@article{calderon_how_2021,
	series = {Cell signaling and gene regulation},
	title = {How retrograde signaling is intertwined with the evolution of photosynthetic eukaryotes},
	volume = {63},
	issn = {1369-5266},
	url = {https://www.sciencedirect.com/science/article/pii/S1369526621000935},
	doi = {10/gmkx8p},
	abstract = {Chloroplasts and mitochondria evolved from free-living prokaryotic organisms that entered the eukaryotic cell through endosymbiosis. The gradual conversion from endosymbiont to organelle during the course of evolution was accompanied by the development of a communication system between the host and the endosymbiont, referred to as retrograde signaling or organelle-to-nucleus signaling. In higher plants, plastid-to-nucleus signaling involves multiple signaling pathways necessary to coordinate plastid function and cellular responses to developmental and environmental stimuli. Phylogenetic reconstructions using sequence information from evolutionarily diverse photosynthetic eukaryotes have begun to provide information about how retrograde signaling pathways were adopted and modified in different lineages over time. A tight communication system was likely a major facilitator of plants conquest of the land because it would have enabled the algal ancestors of land plants to better allocate their cellular resources in response to high light and desiccation, the major stressor for streptophyte algae in a terrestrial habitat. In this review, we aim to give an evolutionary perspective on plastid-to-nucleus signaling.},
	language = {en},
	urldate = {2021-11-12},
	journal = {Current Opinion in Plant Biology},
	author = {Calderon, Robert H. and Strand, Åsa},
	month = oct,
	year = {2021},
	keywords = {Cyanobacteria, Endosymbiosis event, Mitochondria, Plastids, Retrograde signals, Stress, lncRNA.},
	pages = {102093},
}

Chloroplasts and mitochondria evolved from free-living prokaryotic organisms that entered the eukaryotic cell through endosymbiosis. The gradual conversion from endosymbiont to organelle during the course of evolution was accompanied by the development of a communication system between the host and the endosymbiont, referred to as retrograde signaling or organelle-to-nucleus signaling. In higher plants, plastid-to-nucleus signaling involves multiple signaling pathways necessary to coordinate plastid function and cellular responses to developmental and environmental stimuli. Phylogenetic reconstructions using sequence information from evolutionarily diverse photosynthetic eukaryotes have begun to provide information about how retrograde signaling pathways were adopted and modified in different lineages over time. A tight communication system was likely a major facilitator of plants conquest of the land because it would have enabled the algal ancestors of land plants to better allocate their cellular resources in response to high light and desiccation, the major stressor for streptophyte algae in a terrestrial habitat. In this review, we aim to give an evolutionary perspective on plastid-to-nucleus signaling.

@article{le_temporary_2021,
	title = {Temporary immersion bioreactor system for propagation by somatic embryogenesis of hybrid larch ({Larix} × eurolepis {Henry})},
	volume = {32},
	issn = {2215-017X},
	url = {https://www.sciencedirect.com/science/article/pii/S2215017X21001004},
	doi = {10/gnj3pm},
	abstract = {Somatic embryogenesis (SE) has high potential for large-scale clonal propagation of conifers. Different types of bioreactor cultures have been tested for the conifer SE process where the temporary immersion bioreactors (TIBs) have proved to be useful across the different developmental steps of the SE process. In the present study the use of TIBs was tested for hybrid larch (Larix × eurolepis Henry). The results showed two-fold increases in both fresh weight (FW) of pro-embryogenic masses (PEMs) and yield of cotyledonary embryos in the TIBs compared to solid medium in plates. For the germination phase, the highest number of roots per plant, the root length and height of plants were also obtained in the TIBs. The results show that the TIB system can be successfully used to support scale up of plant production in all steps of the SE process from proliferation to germination of hybrid larch (Larix × eurolepis Henry).},
	language = {en},
	urldate = {2021-11-12},
	journal = {Biotechnology Reports},
	author = {Le, Kim-Cuong and Dedicova, Beata and Johansson, Sofie and Lelu-Walter, Marie-Anne and Egertsdotter, Ulrika},
	month = dec,
	year = {2021},
	keywords = {Germination, Horizontal TIB, Larix × eurolepis, Scale up, Somatic embryogenesis, Vertical TIB, ×},
	pages = {e00684},
}

Somatic embryogenesis (SE) has high potential for large-scale clonal propagation of conifers. Different types of bioreactor cultures have been tested for the conifer SE process where the temporary immersion bioreactors (TIBs) have proved to be useful across the different developmental steps of the SE process. In the present study the use of TIBs was tested for hybrid larch (Larix × eurolepis Henry). The results showed two-fold increases in both fresh weight (FW) of pro-embryogenic masses (PEMs) and yield of cotyledonary embryos in the TIBs compared to solid medium in plates. For the germination phase, the highest number of roots per plant, the root length and height of plants were also obtained in the TIBs. The results show that the TIB system can be successfully used to support scale up of plant production in all steps of the SE process from proliferation to germination of hybrid larch (Larix × eurolepis Henry).

@article{parker_biohybrid_2021,
	title = {Biohybrid plants with electronic roots via in vivo polymerization of conjugated oligomers},
	issn = {2051-6355},
	url = {https://pubs.rsc.org/en/content/articlelanding/2021/mh/d1mh01423d},
	doi = {10/gnh3cp},
	abstract = {Plant processes, ranging from photosynthesis through production of biomaterials to environmental sensing and adaptation, can be used in technology via integration of functional materials and devices. Previously, plants with integrated organic electronic devices and circuits distributed in their vascular tissue and organs have been demonstrated. To circumvent biological barriers, and thereby access the internal tissue, plant cuttings were used, which resulted in biohybrids with limited lifetime and use. Here, we report intact plants with electronic functionality that continue to grow and develop enabling plant-biohybrid systems that fully maintain their biological processes. The biocatalytic machinery of the plant cell wall was leveraged to seamlessly integrate conductors with mixed ionic–electronic conductivity along the root system of the plants. Cell wall peroxidases catalyzed ETE-S polymerization while the plant tissue served as the template, organizing the polymer in a favorable manner. The conductivity of the resulting p(ETE-S) roots reached the order of 10 S cm−1 and remained stable over the course of 4 weeks while the roots continued to grow. The p(ETE-S) roots were used to build supercapacitors that outperform previous plant-biohybrid charge storage demonstrations. Plants were not affected by the electronic functionalization but adapted to this new hybrid state by developing a more complex root system. Biohybrid plants with electronic roots pave the way for autonomous systems with potential applications in energy, sensing and robotics.},
	language = {en},
	urldate = {2021-11-18},
	journal = {Materials Horizons},
	author = {Parker, Daniela and Daguerre, Yohann and Dufil, Gwennaël and Mantione, Daniele and Solano, Eduardo and Cloutet, Eric and Hadziioannou, Georges and Näsholm, Torgny and Berggren, Magnus and Pavlopoulou, Eleni and Stavrinidou, Eleni},
	month = nov,
	year = {2021},
	note = {Publisher: The Royal Society of Chemistry},
}

Plant processes, ranging from photosynthesis through production of biomaterials to environmental sensing and adaptation, can be used in technology via integration of functional materials and devices. Previously, plants with integrated organic electronic devices and circuits distributed in their vascular tissue and organs have been demonstrated. To circumvent biological barriers, and thereby access the internal tissue, plant cuttings were used, which resulted in biohybrids with limited lifetime and use. Here, we report intact plants with electronic functionality that continue to grow and develop enabling plant-biohybrid systems that fully maintain their biological processes. The biocatalytic machinery of the plant cell wall was leveraged to seamlessly integrate conductors with mixed ionic–electronic conductivity along the root system of the plants. Cell wall peroxidases catalyzed ETE-S polymerization while the plant tissue served as the template, organizing the polymer in a favorable manner. The conductivity of the resulting p(ETE-S) roots reached the order of 10 S cm−1 and remained stable over the course of 4 weeks while the roots continued to grow. The p(ETE-S) roots were used to build supercapacitors that outperform previous plant-biohybrid charge storage demonstrations. Plants were not affected by the electronic functionalization but adapted to this new hybrid state by developing a more complex root system. Biohybrid plants with electronic roots pave the way for autonomous systems with potential applications in energy, sensing and robotics.

@article{singh_when_2021,
	title = {When to branch: seasonal control of shoot architecture in trees},
	copyright = {© 2021 The Authors. The FEBS Journal published by John Wiley \& Sons Ltd on behalf of Federation of European Biochemical Societies},
	issn = {1742-4658},
	shorttitle = {When to branch},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/febs.16227},
	doi = {10/gnj3pj},
	abstract = {Long-lived perennial plants optimize their shoot architecture by responding to seasonal cues. The main strategy used by plants of temperate and boreal regions with respect to surviving the extremely unfavourable conditions of winter comprises the protection of their apical and lateral meristematic tissues. This involves myriads of transcriptional, translational and metabolic changes in the plants because shoot architecture is controlled by multiple pathways that regulate processes such as bud formation and flowering, small RNAs, environmental factors (especially light quality, photoperiod and temperature), hormones, and sugars. Recent studies have begun to reveal how these pathways are recruited for the seasonal adaptation and regulation of shoot architecture in perennial plants, including the role of a regulatory module consisting of antagonistic players terminal flower 1 (TFL1) and like-ap1 (LAP1) in the hybrid aspen. Here, we review recent progress in our understanding of the genetic control of shoot architecture in perennials compared to in annuals.},
	language = {en},
	urldate = {2021-11-12},
	journal = {The FEBS Journal},
	author = {Singh, Rajesh Kumar and Bhalerao, Rishikesh P. and Maurya, Jay P.},
	month = oct,
	year = {2021},
	keywords = {Axillary buds, Branching, Photoperiod, Seasonal growth, Shoot Architecture, axillary buds, branching, photoperiod, seasonal growth, shoot architecture, temperature},
}

Long-lived perennial plants optimize their shoot architecture by responding to seasonal cues. The main strategy used by plants of temperate and boreal regions with respect to surviving the extremely unfavourable conditions of winter comprises the protection of their apical and lateral meristematic tissues. This involves myriads of transcriptional, translational and metabolic changes in the plants because shoot architecture is controlled by multiple pathways that regulate processes such as bud formation and flowering, small RNAs, environmental factors (especially light quality, photoperiod and temperature), hormones, and sugars. Recent studies have begun to reveal how these pathways are recruited for the seasonal adaptation and regulation of shoot architecture in perennial plants, including the role of a regulatory module consisting of antagonistic players terminal flower 1 (TFL1) and like-ap1 (LAP1) in the hybrid aspen. Here, we review recent progress in our understanding of the genetic control of shoot architecture in perennials compared to in annuals.

@article{chen_determination_2021,
	title = {Determination of conifer age biomarker {DAL1} interactome using {Y2H}-seq},
	volume = {1},
	copyright = {2021 The Author(s)},
	issn = {2767-3812},
	url = {http://www.maxapress.com/rticle/doi/10.48130/FR-2021-0012},
	doi = {10/gnj3pg},
	abstract = {Age is a sophisticated physiological signal that ensures the sequence of different developmental stages in organisms. The regulation of ageing pathways appears to differ between gymnosperms and angiosperms. We previously identified \textit{DAL1} as a conserved conifer age biomarker that plays a crucial role in the transition from vegetative to reproductive life-history phases in pines. Therefore, elucidating the specific interaction events related to DAL1 is key to understanding how age drives conifer development. Large-scale yeast two-hybrid (Y2H) analysis followed by next-generation high-throughput sequencing (Y2H-seq) allowed us to identify 135 PtDAL1 interacting proteins in \textit{Pinus tabuliformis}. Our study found that PtDAL1 interacting proteins showed an ageing-related module, with sophisticated interacting networks composed of transcription factors (TFs), transcriptional regulators (TRs), and kinases. These interacting proteins are produced in response to a variety of phytohormones and environmental signals, and are likely involved in wood formation, needle development, oleoresin terpenoids biosynthesis, and reproductive development. In this study, we propose a novel regulation model of conifer ageing pathways whereby PtDAL1 coordinates different environmental stimuli and interacts with corresponding proteins to regulate appropriate development.},
	language = {en},
	number = {1},
	urldate = {2021-11-22},
	journal = {Forestry Research},
	author = {Chen, Xi and Zhu, Qianya and Nie, Yumeng and Han, Fangxu and Li, Yue and Wu, Harry X. and Niu, Shihui},
	month = jul,
	year = {2021},
	pages = {1--12},
}

Age is a sophisticated physiological signal that ensures the sequence of different developmental stages in organisms. The regulation of ageing pathways appears to differ between gymnosperms and angiosperms. We previously identified DAL1 as a conserved conifer age biomarker that plays a crucial role in the transition from vegetative to reproductive life-history phases in pines. Therefore, elucidating the specific interaction events related to DAL1 is key to understanding how age drives conifer development. Large-scale yeast two-hybrid (Y2H) analysis followed by next-generation high-throughput sequencing (Y2H-seq) allowed us to identify 135 PtDAL1 interacting proteins in Pinus tabuliformis. Our study found that PtDAL1 interacting proteins showed an ageing-related module, with sophisticated interacting networks composed of transcription factors (TFs), transcriptional regulators (TRs), and kinases. These interacting proteins are produced in response to a variety of phytohormones and environmental signals, and are likely involved in wood formation, needle development, oleoresin terpenoids biosynthesis, and reproductive development. In this study, we propose a novel regulation model of conifer ageing pathways whereby PtDAL1 coordinates different environmental stimuli and interacts with corresponding proteins to regulate appropriate development.