a nuanced picture of how knowledge and acting are connected. Meaning-making, cultural frames, and techno-scientific knowledge conceptions converge, interact, and, at times, replace or diminish each other. The connection and interplay of these dimensions, we suggest, can be understood as a knowledge spectrum. These insights into integrated knowledge, based on an empirical case, must be addressed in the production of knowledge, both to grasp the climate and sustainability issues that face us and to support action in response to them.},
	language = {en},
	urldate = {2023-04-21},
	journal = {Sustainability Science},
	author = {Priebe, Janina and Hallberg-Sramek, Isabella and Reimerson, Elsa and Mårald, Erland},
	month = mar,
	year = {2023},
	keywords = {Climate change, Forests, Knowledge, Sustainability, Sweden, Transformation},
}

Integrated approaches to knowledge that recognize meaning, behavior, culture, and systems as domains of knowledge are increasingly employed in holistic views on sustainability transformation but often remain conceptually driven. In this study, we analyze empirical data from a collaborative process with local forest stakeholders in Sweden through the lens of individual, collective, interior, and exterior knowledge dimensions. We show that the participants’ understanding of knowledge about forests and climate change presents a nuanced picture of how knowledge and acting are connected. Meaning-making, cultural frames, and techno-scientific knowledge conceptions converge, interact, and, at times, replace or diminish each other. The connection and interplay of these dimensions, we suggest, can be understood as a knowledge spectrum. These insights into integrated knowledge, based on an empirical case, must be addressed in the production of knowledge, both to grasp the climate and sustainability issues that face us and to support action in response to them.

@article{bai_seedtransnet_2023,
	title = {{SeedTransNet}: a directional translational network revealing regulatory patterns during seed maturation and germination},
	volume = {74},
	issn = {0022-0957},
	shorttitle = {{SeedTransNet}},
	url = {https://doi.org/10.1093/jxb/erac394},
	doi = {10.1093/jxb/erac394},
	abstract = {Seed maturation is the developmental process that prepares the embryo for the desiccated waiting period before germination. It is associated with a series of physiological changes leading to the establishment of seed dormancy, seed longevity, and desiccation tolerance. We studied translational changes during seed maturation and observed a gradual reduction in global translation during seed maturation. Transcriptome and translatome profiling revealed specific reduction in the translation of thousands of genes. By including previously published data on germination and seedling establishment, a regulatory network based on polysome occupancy data was constructed: SeedTransNet. Network analysis predicted translational regulatory pathways involving hundreds of genes with distinct functions. The network identified specific transcript sequence features suggesting separate translational regulatory circuits. The network revealed several seed maturation-associated genes as central nodes, and this was confirmed by specific seed phenotypes of the respective mutants. One of the regulators identified, an AWPM19 family protein, PM19-Like1 (PM19L1), was shown to regulate seed dormancy and longevity. This putative RNA-binding protein also affects the translational regulation of its target mRNA, as identified by SeedTransNet. Our data show the usefulness of SeedTransNet in identifying regulatory pathways during seed phase transitions.},
	number = {7},
	urldate = {2023-04-14},
	journal = {Journal of Experimental Botany},
	author = {Bai, Bing and Schiffthaler, Bastian and van der Horst, Sjors and Willems, Leo and Vergara, Alexander and Karlström, Jacob and Mähler, Niklas and Delhomme, Nicolas and Bentsink, Leónie and Hanson, Johannes},
	month = apr,
	year = {2023},
	pages = {2416--2432},
}

Seed maturation is the developmental process that prepares the embryo for the desiccated waiting period before germination. It is associated with a series of physiological changes leading to the establishment of seed dormancy, seed longevity, and desiccation tolerance. We studied translational changes during seed maturation and observed a gradual reduction in global translation during seed maturation. Transcriptome and translatome profiling revealed specific reduction in the translation of thousands of genes. By including previously published data on germination and seedling establishment, a regulatory network based on polysome occupancy data was constructed: SeedTransNet. Network analysis predicted translational regulatory pathways involving hundreds of genes with distinct functions. The network identified specific transcript sequence features suggesting separate translational regulatory circuits. The network revealed several seed maturation-associated genes as central nodes, and this was confirmed by specific seed phenotypes of the respective mutants. One of the regulators identified, an AWPM19 family protein, PM19-Like1 (PM19L1), was shown to regulate seed dormancy and longevity. This putative RNA-binding protein also affects the translational regulation of its target mRNA, as identified by SeedTransNet. Our data show the usefulness of SeedTransNet in identifying regulatory pathways during seed phase transitions.

@article{escamez_genetic_2023,
	title = {Genetic markers and tree properties predicting wood biorefining potential in aspen ({Populus} tremula) bioenergy feedstock},
	volume = {16},
	issn = {2731-3654},
	url = {https://doi.org/10.1186/s13068-023-02315-1},
	doi = {10.1186/s13068-023-02315-1},
	abstract = {Wood represents the majority of the biomass on land and constitutes a renewable source of biofuels and other bioproducts. However, wood is recalcitrant to bioconversion, raising a need for feedstock improvement in production of, for instance, biofuels. We investigated the properties of wood that affect bioconversion, as well as the underlying genetics, to help identify superior tree feedstocks for biorefining.},
	number = {1},
	urldate = {2023-04-14},
	journal = {Biotechnology for Biofuels and Bioproducts},
	author = {Escamez, Sacha and Robinson, Kathryn M. and Luomaranta, Mikko and Gandla, Madhavi Latha and Mähler, Niklas and Yassin, Zakiya and Grahn, Thomas and Scheepers, Gerhard and Stener, Lars-Göran and Jansson, Stefan and Jönsson, Leif J. and Street, Nathaniel R. and Tuominen, Hannele},
	month = apr,
	year = {2023},
	keywords = {Bioenergy, Biomass, Biorefining, Feedstock recalcitrance, Forest feedstocks, Saccharification},
	pages = {65},
}

Wood represents the majority of the biomass on land and constitutes a renewable source of biofuels and other bioproducts. However, wood is recalcitrant to bioconversion, raising a need for feedstock improvement in production of, for instance, biofuels. We investigated the properties of wood that affect bioconversion, as well as the underlying genetics, to help identify superior tree feedstocks for biorefining.

@article{chen_preselection_2023,
	title = {Preselection of {QTL} markers enhances accuracy of genomic selection in {Norway} spruce},
	volume = {24},
	issn = {1471-2164},
	url = {https://doi.org/10.1186/s12864-023-09250-3},
	doi = {10.1186/s12864-023-09250-3},
	abstract = {Genomic prediction (GP) or genomic selection is a method to predict the accumulative effect of all quantitative trait loci (QTLs) in a population by estimating the realized genomic relationships between the individuals and by capturing the linkage disequilibrium between markers and QTLs. Thus, marker preselection is considered a promising method to capture Mendelian segregation effects. Using QTLs detected in a genome-wide association study (GWAS) may improve GP. Here, we performed GWAS and GP in a population with 904 clones from 32 full-sib families using a newly developed 50 k SNP Norway spruce array. Through GWAS we identified 41 SNPs associated with budburst stage (BB) and the largest effect association explained 5.1\% of the phenotypic variation (PVE). For the other five traits such as growth and wood quality traits, only 2 – 13 associations were observed and the PVE of the strongest effects ranged from 1.2\% to 2.0\%. GP using approximately 100 preselected SNPs, based on the smallest p-values from GWAS showed the greatest predictive ability (PA) for the trait BB. For the other traits, a preselection of 2000–4000 SNPs, was found to offer the best model fit according to the Akaike information criterion being minimized. But PA-magnitudes from GP using such selections were still similar to that of GP using all markers. Analyses on both real-life and simulated data also showed that the inclusion of a large QTL SNP in the model as a fixed effect could improve PA and accuracy of GP provided that the PVE of the QTL was ≥ 2.5\%.},
	number = {1},
	urldate = {2023-04-11},
	journal = {BMC Genomics},
	author = {Chen, Zhi-Qiang and Klingberg, Adam and Hallingbäck, Henrik R. and Wu, Harry X.},
	month = mar,
	year = {2023},
	keywords = {GWAS, Genomic prediction, Marker preselection, Picea abies},
	pages = {147},
}

Genomic prediction (GP) or genomic selection is a method to predict the accumulative effect of all quantitative trait loci (QTLs) in a population by estimating the realized genomic relationships between the individuals and by capturing the linkage disequilibrium between markers and QTLs. Thus, marker preselection is considered a promising method to capture Mendelian segregation effects. Using QTLs detected in a genome-wide association study (GWAS) may improve GP. Here, we performed GWAS and GP in a population with 904 clones from 32 full-sib families using a newly developed 50 k SNP Norway spruce array. Through GWAS we identified 41 SNPs associated with budburst stage (BB) and the largest effect association explained 5.1% of the phenotypic variation (PVE). For the other five traits such as growth and wood quality traits, only 2 – 13 associations were observed and the PVE of the strongest effects ranged from 1.2% to 2.0%. GP using approximately 100 preselected SNPs, based on the smallest p-values from GWAS showed the greatest predictive ability (PA) for the trait BB. For the other traits, a preselection of 2000–4000 SNPs, was found to offer the best model fit according to the Akaike information criterion being minimized. But PA-magnitudes from GP using such selections were still similar to that of GP using all markers. Analyses on both real-life and simulated data also showed that the inclusion of a large QTL SNP in the model as a fixed effect could improve PA and accuracy of GP provided that the PVE of the QTL was ≥ 2.5%.

@article{rohricht_mitochondrial_2023,
	title = {Mitochondrial ferredoxin-like is essential for forming complex {I}-containing supercomplexes in {Arabidopsis}},
	volume = {191},
	issn = {0032-0889},
	url = {https://doi.org/10.1093/plphys/kiad040},
	doi = {10.1093/plphys/kiad040},
	abstract = {In eukaryotes, mitochondrial ATP is mainly produced by the oxidative phosphorylation (OXPHOS) system, which is composed of 5 multiprotein complexes (complexes I–V). Analyses of the OXPHOS system by native gel electrophoresis have revealed an organization of OXPHOS complexes into supercomplexes, but their roles and assembly pathways remain unclear. In this study, we characterized an atypical mitochondrial ferredoxin (mitochondrial ferredoxin-like, mFDX-like). This protein was previously found to be part of the bridge domain linking the matrix and membrane arms of the complex I. Phylogenetic analysis suggested that the Arabidopsis (Arabidopsis thaliana) mFDX-like evolved from classical mitochondrial ferredoxins (mFDXs) but lost one of the cysteines required for the coordination of the iron-sulfur (Fe-S) cluster, supposedly essential for the electron transfer function of FDXs. Accordingly, our biochemical study showed that AtmFDX-like does not bind an Fe-S cluster and is therefore unlikely to be involved in electron transfer reactions. To study the function of mFDX-like, we created deletion lines in Arabidopsis using a CRISPR/Cas9-based strategy. These lines did not show any abnormal phenotype under standard growth conditions. However, the characterization of the OXPHOS system demonstrated that mFDX-like is important for the assembly of complex I and essential for the formation of complex I-containing supercomplexes. We propose that mFDX-like and the bridge domain are required for the correct conformation of the membrane arm of complex I that is essential for the association of complex I with complex III2 to form supercomplexes.},
	number = {4},
	urldate = {2023-04-11},
	journal = {Plant Physiology},
	author = {Röhricht, Helene and Przybyla-Toscano, Jonathan and Forner, Joachim and Boussardon, Clément and Keech, Olivier and Rouhier, Nicolas and Meyer, Etienne H},
	month = apr,
	year = {2023},
	pages = {2170--2184},
}

In eukaryotes, mitochondrial ATP is mainly produced by the oxidative phosphorylation (OXPHOS) system, which is composed of 5 multiprotein complexes (complexes I–V). Analyses of the OXPHOS system by native gel electrophoresis have revealed an organization of OXPHOS complexes into supercomplexes, but their roles and assembly pathways remain unclear. In this study, we characterized an atypical mitochondrial ferredoxin (mitochondrial ferredoxin-like, mFDX-like). This protein was previously found to be part of the bridge domain linking the matrix and membrane arms of the complex I. Phylogenetic analysis suggested that the Arabidopsis (Arabidopsis thaliana) mFDX-like evolved from classical mitochondrial ferredoxins (mFDXs) but lost one of the cysteines required for the coordination of the iron-sulfur (Fe-S) cluster, supposedly essential for the electron transfer function of FDXs. Accordingly, our biochemical study showed that AtmFDX-like does not bind an Fe-S cluster and is therefore unlikely to be involved in electron transfer reactions. To study the function of mFDX-like, we created deletion lines in Arabidopsis using a CRISPR/Cas9-based strategy. These lines did not show any abnormal phenotype under standard growth conditions. However, the characterization of the OXPHOS system demonstrated that mFDX-like is important for the assembly of complex I and essential for the formation of complex I-containing supercomplexes. We propose that mFDX-like and the bridge domain are required for the correct conformation of the membrane arm of complex I that is essential for the association of complex I with complex III2 to form supercomplexes.

@article{calderon_rubredoxin_2023,
	title = {Rubredoxin 1 promotes the proper folding of {D1} and is not required for heme b559 assembly in {Chlamydomonas} photosystem {II}},
	volume = {299},
	issn = {0021-9258, 1083-351X},
	url = {https://www.jbc.org/article/S0021-9258(23)00100-X/abstract},
	doi = {10.1016/j.jbc.2023.102968},
	abstract = {{\textless}p{\textgreater}Photosystem II (PSII), the water:plastoquinone oxidoreductase of oxygenic photosynthesis, contains a heme \textit{b}$_{\textrm{559}}$ iron whose axial ligands are provided by histidine residues from the α (PsbE) and β (PsbF) subunits. PSII assembly depends on accessory proteins that facilitate the step-wise association of its protein and pigment components into a functional complex, a process that is challenging to study due to the low accumulation of assembly intermediates. Here, we examined the putative role of the iron[1Fe-0S]-containing protein rubredoxin 1 (RBD1) as an assembly factor for cytochrome \textit{b}$_{\textrm{559}}$, using the RBD1-lacking \textit{2pac} mutant from \textit{Chlamydomonas reinhardtii}, in which the accumulation of PSII was rescued by the inactivation of the thylakoid membrane FtsH protease. To this end, we constructed the double mutant \textit{2pac ftsh1-1}, which harbored PSII dimers that sustained its photoautotrophic growth. We purified PSII from the \textit{2pac ftsh1-1} background and found that α and β cytochrome \textit{b}$_{\textrm{559}}$ subunits are still present and coordinate heme \textit{b}$_{\textrm{559}}$ as in the WT. Interestingly, immunoblot analysis of dark- and low light–grown \textit{2pac ftsh1-1} showed the accumulation of a 23-kDa fragment of the D1 protein, a marker typically associated with structural changes resulting from photodamage of PSII. Its cleavage occurs in the vicinity of a nonheme iron which binds to PSII on its electron acceptor side. Altogether, our findings demonstrate that RBD1 is not required for heme \textit{b}$_{\textrm{559}}$ assembly and point to a role for RBD1 in promoting the proper folding of D1, possibly \textit{via} delivery or reduction of the nonheme iron during PSII assembly.{\textless}/p{\textgreater}},
	language = {English},
	number = {3},
	urldate = {2023-03-31},
	journal = {Journal of Biological Chemistry},
	author = {Calderon, Robert H. and Vitry, Catherine de and Wollman, Francis-André and Niyogi, Krishna K.},
	month = mar,
	year = {2023},
	pmid = {36736898},
	note = {Publisher: Elsevier},
}

\textlessp\textgreaterPhotosystem II (PSII), the water:plastoquinone oxidoreductase of oxygenic photosynthesis, contains a heme b$_{\textrm{559}}$ iron whose axial ligands are provided by histidine residues from the α (PsbE) and β (PsbF) subunits. PSII assembly depends on accessory proteins that facilitate the step-wise association of its protein and pigment components into a functional complex, a process that is challenging to study due to the low accumulation of assembly intermediates. Here, we examined the putative role of the iron[1Fe-0S]-containing protein rubredoxin 1 (RBD1) as an assembly factor for cytochrome b$_{\textrm{559}}$, using the RBD1-lacking 2pac mutant from Chlamydomonas reinhardtii, in which the accumulation of PSII was rescued by the inactivation of the thylakoid membrane FtsH protease. To this end, we constructed the double mutant 2pac ftsh1-1, which harbored PSII dimers that sustained its photoautotrophic growth. We purified PSII from the 2pac ftsh1-1 background and found that α and β cytochrome b$_{\textrm{559}}$ subunits are still present and coordinate heme b$_{\textrm{559}}$ as in the WT. Interestingly, immunoblot analysis of dark- and low light–grown 2pac ftsh1-1 showed the accumulation of a 23-kDa fragment of the D1 protein, a marker typically associated with structural changes resulting from photodamage of PSII. Its cleavage occurs in the vicinity of a nonheme iron which binds to PSII on its electron acceptor side. Altogether, our findings demonstrate that RBD1 is not required for heme b$_{\textrm{559}}$ assembly and point to a role for RBD1 in promoting the proper folding of D1, possibly via delivery or reduction of the nonheme iron during PSII assembly.\textless/p\textgreater

@article{gao_phylogeography_2023,
	title = {Phylogeography and introgression between {Pinus} kesiya and {Pinus} yunnanensis in {Southeast} {Asia}},
	volume = {n/a},
	issn = {1759-6831},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/jse.12949},
	doi = {10.1111/jse.12949},
	abstract = {Southeast Asia (SEA) has seen strong climatic oscillations and fluctuations in sea levels during the Quaternary. The impact of past climate changes on the evolution and distribution of local flora in SEA is still poorly understood. Here we aim to infer how the Quaternary climate change affects the evolutionary process and range shifts in two pine species. We investigated the population genetic structure and diversity using cytoplasmic DNA markers, and performed ecological niche modeling to reconstruct the species past distribution and to project range shift under future climates. We found substantial gene flow across the continuous distribution of the subtropical Pinus yunnanensis. In contrast, the tropical Pinus kesiya showed a strong population structure in accordance with its disjunct distribution across montane islands in Indochina and the Philippines. A broad hybrid zone of the two species occurs in southern Yunnan. Asymmetric introgression from the two species was detected in this zone with dominant mitochondrial gene flow from P. yunnanensis and chloroplast gene flow from P. kesiya. The observed population structure suggests a typical postglaciation expansion in P. yunnanensis, and a glacial expansion and interglacial contraction in P. kesiya. Ecological niche modeling supports the inferred demographic history and predicts a decrease in range size for P. kesiya under future climates. Our results suggest that tropical pine species in SEA have undergone evolutionary trajectories different from high latitude species related to their Quaternary climate histories. We also illustrate the need for urgent conservation actions in this fragmented landscape.},
	language = {en},
	number = {n/a},
	urldate = {2023-03-31},
	journal = {Journal of Systematics and Evolution},
	author = {Gao, Jie and Tomlinson, Kyle W. and Zhao, Wei and Wang, Baosheng and Lapuz, Ralph Sedricke and Liu, Jing-Xin and Pasion, Bonifacio O. and Hai, Bach T. and Chanthayod, Souvick and Chen, Jin and Wang, Xiao-Ru},
	month = jan,
	year = {2023},
	note = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1111/jse.12949},
	keywords = {Pinus kesiya, Pinus yunnanensis, cpDNA, introgression, mtDNA capture, phylogeography},
}

Southeast Asia (SEA) has seen strong climatic oscillations and fluctuations in sea levels during the Quaternary. The impact of past climate changes on the evolution and distribution of local flora in SEA is still poorly understood. Here we aim to infer how the Quaternary climate change affects the evolutionary process and range shifts in two pine species. We investigated the population genetic structure and diversity using cytoplasmic DNA markers, and performed ecological niche modeling to reconstruct the species past distribution and to project range shift under future climates. We found substantial gene flow across the continuous distribution of the subtropical Pinus yunnanensis. In contrast, the tropical Pinus kesiya showed a strong population structure in accordance with its disjunct distribution across montane islands in Indochina and the Philippines. A broad hybrid zone of the two species occurs in southern Yunnan. Asymmetric introgression from the two species was detected in this zone with dominant mitochondrial gene flow from P. yunnanensis and chloroplast gene flow from P. kesiya. The observed population structure suggests a typical postglaciation expansion in P. yunnanensis, and a glacial expansion and interglacial contraction in P. kesiya. Ecological niche modeling supports the inferred demographic history and predicts a decrease in range size for P. kesiya under future climates. Our results suggest that tropical pine species in SEA have undergone evolutionary trajectories different from high latitude species related to their Quaternary climate histories. We also illustrate the need for urgent conservation actions in this fragmented landscape.

@article{tian_unique_2023,
	title = {Unique gene duplications and conserved microsynteny potentially associated with resistance to wood decay in the {Lauraceae}},
	volume = {14},
	issn = {1664-462X},
	url = {https://www.frontiersin.org/articles/10.3389/fpls.2023.1122549},
	abstract = {Wood decay resistance (WDR) is marking the value of wood utilization. Many trees of the Lauraceae have exceptional WDR, as evidenced by their use in ancient royal palace buildings in China. However, the genetics of WDR remain elusive. Here, through comparative genomics, we revealed the unique characteristics related to the high WDR in Lauraceae trees. We present a 1.27-Gb chromosome-level assembly for Lindera megaphylla (Lauraceae). Comparative genomics integrating major groups of angiosperm revealed Lauraceae species have extensively shared gene microsynteny associated with the biosynthesis of specialized metabolites such as isoquinoline alkaloids, flavonoid, lignins and terpenoid, which play significant roles in WDR. In Lauraceae genomes, tandem and proximal duplications (TD/PD) significantly expanded the coding space of key enzymes of biosynthesis pathways related to WDR, which may enhance the decay resistance of wood by increasing the accumulation of these compounds. Among Lauraceae species, genes of WDR-related biosynthesis pathways showed remarkable expansion by TD/PD and conveyed unique and conserved motifs in their promoter and protein sequences, suggesting conserved gene collinearity, gene expansion and gene regulation supporting the high WDR. Our study thus reveals genomic profiles related to biochemical transitions among major plant groups and the genomic basis of WDR in the Lauraceae.},
	urldate = {2023-03-31},
	journal = {Frontiers in Plant Science},
	author = {Tian, Xue-Chan and Guo, Jing-Fang and Yan, Xue-Mei and Shi, Tian-Le and Nie, Shuai and Zhao, Shi-Wei and Bao, Yu-Tao and Li, Zhi-Chao and Kong, Lei and Su, Guang-Ju and Mao, Jian-Feng and Lin, Jinxing},
	month = mar,
	year = {2023},
}

Wood decay resistance (WDR) is marking the value of wood utilization. Many trees of the Lauraceae have exceptional WDR, as evidenced by their use in ancient royal palace buildings in China. However, the genetics of WDR remain elusive. Here, through comparative genomics, we revealed the unique characteristics related to the high WDR in Lauraceae trees. We present a 1.27-Gb chromosome-level assembly for Lindera megaphylla (Lauraceae). Comparative genomics integrating major groups of angiosperm revealed Lauraceae species have extensively shared gene microsynteny associated with the biosynthesis of specialized metabolites such as isoquinoline alkaloids, flavonoid, lignins and terpenoid, which play significant roles in WDR. In Lauraceae genomes, tandem and proximal duplications (TD/PD) significantly expanded the coding space of key enzymes of biosynthesis pathways related to WDR, which may enhance the decay resistance of wood by increasing the accumulation of these compounds. Among Lauraceae species, genes of WDR-related biosynthesis pathways showed remarkable expansion by TD/PD and conveyed unique and conserved motifs in their promoter and protein sequences, suggesting conserved gene collinearity, gene expansion and gene regulation supporting the high WDR. Our study thus reveals genomic profiles related to biochemical transitions among major plant groups and the genomic basis of WDR in the Lauraceae.

@article{routier_chitosan-modified_2023,
	title = {Chitosan-{Modified} {Polyethyleneimine} {Nanoparticles} for {Enhancing} the {Carboxylation} {Reaction} and {Plants}’ {CO2} {Uptake}},
	volume = {17},
	issn = {1936-0851},
	url = {https://doi.org/10.1021/acsnano.2c09255},
	doi = {10.1021/acsnano.2c09255},
	abstract = {Increasing plants’ photosynthetic efficiency is a major challenge that must be addressed in order to cover the food demands of the growing population in the changing climate. Photosynthesis is greatly limited at the initial carboxylation reaction, where CO2 is converted to the organic acid 3-PGA, catalyzed by the RuBisCO enzyme. RuBisCO has poor affinity for CO2, but also the CO2 concentration at the RuBisCO site is limited by the diffusion of atmospheric CO2 through the various leaf compartments to the reaction site. Beyond genetic engineering, nanotechnology can offer a materials-based approach for enhancing photosynthesis, and yet, it has mostly been explored for the light-dependent reactions. In this work, we developed polyethyleneimine-based nanoparticles for enhancing the carboxylation reaction. We demonstrate that the nanoparticles can capture CO2 in the form of bicarbonate and increase the CO2 that reacts with the RuBisCO enzyme, enhancing the 3-PGA production in in vitro assays by 20\%. The nanoparticles can be introduced to the plant via leaf infiltration and, because of the functionalization with chitosan oligomers, they do not induce any toxic effect to the plant. In the leaves, the nanoparticles localize in the apoplastic space but also spontaneously reach the chloroplasts where photosynthetic activity takes place. Their CO2 loading-dependent fluorescence verifies that, in vivo, they maintain their ability to capture CO2 and can be therefore reloaded with atmospheric CO2 while in planta. Our results contribute to the development of a nanomaterials-based CO2-concentrating mechanism in plants that can potentially increase photosynthetic efficiency and overall plants’ CO2 storage.},
	number = {4},
	urldate = {2023-03-10},
	journal = {ACS Nano},
	author = {Routier, Cyril and Vallan, Lorenzo and Daguerre, Yohann and Juvany, Marta and Istif, Emin and Mantione, Daniele and Brochon, Cyril and Hadziioannou, Georges and Strand, Åsa and Näsholm, Torgny and Cloutet, Eric and Pavlopoulou, Eleni and Stavrinidou, Eleni},
	month = feb,
	year = {2023},
	note = {Publisher: American Chemical Society},
	pages = {3430--3441},
}

Increasing plants’ photosynthetic efficiency is a major challenge that must be addressed in order to cover the food demands of the growing population in the changing climate. Photosynthesis is greatly limited at the initial carboxylation reaction, where CO2 is converted to the organic acid 3-PGA, catalyzed by the RuBisCO enzyme. RuBisCO has poor affinity for CO2, but also the CO2 concentration at the RuBisCO site is limited by the diffusion of atmospheric CO2 through the various leaf compartments to the reaction site. Beyond genetic engineering, nanotechnology can offer a materials-based approach for enhancing photosynthesis, and yet, it has mostly been explored for the light-dependent reactions. In this work, we developed polyethyleneimine-based nanoparticles for enhancing the carboxylation reaction. We demonstrate that the nanoparticles can capture CO2 in the form of bicarbonate and increase the CO2 that reacts with the RuBisCO enzyme, enhancing the 3-PGA production in in vitro assays by 20%. The nanoparticles can be introduced to the plant via leaf infiltration and, because of the functionalization with chitosan oligomers, they do not induce any toxic effect to the plant. In the leaves, the nanoparticles localize in the apoplastic space but also spontaneously reach the chloroplasts where photosynthetic activity takes place. Their CO2 loading-dependent fluorescence verifies that, in vivo, they maintain their ability to capture CO2 and can be therefore reloaded with atmospheric CO2 while in planta. Our results contribute to the development of a nanomaterials-based CO2-concentrating mechanism in plants that can potentially increase photosynthetic efficiency and overall plants’ CO2 storage.

@article{pateras_short_2023,
	title = {Short term starvation potentiates the efficacy of chemotherapy in triple negative breast cancer via metabolic reprogramming},
	volume = {21},
	issn = {1479-5876},
	url = {https://doi.org/10.1186/s12967-023-03935-9},
	doi = {10.1186/s12967-023-03935-9},
	abstract = {Chemotherapy (CT) is central to the treatment of triple negative breast cancer (TNBC), but drug toxicity and resistance place strong restrictions on treatment regimes. Fasting sensitizes cancer cells to a range of chemotherapeutic agents and also ameliorates CT-associated adverse effects. However, the molecular mechanism(s) by which fasting, or short-term starvation (STS), improves the efficacy of CT is poorly characterized.},
	number = {1},
	urldate = {2023-03-10},
	journal = {Journal of Translational Medicine},
	author = {Pateras, Ioannis S. and Williams, Chloe and Gianniou, Despoina D. and Margetis, Aggelos T. and Avgeris, Margaritis and Rousakis, Pantelis and Legaki, Aigli-Ioanna and Mirtschink, Peter and Zhang, Wei and Panoutsopoulou, Konstantina and Delis, Anastasios D. and Pagakis, Stamatis N. and Tang, Wei and Ambs, Stefan and Warpman Berglund, Ulrika and Helleday, Thomas and Varvarigou, Anastasia and Chatzigeorgiou, Antonios and Nordström, Anders and Tsitsilonis, Ourania E. and Trougakos, Ioannis P. and Gilthorpe, Jonathan D. and Frisan, Teresa},
	month = mar,
	year = {2023},
	keywords = {Breast cancer, Caloric restriction, Fasting, Metabolic reprogramming, Mitochondria, Oncological treatment, Oxidative stress, Reactive oxygen species, Starvation, Triple negative breast cancer},
	pages = {169},
}

Chemotherapy (CT) is central to the treatment of triple negative breast cancer (TNBC), but drug toxicity and resistance place strong restrictions on treatment regimes. Fasting sensitizes cancer cells to a range of chemotherapeutic agents and also ameliorates CT-associated adverse effects. However, the molecular mechanism(s) by which fasting, or short-term starvation (STS), improves the efficacy of CT is poorly characterized.

@article{hallberg-sramek_combining_2023,
	title = {Combining scientific and local knowledge improves evaluating future scenarios of forest ecosystem services},
	volume = {60},
	issn = {2212-0416},
	url = {https://www.sciencedirect.com/science/article/pii/S2212041623000049},
	doi = {10.1016/j.ecoser.2023.101512},
	abstract = {Forest scenario analysis can help tackle sustainability issues by generating insight into the potential long-term effects of present-day management. In northern Sweden, forests provide important benefits including climate change mitigation, biodiversity conservation, reindeer husbandry, local livelihoods, and recreation. Informed by local stakeholders’ views on how forests can be enabled to deliver these benefits, we created four forest management scenarios: the close-to-nature scenario (CTN) which emphasises biodiversity conservation, the classic management scenario (CLA) optimising the forests’ net present value, the intensified scenario (INT) maximising harvested wood from the forest, and the combined scenario (COM) applying a combination of measures from the CTN and INT. The scenarios were applied to the local forest landscape and modelled over a 100-year simulation period, and the results of the modelling were then evaluated by a diverse group of stakeholders. For most ecosystem services, there was a time lag of 10–50 years before noticeable effects and differences between the scenarios became evident, highlighting the need to consider both the short- and long-term effects of forest management. Evaluation by the stakeholders put the modelled results into a local context. They raised considerations relating to wildlife and hunting, climate change risks, social acceptability, and conflict, highlighting the value of evaluating the scenarios qualitatively as well as quantitatively. Overall, stakeholders thought that the CTN and CLA scenarios promoted more ecosystem services and posed fewer climate risks, while also creating less conflict among stakeholders. Our results emphasise the value of combining scientific and local knowledge when developing and evaluating future forest scenarios.},
	language = {en},
	urldate = {2023-03-10},
	journal = {Ecosystem Services},
	author = {Hallberg-Sramek, Isabella and Nordström, Eva-Maria and Priebe, Janina and Reimerson, Elsa and Mårald, Erland and Nordin, Annika},
	month = apr,
	year = {2023},
	keywords = {Forest management, Indigenous and local knowledge, Inter- and transdisciplinary research, Knowledge co-production, Scenario modelling, Stakeholder participation},
	pages = {101512},
}

Forest scenario analysis can help tackle sustainability issues by generating insight into the potential long-term effects of present-day management. In northern Sweden, forests provide important benefits including climate change mitigation, biodiversity conservation, reindeer husbandry, local livelihoods, and recreation. Informed by local stakeholders’ views on how forests can be enabled to deliver these benefits, we created four forest management scenarios: the close-to-nature scenario (CTN) which emphasises biodiversity conservation, the classic management scenario (CLA) optimising the forests’ net present value, the intensified scenario (INT) maximising harvested wood from the forest, and the combined scenario (COM) applying a combination of measures from the CTN and INT. The scenarios were applied to the local forest landscape and modelled over a 100-year simulation period, and the results of the modelling were then evaluated by a diverse group of stakeholders. For most ecosystem services, there was a time lag of 10–50 years before noticeable effects and differences between the scenarios became evident, highlighting the need to consider both the short- and long-term effects of forest management. Evaluation by the stakeholders put the modelled results into a local context. They raised considerations relating to wildlife and hunting, climate change risks, social acceptability, and conflict, highlighting the value of evaluating the scenarios qualitatively as well as quantitatively. Overall, stakeholders thought that the CTN and CLA scenarios promoted more ecosystem services and posed fewer climate risks, while also creating less conflict among stakeholders. Our results emphasise the value of combining scientific and local knowledge when developing and evaluating future forest scenarios.

@article{derba-maceluch_xylan_2023,
	title = {Xylan glucuronic acid side chains fix suberin-like aliphatic compounds to wood cell walls},
	volume = {238},
	issn = {1469-8137},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/nph.18712},
	doi = {10.1111/nph.18712},
	abstract = {Wood is the most important repository of assimilated carbon in the biosphere, in the form of large polymers (cellulose, hemicelluloses including glucuronoxylan, and lignin) that interactively form a composite, together with soluble extractives including phenolic and aliphatic compounds. Molecular interactions among these compounds are not fully understood. We have targeted the expression of a fungal α-glucuronidase to the wood cell wall of aspen (Populus tremula L. × tremuloides Michx.) and Arabidopsis (Arabidopsis thaliana (L.) Heynh), to decrease contents of the 4-O-methyl glucuronopyranose acid (mGlcA) substituent of xylan, to elucidate mGlcA's functions. The enzyme affected the content of aliphatic insoluble cell wall components having composition similar to suberin, which required mGlcA for binding to cell walls. Such suberin-like compounds have been previously identified in decayed wood, but here, we show their presence in healthy wood of both hardwood and softwood species. By contrast, γ-ester bonds between mGlcA and lignin were insensitive to cell wall-localized α-glucuronidase, supporting the intracellular formation of these bonds. These findings challenge the current view of the wood cell wall composition and reveal a novel function of mGlcA substituent of xylan in fastening of suberin-like compounds to cell wall. They also suggest an intracellular initiation of lignin–carbohydrate complex assembly.},
	language = {en},
	number = {1},
	urldate = {2023-03-10},
	journal = {New Phytologist},
	author = {Derba-Maceluch, Marta and Mitra, Madhusree and Hedenström, Mattias and Liu, Xiaokun and Gandla, Madhavi L. and Barbut, Félix R. and Abreu, Ilka N. and Donev, Evgeniy N. and Urbancsok, János and Moritz, Thomas and Jönsson, Leif J. and Tsang, Adrian and Powlowski, Justin and Master, Emma R. and Mellerowicz, Ewa J.},
	month = jan,
	year = {2023},
	note = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1111/nph.18712},
	keywords = {Populus, lignin-carbohydrate complexes (LCCs), lignin–carbohydrate complexes, saccharification, suberin, wood cell wall, xylan},
	pages = {297--312},
}

Wood is the most important repository of assimilated carbon in the biosphere, in the form of large polymers (cellulose, hemicelluloses including glucuronoxylan, and lignin) that interactively form a composite, together with soluble extractives including phenolic and aliphatic compounds. Molecular interactions among these compounds are not fully understood. We have targeted the expression of a fungal α-glucuronidase to the wood cell wall of aspen (Populus tremula L. × tremuloides Michx.) and Arabidopsis (Arabidopsis thaliana (L.) Heynh), to decrease contents of the 4-O-methyl glucuronopyranose acid (mGlcA) substituent of xylan, to elucidate mGlcA's functions. The enzyme affected the content of aliphatic insoluble cell wall components having composition similar to suberin, which required mGlcA for binding to cell walls. Such suberin-like compounds have been previously identified in decayed wood, but here, we show their presence in healthy wood of both hardwood and softwood species. By contrast, γ-ester bonds between mGlcA and lignin were insensitive to cell wall-localized α-glucuronidase, supporting the intracellular formation of these bonds. These findings challenge the current view of the wood cell wall composition and reveal a novel function of mGlcA substituent of xylan in fastening of suberin-like compounds to cell wall. They also suggest an intracellular initiation of lignin–carbohydrate complex assembly.

@article{chowdhury_fluorogenic_2023,
	title = {Fluorogenic properties of 4-dimethylaminocinnamaldehyde ({DMACA}) enable high resolution imaging of cell-wall-bound proanthocyanidins in plant root tissues},
	volume = {13},
	issn = {1664-462X},
	url = {https://www.frontiersin.org/articles/10.3389/fpls.2022.1060804},
	doi = {10.3389/fpls.2022.1060804},
	abstract = {Proanthocyanidins (PAs) are polymeric phenolic compounds found in plants and used in many industrial applications. Despite strong evidence of herbivore and pathogen resistance-related properties of PAs, their in planta function is not fully understood. Determining the location and dynamics of PAs in plant tissues and cellular compartments is crucial to understand their mode of action. Such an approach requires microscopic localization with fluorescent dyes that specifically bind to PAs. Such dyes have hitherto been lacking. Here, we show that 4-dimethylaminocinnamaldehyde (DMACA) can be used as a PA-specific fluorescent dye that allows localization of PAs at high resolution in cell walls and inside cells using confocal microscopy, revealing features of previously unreported wall-bound PAs. We demonstrate several novel usages of DMACA as a fluorophore by taking advantage of its double staining compatibility with other fluorescent dyes. We illustrate the use of the dye alone and its co-localization with cell wall polymers in different Populus root tissues. The easy-to-use fluorescent staining method, together with its high photostability and compatibility with other fluorogenic dyes, makes DMACA a valuable tool for uncovering the biological function of PAs at a cellular level in plant tissues. DMACA can also be used in other plant tissues than roots, however care needs to be taken when tissues contain compounds that autofluoresce in the red spectral region which can be confounded with the PA-specific DMACA signal.},
	urldate = {2023-02-10},
	journal = {Frontiers in Plant Science},
	author = {Chowdhury, Jamil and Ferdous, Jannatul and Lihavainen, Jenna and Albrectsen, Benedicte Riber and Lundberg-Felten, Judith},
	month = feb,
	year = {2023},
	keywords = {⛔ No DOI found},
}

Proanthocyanidins (PAs) are polymeric phenolic compounds found in plants and used in many industrial applications. Despite strong evidence of herbivore and pathogen resistance-related properties of PAs, their in planta function is not fully understood. Determining the location and dynamics of PAs in plant tissues and cellular compartments is crucial to understand their mode of action. Such an approach requires microscopic localization with fluorescent dyes that specifically bind to PAs. Such dyes have hitherto been lacking. Here, we show that 4-dimethylaminocinnamaldehyde (DMACA) can be used as a PA-specific fluorescent dye that allows localization of PAs at high resolution in cell walls and inside cells using confocal microscopy, revealing features of previously unreported wall-bound PAs. We demonstrate several novel usages of DMACA as a fluorophore by taking advantage of its double staining compatibility with other fluorescent dyes. We illustrate the use of the dye alone and its co-localization with cell wall polymers in different Populus root tissues. The easy-to-use fluorescent staining method, together with its high photostability and compatibility with other fluorogenic dyes, makes DMACA a valuable tool for uncovering the biological function of PAs at a cellular level in plant tissues. DMACA can also be used in other plant tissues than roots, however care needs to be taken when tissues contain compounds that autofluoresce in the red spectral region which can be confounded with the PA-specific DMACA signal.

@article{siddique_molecular_2023,
	title = {Molecular studies of rust on {European} aspen suggest an autochthonous relationship shaped by genotype},
	volume = {14},
	issn = {1664-462X},
	url = {https://www.frontiersin.org/articles/10.3389/fpls.2023.1111001},
	doi = {10.3389/fpls.2023.1111001},
	abstract = {Forests are at increasing risk from pathogen outbreak. Climate change for example enhance the risk of local disease outbreaks, and naturalization of exotic pathogens may follow human activities, warranting robust pest surveillance routines to support forest management. Melampsora pinitorqua (pine twisting rust) is of concern in Swedish forestry, and here we evaluate the use of visible rust scores (VRS) on its obligate summer host, European aspen (Populus tremula) as a tool for quantification of the pathogen. With use of species-specific primers, we could detect the native rust, but we failed to detect two exotic rusts (M. medusae and M. larici-populina). We found that aspen genotype determined the presence of fungal genetic markers (amplifying the ITS2 region of the fungal rDNA sequence) as well as DNA sequences specific to M. pinitorqua. We correlated VRS with the amount of fungal DNA in the same leaf, and we related the findings to aspen genotype-specific parameters such as the ability to synthesize and store leaf condensed tannins (CT).  At the genotype level both positive and negative relationships were observed between CTs, fungal markers, and rust infestations. However, at the population level, foliar CT concentrations correlated negatively with general fungal- and rust-specific marker abundances.  Our results, therefore, do not support the use of VRS to assess Melampsora infestation in Aspen. They do, however, suggest that the relationship between European aspen and rust infestation may be characterized as autochthonous in northern Sweden.},
	urldate = {2023-02-24},
	journal = {Frontiers in Plant Science},
	author = {Siddique, Abu Bakar and Menke, Laura and Dinedurga, Melis and Albrectsen, Benedicte Riber},
	month = feb,
	year = {2023},
}

Forests are at increasing risk from pathogen outbreak. Climate change for example enhance the risk of local disease outbreaks, and naturalization of exotic pathogens may follow human activities, warranting robust pest surveillance routines to support forest management. Melampsora pinitorqua (pine twisting rust) is of concern in Swedish forestry, and here we evaluate the use of visible rust scores (VRS) on its obligate summer host, European aspen (Populus tremula) as a tool for quantification of the pathogen. With use of species-specific primers, we could detect the native rust, but we failed to detect two exotic rusts (M. medusae and M. larici-populina). We found that aspen genotype determined the presence of fungal genetic markers (amplifying the ITS2 region of the fungal rDNA sequence) as well as DNA sequences specific to M. pinitorqua. We correlated VRS with the amount of fungal DNA in the same leaf, and we related the findings to aspen genotype-specific parameters such as the ability to synthesize and store leaf condensed tannins (CT). At the genotype level both positive and negative relationships were observed between CTs, fungal markers, and rust infestations. However, at the population level, foliar CT concentrations correlated negatively with general fungal- and rust-specific marker abundances. Our results, therefore, do not support the use of VRS to assess Melampsora infestation in Aspen. They do, however, suggest that the relationship between European aspen and rust infestation may be characterized as autochthonous in northern Sweden.

@article{ntefidou_physcomitrium_2023,
	title = {Physcomitrium patens {PpRIC}, an ancestral {CRIB}-domain {ROP} effector, inhibits auxin-induced differentiation of apical initial cells},
	volume = {42},
	issn = {2211-1247},
	url = {https://www.cell.com/cell-reports/abstract/S2211-1247(23)00141-9},
	doi = {10.1016/j.celrep.2023.112130},
	abstract = {RHO guanosine triphosphatases are important eukaryotic regulators of cell differentiation and behavior. Plant ROP (RHO of plant) family members activate specific, incompletely characterized downstream signaling. The structurally simple land plant Physcomitrium patens is missing homologs of key animal and flowering plant RHO effectors but contains a single CRIB (CDC42/RAC interactive binding)-domain-containing RIC (ROP-interacting CRIB-containing) protein (PpRIC). Protonemal P. patens filaments elongate based on regular division and PpROP-dependent tip growth of apical initial cells, which upon stimulation by the hormone auxin differentiate caulonemal characteristics. PpRIC interacts with active PpROP1, co-localizes with this protein at the plasma membrane at the tip of apical initial cells, and accumulates in the nucleus. Remarkably, PpRIC is not required for tip growth but is targeted to the nucleus to block caulonema differentiation downstream of auxin-controlled gene expression. These observations establish functions of PpRIC in mediating crosstalk between ROP and auxin signaling, which contributes to the maintenance of apical initial cell identity.},
	language = {English},
	number = {2},
	urldate = {2023-02-23},
	journal = {Cell Reports},
	author = {Ntefidou, Maria and Eklund, D. Magnus and Bail, Aude Le and Schulmeister, Sylwia and Scherbel, Franziska and Brandl, Lisa and Dörfler, Wolfgang and Eichstädt, Chantal and Bannmüller, Anna and Ljung, Karin and Kost, Benedikt},
	month = feb,
	year = {2023},
	pmid = {36790931},
	note = {Publisher: Elsevier},
	keywords = {CP: Developmental biology, CP: Plants, CRIB domain, Physcomitrium patens, RHO/ROP GTPases, RHO/ROP effectors, auxin, cell differentiation, initial cells, land plant evolution, nuclear targeting, tip growth},
}

RHO guanosine triphosphatases are important eukaryotic regulators of cell differentiation and behavior. Plant ROP (RHO of plant) family members activate specific, incompletely characterized downstream signaling. The structurally simple land plant Physcomitrium patens is missing homologs of key animal and flowering plant RHO effectors but contains a single CRIB (CDC42/RAC interactive binding)-domain-containing RIC (ROP-interacting CRIB-containing) protein (PpRIC). Protonemal P. patens filaments elongate based on regular division and PpROP-dependent tip growth of apical initial cells, which upon stimulation by the hormone auxin differentiate caulonemal characteristics. PpRIC interacts with active PpROP1, co-localizes with this protein at the plasma membrane at the tip of apical initial cells, and accumulates in the nucleus. Remarkably, PpRIC is not required for tip growth but is targeted to the nucleus to block caulonema differentiation downstream of auxin-controlled gene expression. These observations establish functions of PpRIC in mediating crosstalk between ROP and auxin signaling, which contributes to the maintenance of apical initial cell identity.

@article{le_provost_oak_2023,
	title = {Oak stands along an elevation gradient have different molecular strategies for regulating bud phenology},
	volume = {23},
	issn = {1471-2229},
	url = {https://doi.org/10.1186/s12870-023-04069-2},
	doi = {10.1186/s12870-023-04069-2},
	abstract = {Global warming raises serious concerns about the persistence of species and populations locally adapted to their environment, simply because of the shift it produces in their adaptive landscape. For instance, the phenological cycle of tree species may be strongly affected by higher winter temperatures and late frost in spring. Given the variety of ecosystem services they provide, the question of forest tree adaptation has received increasing attention in the scientific community and catalyzed research efforts in ecology, evolutionary biology and functional genomics to study their adaptive capacity to respond to such perturbations.},
	number = {1},
	urldate = {2023-03-03},
	journal = {BMC Plant Biology},
	author = {Le Provost, Gregoire and Lalanne, Céline and Lesur, Isabelle and Louvet, Jean-Marc and Delzon, Sylvain and Kremer, Antoine and Labadie, Karine and Aury, Jean-Marc and Da Silva, Corinne and Moritz, Thomas and Plomion, Christophe},
	month = feb,
	year = {2023},
	keywords = {Bud phenology, Elevation cline, Gene expression, Hormone quantification, Response to temperature, Sessile oak},
	pages = {108},
}

Global warming raises serious concerns about the persistence of species and populations locally adapted to their environment, simply because of the shift it produces in their adaptive landscape. For instance, the phenological cycle of tree species may be strongly affected by higher winter temperatures and late frost in spring. Given the variety of ecosystem services they provide, the question of forest tree adaptation has received increasing attention in the scientific community and catalyzed research efforts in ecology, evolutionary biology and functional genomics to study their adaptive capacity to respond to such perturbations.

@article{nie_gapless_2023,
	title = {Gapless genome assembly of azalea and multi-omics investigation into divergence between two species with distinct flower color},
	volume = {10},
	issn = {2052-7276},
	url = {https://doi.org/10.1093/hr/uhac241},
	doi = {10.1093/hr/uhac241},
	abstract = {The genus Rhododendron (Ericaceae), with more than 1000 species highly diverse in flower color, is providing distinct ornamental values and a model system for flower color studies. Here, we investigated the divergence between two parental species with different flower color widely used for azalea breeding. Gapless genome assembly was generated for the yellow-flowered azalea, Rhododendron molle. Comparative genomics found recent proliferation of  long terminal repeat retrotransposons (LTR-RTs), especially Gypsy, has resulted in a 125 Mb (19\%) genome size increase in species-specific regions, and a significant amount of dispersed gene duplicates (13 402) and pseudogenes (17 437). Metabolomic assessment revealed that yellow flower coloration is attributed to the dynamic changes of carotenoids/flavonols biosynthesis and chlorophyll degradation. Time-ordered gene co-expression networks (TO-GCNs) and the comparison confirmed the metabolome and uncovered the specific gene regulatory changes underpinning the distinct flower pigmentation. B3 and ERF TFs were found dominating the gene regulation of carotenoids/flavonols characterized pigmentation in R. molle, while WRKY, ERF, WD40, C2H2, and NAC TFs collectively regulated the anthocyanins characterized pigmentation in the red-flowered R simsii. This study employed a multi-omics strategy in disentangling the complex divergence between two important azaleas and provided references for further functional genetics and molecular breeding.},
	number = {1},
	urldate = {2023-03-03},
	journal = {Horticulture Research},
	author = {Nie, Shuai and Zhao, Shi-Wei and Shi, Tian-Le and Zhao, Wei and Zhang, Ren-Gang and Tian, Xue-Chan and Guo, Jing-Fang and Yan, Xue-Mei and Bao, Yu-Tao and Li, Zhi-Chao and Kong, Lei and Ma, Hai-Yao and Chen, Zhao-Yang and Liu, Hui and El-Kassaby, Yousry A and Porth, Ilga and Yang, Fu-Sheng and Mao, Jian-Feng},
	month = jan,
	year = {2023},
	pages = {uhac241},
}

The genus Rhododendron (Ericaceae), with more than 1000 species highly diverse in flower color, is providing distinct ornamental values and a model system for flower color studies. Here, we investigated the divergence between two parental species with different flower color widely used for azalea breeding. Gapless genome assembly was generated for the yellow-flowered azalea, Rhododendron molle. Comparative genomics found recent proliferation of long terminal repeat retrotransposons (LTR-RTs), especially Gypsy, has resulted in a 125 Mb (19%) genome size increase in species-specific regions, and a significant amount of dispersed gene duplicates (13 402) and pseudogenes (17 437). Metabolomic assessment revealed that yellow flower coloration is attributed to the dynamic changes of carotenoids/flavonols biosynthesis and chlorophyll degradation. Time-ordered gene co-expression networks (TO-GCNs) and the comparison confirmed the metabolome and uncovered the specific gene regulatory changes underpinning the distinct flower pigmentation. B3 and ERF TFs were found dominating the gene regulation of carotenoids/flavonols characterized pigmentation in R. molle, while WRKY, ERF, WD40, C2H2, and NAC TFs collectively regulated the anthocyanins characterized pigmentation in the red-flowered R simsii. This study employed a multi-omics strategy in disentangling the complex divergence between two important azaleas and provided references for further functional genetics and molecular breeding.

@article{boussardon_tissue-specific_2023,
	title = {Tissue-{Specific} {Isolation} of {Tagged} {Arabidopsis} {Plastids}},
	volume = {3},
	issn = {2691-1299},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1002/cpz1.673},
	doi = {10.1002/cpz1.673},
	abstract = {Plastids are found in all plant cell types. However, most extraction methods to study these organelles are performed at the organ level (e.g., leaf, root, fruit) and do not allow for tissue-specific resolution, which hinders our understanding of their physiology. Therefore, IPTACT (Isolation of Plastids TAgged in specific Cell Types) was developed to isolate plastids in a tissue-specific manner in Arabidopsis thaliana (Arabidopsis). Plastids are biotinylated using one-shot transgenic lines, and tissue specificity is achieved with a suitable promoter as long as such a promoter exists. Cell-specific biotinylated plastids are then isolated with 2.8-µm streptavidin beads. Plastids extracted by IPTACT are suitable for RNA or protein isolation and subsequent tissue-specific OMICs analyses. This method provides the user with a powerful tool to investigate plastidial functions at cell-type resolution. Furthermore, it can easily be combined with studies using diverse genetic backgrounds and/or different developmental or stress conditions. © 2022 The Authors. Current Protocols published by Wiley Periodicals LLC. Basic Protocol 1: Promoter cloning and plant selection Basic Protocol 2: Isolation of biotinylated plastids Basic Protocol 3: Quality control of isolated plastids},
	language = {en},
	number = {2},
	urldate = {2023-02-22},
	journal = {Current Protocols},
	author = {Boussardon, Clément and Keech, Olivier},
	year = {2023},
	note = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1002/cpz1.673},
	keywords = {Arabidopsis, biotin-streptavidin interaction, editable Golden Gate plasmids, plastids, tissue-specific isolation},
	pages = {e673},
}

Plastids are found in all plant cell types. However, most extraction methods to study these organelles are performed at the organ level (e.g., leaf, root, fruit) and do not allow for tissue-specific resolution, which hinders our understanding of their physiology. Therefore, IPTACT (Isolation of Plastids TAgged in specific Cell Types) was developed to isolate plastids in a tissue-specific manner in Arabidopsis thaliana (Arabidopsis). Plastids are biotinylated using one-shot transgenic lines, and tissue specificity is achieved with a suitable promoter as long as such a promoter exists. Cell-specific biotinylated plastids are then isolated with 2.8-µm streptavidin beads. Plastids extracted by IPTACT are suitable for RNA or protein isolation and subsequent tissue-specific OMICs analyses. This method provides the user with a powerful tool to investigate plastidial functions at cell-type resolution. Furthermore, it can easily be combined with studies using diverse genetic backgrounds and/or different developmental or stress conditions. © 2022 The Authors. Current Protocols published by Wiley Periodicals LLC. Basic Protocol 1: Promoter cloning and plant selection Basic Protocol 2: Isolation of biotinylated plastids Basic Protocol 3: Quality control of isolated plastids

@article{jonsson_multiple_2023,
	title = {Multiple mechanisms behind plant bending},
	volume = {9},
	copyright = {2022 Springer Nature Limited},
	issn = {2055-0278},
	url = {https://www.nature.com/articles/s41477-022-01310-y},
	doi = {10.1038/s41477-022-01310-y},
	abstract = {To survive, plants constantly adapt their body shape to their environment. This often involves remarkably rapid bending of their organs such as stems, leaves and roots. Since plant cells are enclosed by stiff cell walls, they use various strategies for bending their organs, which differ from bending mechanisms of soft animal tissues and involve larger physical forces. Here we attempt to summarize and link different viewpoints on bending mechanisms: genes and signalling, mathematical modelling and biomechanics. We argue that quantifying cell growth and physical forces could open a new level in our understanding of bending and resolve some of its paradoxes.},
	language = {en},
	number = {1},
	urldate = {2023-02-03},
	journal = {Nature Plants},
	author = {Jonsson, Kristoffer and Ma, Yuan and Routier-Kierzkowska, Anne-Lise and Bhalerao, Rishikesh P.},
	month = jan,
	year = {2023},
	keywords = {Plant morphogenesis, Tropism},
	pages = {13--21},
}

To survive, plants constantly adapt their body shape to their environment. This often involves remarkably rapid bending of their organs such as stems, leaves and roots. Since plant cells are enclosed by stiff cell walls, they use various strategies for bending their organs, which differ from bending mechanisms of soft animal tissues and involve larger physical forces. Here we attempt to summarize and link different viewpoints on bending mechanisms: genes and signalling, mathematical modelling and biomechanics. We argue that quantifying cell growth and physical forces could open a new level in our understanding of bending and resolve some of its paradoxes.

@article{igamberdiev_toward_2023,
	title = {Toward understanding the emergence of life: {A} dual function of the system of nucleotides in the metabolically closed autopoietic organization},
	volume = {224},
	issn = {0303-2647},
	shorttitle = {Toward understanding the emergence of life},
	url = {https://www.sciencedirect.com/science/article/pii/S0303264723000126},
	doi = {10.1016/j.biosystems.2023.104837},
	abstract = {General structure of metabolism includes the reproduction of catalysts that govern metabolism. In this structure, the system becomes autopoietic in the sense of Maturana and Varela, and it is closed to efficient causation as defined by Robert Rosen. The autopoietic maintenance and operation of the catalysts takes place via the set of free nucleotides while the synthesis of catalysts occurs via the information encoded by the set of nucleotides arranged in polymers of RNA and DNA. Both energy charge and genetic information use the components of the same pool of nucleoside triphosphates, which is equilibrated by thermodynamic buffering enzymes such as nucleoside diphosphate kinase and adenylate kinase. This occurs in a way that the system becomes internally stable and metabolically closed, which initially could be realized at the level of ribozymes catalyzing basic metabolic reactions as well as own reproduction. The function of ATP, GTP, UTP, and CTP is dual, as these species participate both in the general metabolism as free nucleotides and in the transfer of genetic information via covalent polymerization to nucleic acids. The changes in their pools directly impact both bioenergetic pathways and nucleic acid turnover. Here we outline the concept of metabolic closure of biosystems grounded in the dual function of nucleotide coenzymes that serve both as energetic and informational molecules and through this duality generate the autopoietic performance and the ability for codepoietic evolutionary transformations of living systems starting from the emergence of prebiotic systems.},
	language = {en},
	urldate = {2023-01-20},
	journal = {Biosystems},
	author = {Igamberdiev, Abir U. and Kleczkowski, Leszek A.},
	month = feb,
	year = {2023},
	keywords = {Autopoiesis, Codepoiesis, Coenzyme, Metabolic closure, Nucleoside triphosphates, Ribozymes, Thermodynamic buffering},
	pages = {104837},
}

General structure of metabolism includes the reproduction of catalysts that govern metabolism. In this structure, the system becomes autopoietic in the sense of Maturana and Varela, and it is closed to efficient causation as defined by Robert Rosen. The autopoietic maintenance and operation of the catalysts takes place via the set of free nucleotides while the synthesis of catalysts occurs via the information encoded by the set of nucleotides arranged in polymers of RNA and DNA. Both energy charge and genetic information use the components of the same pool of nucleoside triphosphates, which is equilibrated by thermodynamic buffering enzymes such as nucleoside diphosphate kinase and adenylate kinase. This occurs in a way that the system becomes internally stable and metabolically closed, which initially could be realized at the level of ribozymes catalyzing basic metabolic reactions as well as own reproduction. The function of ATP, GTP, UTP, and CTP is dual, as these species participate both in the general metabolism as free nucleotides and in the transfer of genetic information via covalent polymerization to nucleic acids. The changes in their pools directly impact both bioenergetic pathways and nucleic acid turnover. Here we outline the concept of metabolic closure of biosystems grounded in the dual function of nucleotide coenzymes that serve both as energetic and informational molecules and through this duality generate the autopoietic performance and the ability for codepoietic evolutionary transformations of living systems starting from the emergence of prebiotic systems.

@article{kidwai_species-specific_2023,
	title = {Species-specific transcriptional reprogramming during adventitious root initiation},
	volume = {28},
	issn = {1360-1385},
	url = {https://www.sciencedirect.com/science/article/pii/S1360138522003028},
	doi = {10.1016/j.tplants.2022.11.003},
	abstract = {Adventitious roots or shoot-borne roots transdifferentiate from cells close to vascular tissues after cell reprogramming, which is associated with increased transcriptional activity. Recently, Garg et al. provided a genome-wide landscape of transcriptional signatures during the early stages of adventitious root initiation in rice and showed that conserved transcription factors acquire species-specific function.},
	language = {en},
	number = {2},
	urldate = {2023-01-26},
	journal = {Trends in Plant Science},
	author = {Kidwai, Maria and Mishra, Priyanka and Bellini, Catherine},
	month = feb,
	year = {2023},
	keywords = {adventitious root, dicotyledons, epigenetic regulation, monocotyledons, transcription factors},
	pages = {128--130},
}

Adventitious roots or shoot-borne roots transdifferentiate from cells close to vascular tissues after cell reprogramming, which is associated with increased transcriptional activity. Recently, Garg et al. provided a genome-wide landscape of transcriptional signatures during the early stages of adventitious root initiation in rice and showed that conserved transcription factors acquire species-specific function.

@article{chandra_transformer-based_2023,
	title = {Transformer-based deep learning for predicting protein properties in the life sciences},
	volume = {12},
	issn = {2050-084X},
	url = {https://doi.org/10.7554/eLife.82819},
	doi = {10.7554/eLife.82819},
	abstract = {Recent developments in deep learning, coupled with an increasing number of sequenced proteins, have led to a breakthrough in life science applications, in particular in protein property prediction. There is hope that deep learning can close the gap between the number of sequenced proteins and proteins with known properties based on lab experiments. Language models from the field of natural language processing have gained popularity for protein property predictions and have led to a new computational revolution in biology, where old prediction results are being improved regularly. Such models can learn useful multipurpose representations of proteins from large open repositories of protein sequences and can be used, for instance, to predict protein properties. The field of natural language processing is growing quickly because of developments in a class of models based on a particular model—the Transformer model. We review recent developments and the use of large-scale Transformer models in applications for predicting protein characteristics and how such models can be used to predict, for example, post-translational modifications. We review shortcomings of other deep learning models and explain how the Transformer models have quickly proven to be a very promising way to unravel information hidden in the sequences of amino acids.},
	urldate = {2023-01-20},
	journal = {eLife},
	author = {Chandra, Abel and Tünnermann, Laura and Löfstedt, Tommy and Gratz, Regina},
	editor = {Dötsch, Volker},
	month = jan,
	year = {2023},
	keywords = {deep learning, life sciences, machine learning, protein property prediction, transformers},
	pages = {e82819},
}

Recent developments in deep learning, coupled with an increasing number of sequenced proteins, have led to a breakthrough in life science applications, in particular in protein property prediction. There is hope that deep learning can close the gap between the number of sequenced proteins and proteins with known properties based on lab experiments. Language models from the field of natural language processing have gained popularity for protein property predictions and have led to a new computational revolution in biology, where old prediction results are being improved regularly. Such models can learn useful multipurpose representations of proteins from large open repositories of protein sequences and can be used, for instance, to predict protein properties. The field of natural language processing is growing quickly because of developments in a class of models based on a particular model—the Transformer model. We review recent developments and the use of large-scale Transformer models in applications for predicting protein characteristics and how such models can be used to predict, for example, post-translational modifications. We review shortcomings of other deep learning models and explain how the Transformer models have quickly proven to be a very promising way to unravel information hidden in the sequences of amino acids.

@article{tiret_divergent_2023,
	title = {Divergent selection predating the {Last} {Glacial} {Maximum} mainly acted on macro-phenotypes in {Norway} spruce},
	volume = {16},
	issn = {1752-4571},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/eva.13519},
	doi = {10.1111/eva.13519},
	abstract = {The current distribution and population structure of many species were, to a large extent, shaped by cycles of isolation in glacial refugia and subsequent population expansions. Isolation in and postglacial expansion through heterogeneous environments led to either neutral or adaptive divergence. Norway spruce is no exception, and its current distribution is the consequence of a constant interplay between evolutionary and demographic processes. We investigated population differentiation and adaptation of Norway spruce for juvenile growth, diameter of the stem, wood density, and tracheid traits at breast height. Data from 4461 phenotyped and genotyped Norway spruce from 396 half-sib families in two progeny tests were used to test for divergent selection in the framework of QST vs. FST. We show that the macroscopic resultant trait (stem diameter), unlike its microscopic components (tracheid dimensions) and juvenile growth, was under divergent selection that predated the Last Glacial Maximum. Altogether, the current variation in these phenotypic traits in Norway spruce is better explained by local adaptation to ancestral environments than to current ones, where populations were partly preadapted, mainly through growth-related traits.},
	language = {en},
	number = {1},
	urldate = {2023-01-20},
	journal = {Evolutionary Applications},
	author = {Tiret, Mathieu and Olsson, Lars and Grahn, Thomas and Karlsson, Bo and Milesi, Pascal and Lascoux, Martin and Lundqvist, Sven-Olof and García-Gil, Maria Rosario},
	year = {2023},
	keywords = {Norway spruce, QST vs. FST, population structure, wood quality},
	pages = {163--172},
}

The current distribution and population structure of many species were, to a large extent, shaped by cycles of isolation in glacial refugia and subsequent population expansions. Isolation in and postglacial expansion through heterogeneous environments led to either neutral or adaptive divergence. Norway spruce is no exception, and its current distribution is the consequence of a constant interplay between evolutionary and demographic processes. We investigated population differentiation and adaptation of Norway spruce for juvenile growth, diameter of the stem, wood density, and tracheid traits at breast height. Data from 4461 phenotyped and genotyped Norway spruce from 396 half-sib families in two progeny tests were used to test for divergent selection in the framework of QST vs. FST. We show that the macroscopic resultant trait (stem diameter), unlike its microscopic components (tracheid dimensions) and juvenile growth, was under divergent selection that predated the Last Glacial Maximum. Altogether, the current variation in these phenotypic traits in Norway spruce is better explained by local adaptation to ancestral environments than to current ones, where populations were partly preadapted, mainly through growth-related traits.

@article{liu_plant_2023,
	title = {The plant trans-{Golgi} network component {ECHIDNA} regulates defense, cell death, and endoplasmic reticulum stress},
	volume = {191},
	issn = {0032-0889},
	url = {https://doi.org/10.1093/plphys/kiac400},
	doi = {10.1093/plphys/kiac400},
	abstract = {The trans-Golgi network (TGN) acts as a central platform for sorting and secreting various cargoes to the cell surface, thus being essential for the full execution of plant immunity. However, the fine-tuned regulation of TGN components in plant defense and stress response has been not fully elucidated. Our study revealed that despite largely compromising penetration resistance, the loss-of-function mutation of the TGN component protein ECHIDNA (ECH) induced enhanced postinvasion resistance to powdery mildew in Arabidopsis thaliana. Genetic and transcriptome analyses and hormone profiling demonstrated that ECH loss resulted in salicylic acid (SA) hyperaccumulation via the ISOCHORISMATE SYNTHASE 1 biosynthesis pathway, thereby constitutively activating SA-dependent innate immunity that was largely responsible for the enhanced postinvasion resistance. Furthermore, the ech mutant displayed accelerated SA-independent spontaneous cell death and constitutive POWDERY MILDEW RESISTANCE 4-mediated callose depositions. In addition, ECH loss led to a chronically prolonged endoplasmic reticulum stress in the ech mutant. These results provide insights into understanding the role of TGN components in the regulation of plant immunity and stress responses.},
	number = {1},
	urldate = {2023-01-09},
	journal = {Plant Physiology},
	author = {Liu, Lijiang and Qin, Li and Safdar, Luqman Bin and Zhao, Chuanji and Cheng, Xiaohui and Xie, Meili and Zhang, Yi and Gao, Feng and Bai, Zetao and Huang, Junyan and Bhalerao, Rishikesh P and Liu, Shengyi and Wei, Yangdou},
	month = jan,
	year = {2023},
	pages = {558--574},
}

The trans-Golgi network (TGN) acts as a central platform for sorting and secreting various cargoes to the cell surface, thus being essential for the full execution of plant immunity. However, the fine-tuned regulation of TGN components in plant defense and stress response has been not fully elucidated. Our study revealed that despite largely compromising penetration resistance, the loss-of-function mutation of the TGN component protein ECHIDNA (ECH) induced enhanced postinvasion resistance to powdery mildew in Arabidopsis thaliana. Genetic and transcriptome analyses and hormone profiling demonstrated that ECH loss resulted in salicylic acid (SA) hyperaccumulation via the ISOCHORISMATE SYNTHASE 1 biosynthesis pathway, thereby constitutively activating SA-dependent innate immunity that was largely responsible for the enhanced postinvasion resistance. Furthermore, the ech mutant displayed accelerated SA-independent spontaneous cell death and constitutive POWDERY MILDEW RESISTANCE 4-mediated callose depositions. In addition, ECH loss led to a chronically prolonged endoplasmic reticulum stress in the ech mutant. These results provide insights into understanding the role of TGN components in the regulation of plant immunity and stress responses.

@article{walker_cytokinin_2023,
	title = {Cytokinin signaling regulates two-stage inflorescence arrest in {Arabidopsis}},
	volume = {191},
	issn = {0032-0889},
	url = {https://doi.org/10.1093/plphys/kiac514},
	doi = {10.1093/plphys/kiac514},
	abstract = {To maximize reproductive success, flowering plants must correctly time entry and exit from the reproductive phase. While much is known about mechanisms that regulate initiation of flowering, end-of-flowering remains largely uncharacterized. End-of-flowering in Arabidopsis (Arabidopsis thaliana) consists of quasi-synchronous arrest of inflorescences, but it is unclear how arrest is correctly timed with respect to environmental stimuli and reproductive success. Here, we showed that Arabidopsis inflorescence arrest is a complex developmental phenomenon, which includes the arrest of the inflorescence meristem (IM), coupled with a separable “floral arrest” of all unopened floral primordia; these events occur well before visible inflorescence arrest. We showed that global inflorescence removal delays both IM and floral arrest, but that local fruit removal only delays floral arrest, emphasizing their separability. We tested whether cytokinin regulates inflorescence arrest, and found that cytokinin signaling dynamics mirror IM activity, while cytokinin treatment can delay both IM and floral arrest. We further showed that gain-of-function cytokinin receptor mutants can delay IM and floral arrest; conversely, loss-of-function mutants prevented the extension of flowering in response to inflorescence removal. Collectively, our data suggest that the dilution of cytokinin among an increasing number of sink organs leads to end-of-flowering in Arabidopsis by triggering IM and floral arrest.},
	number = {1},
	urldate = {2023-01-09},
	journal = {Plant Physiology},
	author = {Walker, Catriona H and Ware, Alexander and Šimura, Jan and Ljung, Karin and Wilson, Zoe and Bennett, Tom},
	month = jan,
	year = {2023},
	pages = {479--495},
}

To maximize reproductive success, flowering plants must correctly time entry and exit from the reproductive phase. While much is known about mechanisms that regulate initiation of flowering, end-of-flowering remains largely uncharacterized. End-of-flowering in Arabidopsis (Arabidopsis thaliana) consists of quasi-synchronous arrest of inflorescences, but it is unclear how arrest is correctly timed with respect to environmental stimuli and reproductive success. Here, we showed that Arabidopsis inflorescence arrest is a complex developmental phenomenon, which includes the arrest of the inflorescence meristem (IM), coupled with a separable “floral arrest” of all unopened floral primordia; these events occur well before visible inflorescence arrest. We showed that global inflorescence removal delays both IM and floral arrest, but that local fruit removal only delays floral arrest, emphasizing their separability. We tested whether cytokinin regulates inflorescence arrest, and found that cytokinin signaling dynamics mirror IM activity, while cytokinin treatment can delay both IM and floral arrest. We further showed that gain-of-function cytokinin receptor mutants can delay IM and floral arrest; conversely, loss-of-function mutants prevented the extension of flowering in response to inflorescence removal. Collectively, our data suggest that the dilution of cytokinin among an increasing number of sink organs leads to end-of-flowering in Arabidopsis by triggering IM and floral arrest.

@article{kleczkowski_magnesium_2023,
	title = {Magnesium and cell energetics: {At} the junction of metabolism of adenylate and non-adenylate nucleotides},
	volume = {280},
	issn = {0176-1617},
	shorttitle = {Magnesium and cell energetics},
	url = {https://www.sciencedirect.com/science/article/pii/S0176161722002875},
	doi = {10.1016/j.jplph.2022.153901},
	abstract = {Free magnesium (Mg2+) represents a powerful signal arising from interconversions of adenylates (ATP, ADP and AMP). This is a consequence of the involvement of adenylate kinase (AK) which equilibrates adenylates and uses defined species of Mg-complexed and Mg-free adenylates in both directions of its reaction. However, cells contain also other reversible Mg2+-dependent enzymes that equilibrate non-adenylate nucleotides (uridylates, cytidylates and guanylates), i.e. nucleoside monophosphate kinases (NMPKs) and nucleoside diphosphate kinase (NDPK). Here, we propose that AK activity is tightly coupled to activities of NMPK and NDPK, linking adenylate equilibrium to equilibria of other nucleotides, and with [Mg2+] controlling the ratios of Mg-chelated and Mg-free nucleotides. This coupling establishes main hubs for adenylate-driven equilibration of non-adenylate nucleotides, with [Mg2+] acting as signal arising from all nucleotides rather than adenylates only. Further consequences involve an overall adenylate control of UTP-, GTP- and CTP-dependent pathways and the availability of substrates for RNA and DNA synthesis.},
	language = {en},
	urldate = {2022-12-30},
	journal = {Journal of Plant Physiology},
	author = {Kleczkowski, Leszek A. and Igamberdiev, Abir U.},
	month = jan,
	year = {2023},
	keywords = {Adenylate kinase, Guanylate kinase, Magnesium signaling, Nucleoside diphosphate kinase, Nucleoside monophosphate kinase, Uridylate-cytidylate kinase},
	pages = {153901},
}

Free magnesium (Mg2+) represents a powerful signal arising from interconversions of adenylates (ATP, ADP and AMP). This is a consequence of the involvement of adenylate kinase (AK) which equilibrates adenylates and uses defined species of Mg-complexed and Mg-free adenylates in both directions of its reaction. However, cells contain also other reversible Mg2+-dependent enzymes that equilibrate non-adenylate nucleotides (uridylates, cytidylates and guanylates), i.e. nucleoside monophosphate kinases (NMPKs) and nucleoside diphosphate kinase (NDPK). Here, we propose that AK activity is tightly coupled to activities of NMPK and NDPK, linking adenylate equilibrium to equilibria of other nucleotides, and with [Mg2+] controlling the ratios of Mg-chelated and Mg-free nucleotides. This coupling establishes main hubs for adenylate-driven equilibration of non-adenylate nucleotides, with [Mg2+] acting as signal arising from all nucleotides rather than adenylates only. Further consequences involve an overall adenylate control of UTP-, GTP- and CTP-dependent pathways and the availability of substrates for RNA and DNA synthesis.

@article{lecoy_analysis_2023,
	title = {Analysis of the {ASR} and {LP3} homologous gene families reveal positive selection acting on {LP3}-3 gene},
	volume = {850},
	issn = {0378-1119},
	url = {https://www.sciencedirect.com/science/article/pii/S0378111922007557},
	doi = {10.1016/j.gene.2022.146935},
	abstract = {Drought has long been established as a major environmental stress for plants which have in turn developed several coping strategies, ranging from physiological to molecular mechanisms. LP3 that was first discovered in loblolly pine (Pinus taeda L.) is a homolog of the Abscisic Acid, Stress and Ripening (ASR) gene belonging to the ABA/WDS gene family that was first detected in tomato. LP3 has been shown to be present in four different paralogs in loblolly pine called LP3-0, LP3-1, LP3-2 and LP3-3. LP3 in loblolly pine has not been as extensively studied as the ASR in tomato. Similar to ASR, the different LP3 paralogs have been shown to be upregulated in response to water deficit stress and to act as transcription factors for genes likely involved in hexose transport. In the current study, we have investigated the evolutionary history of LP3 gene family, with the aim of relating it to that of ASR from a phylogenetic perspective and comparing the differences in selective pressure and codon usage. Phylogenetic trees revealed that LP3 is less divergent across species than ASR even when the trees were solely based on the different sub-sections of the gene. Phylogenetic, GC content, codon usage and selective pressure analyses suggest that LP3-3 is undergoing positive selection.},
	language = {en},
	urldate = {2022-10-06},
	journal = {Gene},
	author = {Lecoy, Jonathan and Ranade, Sonali Sachin and García-Gil, María Rosario},
	month = jan,
	year = {2023},
	keywords = {ABA/WDS, Codon usage, Drought resistance, GC-content, Selective pressure},
	pages = {146935},
}

Drought has long been established as a major environmental stress for plants which have in turn developed several coping strategies, ranging from physiological to molecular mechanisms. LP3 that was first discovered in loblolly pine (Pinus taeda L.) is a homolog of the Abscisic Acid, Stress and Ripening (ASR) gene belonging to the ABA/WDS gene family that was first detected in tomato. LP3 has been shown to be present in four different paralogs in loblolly pine called LP3-0, LP3-1, LP3-2 and LP3-3. LP3 in loblolly pine has not been as extensively studied as the ASR in tomato. Similar to ASR, the different LP3 paralogs have been shown to be upregulated in response to water deficit stress and to act as transcription factors for genes likely involved in hexose transport. In the current study, we have investigated the evolutionary history of LP3 gene family, with the aim of relating it to that of ASR from a phylogenetic perspective and comparing the differences in selective pressure and codon usage. Phylogenetic trees revealed that LP3 is less divergent across species than ASR even when the trees were solely based on the different sub-sections of the gene. Phylogenetic, GC content, codon usage and selective pressure analyses suggest that LP3-3 is undergoing positive selection.