@article{stojkovic_transcriptome_2024,
	title = {A transcriptome atlas of zygotic and somatic embryogenesis in {Norway} spruce},
	volume = {120},
	copyright = {© 2024 The Author(s). The Plant Journal published by Society for Experimental Biology and John Wiley \& Sons Ltd.},
	issn = {1365-313X},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/tpj.17087},
	doi = {10.1111/tpj.17087},
	abstract = {Somatic embryogenesis (SE) is a powerful model system for studying embryo development and an important method for scaling up availability of elite and climate-adapted genetic material of Norway spruce (Picea abies L. Karst). However, there are several steps during the development of the somatic embryo (Sem) that are suboptimal compared to zygotic embryo (Zem) development. These differences are poorly understood and result in substantial yield losses during plant production, which limits cost-effective large-scale production of SE plants. This study presents a comprehensive data resource profiling gene expression during zygotic and somatic embryo development to support studies aiming to advance understanding of gene regulatory programmes controlling embryo development. Transcriptome expression patterns were analysed during zygotic embryogenesis (ZE) in Norway spruce, including separated samples of the female gametophytes and Zem, and at multiple stages during SE. Expression data from eight developmental stages of SE, starting with pro-embryogenic masses (PEMs) up until germination, revealed extensive modulation of the transcriptome between the early and mid-stage maturing embryos and at the transition of desiccated embryos to germination. Comparative analysis of gene expression changes during ZE and SE identified differences in the pattern of gene expression changes and functional enrichment of these provided insight into the associated biological processes. Orthologs of transcription factors known to regulate embryo development in angiosperms were differentially regulated during Zem and Sem development and in the different zygotic embryo tissues, providing clues to the differences in development observed between Zem and Sem. This resource represents the most comprehensive dataset available for exploring embryo development in conifers.},
	language = {en},
	number = {5},
	urldate = {2024-12-13},
	journal = {The Plant Journal},
	author = {Stojkovič, Katja and Canovi, Camilla and Le, Kim-Cuong and Ahmad, Iftikhar and Gaboreanu, Ioana and Johansson, Sofie and Delhomme, Nicolas and Egertsdotter, Ulrika and Street, Nathaniel R.},
	year = {2024},
	note = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1111/tpj.17087},
	keywords = {Norway spruce, Picea abies, differential expression, embryo, embryogenesis, transcriptome},
	pages = {2238--2252},
}

Somatic embryogenesis (SE) is a powerful model system for studying embryo development and an important method for scaling up availability of elite and climate-adapted genetic material of Norway spruce (Picea abies L. Karst). However, there are several steps during the development of the somatic embryo (Sem) that are suboptimal compared to zygotic embryo (Zem) development. These differences are poorly understood and result in substantial yield losses during plant production, which limits cost-effective large-scale production of SE plants. This study presents a comprehensive data resource profiling gene expression during zygotic and somatic embryo development to support studies aiming to advance understanding of gene regulatory programmes controlling embryo development. Transcriptome expression patterns were analysed during zygotic embryogenesis (ZE) in Norway spruce, including separated samples of the female gametophytes and Zem, and at multiple stages during SE. Expression data from eight developmental stages of SE, starting with pro-embryogenic masses (PEMs) up until germination, revealed extensive modulation of the transcriptome between the early and mid-stage maturing embryos and at the transition of desiccated embryos to germination. Comparative analysis of gene expression changes during ZE and SE identified differences in the pattern of gene expression changes and functional enrichment of these provided insight into the associated biological processes. Orthologs of transcription factors known to regulate embryo development in angiosperms were differentially regulated during Zem and Sem development and in the different zygotic embryo tissues, providing clues to the differences in development observed between Zem and Sem. This resource represents the most comprehensive dataset available for exploring embryo development in conifers.

@article{pandey_regulatory_2024,
	title = {A regulatory module mediating temperature control of cell-cell communication facilitates tree bud dormancy release},
	volume = {43},
	issn = {0261-4189},
	url = {https://www.embopress.org/doi/full/10.1038/s44318-024-00256-5},
	doi = {10.1038/s44318-024-00256-5},
	abstract = {The control of cell–cell communication via plasmodesmata (PD) plays a key role in plant development. In tree buds, low-temperature conditions (LT) induce a switch in plasmodesmata from a closed to an open state, which restores cell-to-cell communication in the shoot apex and releases dormancy. Using genetic and cell-biological approaches, we have identified a previously uncharacterized transcription factor, Low-temperature-Induced MADS-box 1 (LIM1), as an LT-induced, direct upstream activator of the gibberellic acid (GA) pathway. The LIM1-GA module mediates low temperature-induced plasmodesmata opening, by negatively regulating callose accumulation to promote dormancy release. LIM1 also activates expression of FT1 (FLOWERING LOCUS T), another LT-induced factor, with LIM1-FT1 forming a coherent feedforward loop converging on low-temperature regulation of gibberellin signaling in dormancy release. Mathematical modeling and experimental validation suggest that negative feedback regulation of LIM1 by gibberellin could play a crucial role in maintaining the robust temporal regulation of bud responses to low temperature. These results reveal genetic factors linking temperature control of cell–cell communication with regulation of seasonally-aligned growth crucial for adaptation of trees.},
	number = {23},
	urldate = {2024-12-06},
	journal = {The EMBO Journal},
	author = {Pandey, Shashank K and Maurya, Jay Prakash and Aryal, Bibek and Drynda, Kamil and Nair, Aswin and Miskolczi, Pal and Singh, Rajesh Kumar and Wang, Xiaobin and Ma, Yujiao and de Souza Moraes, Tatiana and Bayer, Emmanuelle M and Farcot, Etienne and Bassel, George W and Band, Leah R and Bhalerao, Rishikesh P},
	month = dec,
	year = {2024},
	note = {Num Pages: 5812
Publisher: John Wiley \& Sons, Ltd},
	keywords = {Callose, Dormancy, Gibberellins, Plasmodesmata, Temperature},
	pages = {5793--5812},
}

The control of cell–cell communication via plasmodesmata (PD) plays a key role in plant development. In tree buds, low-temperature conditions (LT) induce a switch in plasmodesmata from a closed to an open state, which restores cell-to-cell communication in the shoot apex and releases dormancy. Using genetic and cell-biological approaches, we have identified a previously uncharacterized transcription factor, Low-temperature-Induced MADS-box 1 (LIM1), as an LT-induced, direct upstream activator of the gibberellic acid (GA) pathway. The LIM1-GA module mediates low temperature-induced plasmodesmata opening, by negatively regulating callose accumulation to promote dormancy release. LIM1 also activates expression of FT1 (FLOWERING LOCUS T), another LT-induced factor, with LIM1-FT1 forming a coherent feedforward loop converging on low-temperature regulation of gibberellin signaling in dormancy release. Mathematical modeling and experimental validation suggest that negative feedback regulation of LIM1 by gibberellin could play a crucial role in maintaining the robust temporal regulation of bud responses to low temperature. These results reveal genetic factors linking temperature control of cell–cell communication with regulation of seasonally-aligned growth crucial for adaptation of trees.

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

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

@article{dufil_glucose-sensitive_2024,
	title = {Glucose-{Sensitive} {Biohybrid} {Roots} for {Supercapacitive} {Bioanodes}},
	url = {https://doi.org/10.1021/acsabm.4c01425},
	doi = {10.1021/acsabm.4c01425},
	abstract = {Plants as living organisms, as well as their material–structural components and physiological processes, offer promising elements for developing more sustainable technologies. Previously, we demonstrated that plants could acquire electronic functionality, as their enzymatic activity catalyzes the in vivo polymerization of water-soluble conjugated oligomers. We then leveraged plant-integrated conductors to develop biohybrid energy storage devices and circuits. Here, we extend the concept of plant biohybrids to develop plant-based energy-harvesting devices. We demonstrate plant biohybrids with modified roots that can convert common root exudates, such as glucose, to electricity. To do so, we developed a simple one-step approach to convert living roots to glucose-sensitive electrodes by dipping the root in a solution of the conjugated trimer ETE-S and the enzyme glucose dehydrogenase flavin adenine dinucleotide. The biohybrid device responds to glucose concentrations down to 100 μM while it saturates at 100 mM. The performance of our approach was compared with a classic mediator-based glucose biosensor functionalization method. While the latter method increases the stability of the sensor, it results in less sensitivity and damages the root structure. Finally, we show that glucose oxidation can be combined with the volumetric capacitance of p(ETE-S)-forming devices that generate current in the presence of glucose and store it in the same biohybrid root electrodes. The plant biohybrid devices open a pathway to biologically integrated technology that finds application in low-power devices, for example, sensors for agriculture or the environment.},
	urldate = {2024-12-06},
	journal = {ACS Applied Bio Materials},
	author = {Dufil, Gwennaël and Pham, Julie and Diacci, Chiara and Daguerre, Yohann and Mantione, Daniele and Zrig, Samia and Näsholm, Torgny and Donahue, Mary J. and Oikonomou, Vasileios K. and Noël, Vincent and Piro, Benoit and Stavrinidou, Eleni},
	month = dec,
	year = {2024},
	note = {Publisher: American Chemical Society},
}

Plants as living organisms, as well as their material–structural components and physiological processes, offer promising elements for developing more sustainable technologies. Previously, we demonstrated that plants could acquire electronic functionality, as their enzymatic activity catalyzes the in vivo polymerization of water-soluble conjugated oligomers. We then leveraged plant-integrated conductors to develop biohybrid energy storage devices and circuits. Here, we extend the concept of plant biohybrids to develop plant-based energy-harvesting devices. We demonstrate plant biohybrids with modified roots that can convert common root exudates, such as glucose, to electricity. To do so, we developed a simple one-step approach to convert living roots to glucose-sensitive electrodes by dipping the root in a solution of the conjugated trimer ETE-S and the enzyme glucose dehydrogenase flavin adenine dinucleotide. The biohybrid device responds to glucose concentrations down to 100 μM while it saturates at 100 mM. The performance of our approach was compared with a classic mediator-based glucose biosensor functionalization method. While the latter method increases the stability of the sensor, it results in less sensitivity and damages the root structure. Finally, we show that glucose oxidation can be combined with the volumetric capacitance of p(ETE-S)-forming devices that generate current in the presence of glucose and store it in the same biohybrid root electrodes. The plant biohybrid devices open a pathway to biologically integrated technology that finds application in low-power devices, for example, sensors for agriculture or the environment.

@article{lazaro-gimeno_circadian_2024,
	title = {The circadian clock participates in seasonal growth in {Norway} spruce ({Picea} abies)},
	volume = {44},
	issn = {1758-4469},
	url = {https://doi.org/10.1093/treephys/tpae139},
	doi = {10.1093/treephys/tpae139},
	abstract = {The boreal forest ecosystems of the northern hemisphere are dominated by conifers, of which Norway spruce (Picea abies [L.] H. Karst.) is one of the most common species. Due to its economic interest to the agroforestry industry, as well as its ecological significance, it is important to understand seasonal growth and biomass production in Norway spruce. Solid evidence that the circadian clock regulates growth in conifers has proved elusive, however, resulting in significant gaps in our knowledge of clock function in these trees. Here, we reassess the impact of the circadian clock on growth in Norway spruce. Using a combination of approaches monitoring the physiology of vegetative growth, transcriptomics and bioinformatics, we determined that the clock could be playing a decisive role in enabling growth, acting in specific developmental processes influenced by season and geographical location to guide bud burst and growth. Thus, the evidence indicates that there is time for spruce.},
	number = {11},
	urldate = {2024-11-29},
	journal = {Tree Physiology},
	author = {Lázaro-Gimeno, David and Ferrari, Camilla and Delhomme, Nico and Johansson, Mikael and Sjölander, Johan and Singh, Rajesh Kumar and Mutwil, Marek and Eriksson, Maria E},
	month = nov,
	year = {2024},
	pages = {tpae139},
}

The boreal forest ecosystems of the northern hemisphere are dominated by conifers, of which Norway spruce (Picea abies [L.] H. Karst.) is one of the most common species. Due to its economic interest to the agroforestry industry, as well as its ecological significance, it is important to understand seasonal growth and biomass production in Norway spruce. Solid evidence that the circadian clock regulates growth in conifers has proved elusive, however, resulting in significant gaps in our knowledge of clock function in these trees. Here, we reassess the impact of the circadian clock on growth in Norway spruce. Using a combination of approaches monitoring the physiology of vegetative growth, transcriptomics and bioinformatics, we determined that the clock could be playing a decisive role in enabling growth, acting in specific developmental processes influenced by season and geographical location to guide bud burst and growth. Thus, the evidence indicates that there is time for spruce.