@article{noauthor_dgat1_2022,
	title = {{DGAT1} activity synchronises with mitophagy to protect cells from metabolic rewiring by iron  depletion},
	volume = {41},
	issn = {0261-4189},
	url = {https://www.embopress.org/doi/full/10.15252/embj.2021109390},
	doi = {10.15252/embj.2021109390},
	abstract = {Abstract Mitophagy removes defective mitochondria via lysosomal elimination. Increased mitophagy coincides with metabolic reprogramming, yet it remains unknown whether mitophagy is a cause or consequence of such state changes. The signalling pathways that integrate with mitophagy to sustain cell and tissue integrity also remain poorly defined. We performed temporal metabolomics on mammalian cells treated with deferiprone, a therapeutic iron chelator that stimulates PINK1/PARKIN-independent mitophagy. Iron depletion profoundly rewired the metabolome, hallmarked by remodelling of lipid metabolism within minutes of treatment. DGAT1-dependent lipid droplet biosynthesis occurred several hours before mitochondrial clearance, with lipid droplets bordering mitochondria upon iron chelation. We demonstrate that DGAT1 inhibition restricts mitophagy in vitro, with impaired lysosomal homeostasis and cell viability. Importantly, genetic depletion of DGAT1 in vivo significantly impaired neuronal mitophagy and locomotor function in Drosophila. Our data define iron depletion as a potent signal that rapidly reshapes metabolism and establishes an unexpected synergy between lipid homeostasis and mitophagy that safeguards cell and tissue integrity.},
	number = {10},
	urldate = {2022-05-20},
	journal = {The EMBO Journal},
	month = may,
	year = {2022},
	note = {Publisher: John Wiley \& Sons, Ltd},
	keywords = {DGAT1, iron, lipid droplet, metabolism, mitophagy},
	pages = {e109390},
}

Abstract Mitophagy removes defective mitochondria via lysosomal elimination. Increased mitophagy coincides with metabolic reprogramming, yet it remains unknown whether mitophagy is a cause or consequence of such state changes. The signalling pathways that integrate with mitophagy to sustain cell and tissue integrity also remain poorly defined. We performed temporal metabolomics on mammalian cells treated with deferiprone, a therapeutic iron chelator that stimulates PINK1/PARKIN-independent mitophagy. Iron depletion profoundly rewired the metabolome, hallmarked by remodelling of lipid metabolism within minutes of treatment. DGAT1-dependent lipid droplet biosynthesis occurred several hours before mitochondrial clearance, with lipid droplets bordering mitochondria upon iron chelation. We demonstrate that DGAT1 inhibition restricts mitophagy in vitro, with impaired lysosomal homeostasis and cell viability. Importantly, genetic depletion of DGAT1 in vivo significantly impaired neuronal mitophagy and locomotor function in Drosophila. Our data define iron depletion as a potent signal that rapidly reshapes metabolism and establishes an unexpected synergy between lipid homeostasis and mitophagy that safeguards cell and tissue integrity.

@article{chardon_natural_2022,
	title = {Natural variation in the long-distance transport of nutrients and photoassimilates in response to {N} availability},
	volume = {273},
	issn = {0176-1617},
	url = {https://www.sciencedirect.com/science/article/pii/S0176161722000931},
	doi = {10.1016/j.jplph.2022.153707},
	abstract = {Phloem and xylem tissues are necessary for the allocation of nutrients and photoassimilates. However, how the long-distance transport of carbon (C) and nitrogen (N) is coordinated with the central metabolism is largely unknown. To better understand how the genetic and environmental factors influence C and N transport, we analysed the metabolite profiles of phloem exudates and xylem saps of five Arabidopsis thaliana accessions grown in low or non-limiting N supply. We observed that xylem saps were composed of 46 or 56\% carbohydrates, 27 or 45\% amino acids, and 5 or 13\% organic acids in low or non-limiting N supply, respectively. In contrast, phloem exudates were composed of 76 or 86\% carbohydrates, 7 or 18\% amino acids, and 5 or 6\% organic acids. Variation in N supply impacted amino acid, organic acid and sugar contents. When comparing low N and non-limiting N, the most striking differences were variations of glutamine, aspartate, and succinate abundance in the xylem saps and citrate and fumarate abundance in phloem exudates. In addition, we observed a substantial variation of metabolite content between genotypes, particularly under high N. The content of several organic acids, such as malate, citrate, fumarate, and succinate was affected by the genotype alone or by the interaction between genotype and N supply. This study confirmed that the response of the transport of nutrients in the phloem and the xylem to N availability is associated with the regulation of the central metabolism and could be an adaptive trait.},
	language = {en},
	urldate = {2022-05-20},
	journal = {Journal of Plant Physiology},
	author = {Chardon, Fabien and De Marco, Federica and Marmagne, Anne and Le Hir, Rozenn and Vilaine, Françoise and Bellini, Catherine and Dinant, Sylvie},
	month = jun,
	year = {2022},
	keywords = {Allocation, Pipecolate, Raffinose, Succinate, Sucrose, Transport},
	pages = {153707},
}

Phloem and xylem tissues are necessary for the allocation of nutrients and photoassimilates. However, how the long-distance transport of carbon (C) and nitrogen (N) is coordinated with the central metabolism is largely unknown. To better understand how the genetic and environmental factors influence C and N transport, we analysed the metabolite profiles of phloem exudates and xylem saps of five Arabidopsis thaliana accessions grown in low or non-limiting N supply. We observed that xylem saps were composed of 46 or 56% carbohydrates, 27 or 45% amino acids, and 5 or 13% organic acids in low or non-limiting N supply, respectively. In contrast, phloem exudates were composed of 76 or 86% carbohydrates, 7 or 18% amino acids, and 5 or 6% organic acids. Variation in N supply impacted amino acid, organic acid and sugar contents. When comparing low N and non-limiting N, the most striking differences were variations of glutamine, aspartate, and succinate abundance in the xylem saps and citrate and fumarate abundance in phloem exudates. In addition, we observed a substantial variation of metabolite content between genotypes, particularly under high N. The content of several organic acids, such as malate, citrate, fumarate, and succinate was affected by the genotype alone or by the interaction between genotype and N supply. This study confirmed that the response of the transport of nutrients in the phloem and the xylem to N availability is associated with the regulation of the central metabolism and could be an adaptive trait.

@article{jonsson_plant_2022,
	title = {Plant cell walls as mechanical signaling hubs for morphogenesis},
	volume = {32},
	issn = {0960-9822},
	url = {https://www.sciencedirect.com/science/article/pii/S0960982222002585},
	doi = {10.1016/j.cub.2022.02.036},
	abstract = {The instructive role of mechanical cues during morphogenesis is increasingly being recognized in all kingdoms. Patterns of mechanical stress depend on shape, growth and external factors. In plants, the cell wall integrates these three parameters to function as a hub for mechanical feedback. Plant cells are interconnected by cell walls that provide structural integrity and yet are flexible enough to act as both targets and transducers of mechanical cues. Such cues may act locally at the subcellular level or across entire tissues, requiring tight control of both cell-wall composition and cell–cell adhesion. Here we focus on how changes in cell-wall chemistry and mechanics act in communicating diverse cues to direct growth asymmetries required for plant morphogenesis. We explore the role of cellulose microfibrils, microtubule arrays and pectin methylesterification in the transduction of mechanical cues during morphogenesis. Plant hormones can affect the mechanochemical composition of the cell wall and, in turn, the cell wall can modulate hormone signaling pathways, as well as the tissue-level distribution of these hormones. This also leads us to revisit the position of biochemical growth factors, such as plant hormones, acting both upstream and downstream of mechanical signaling. Finally, while the structure of the cell wall is being elucidated with increasing precision, existing data clearly show that the integration of genetic, biochemical and theoretical studies will be essential for a better understanding of the role of the cell wall as a hub for the mechanical control of plant morphogenesis.},
	language = {en},
	number = {7},
	urldate = {2022-05-20},
	journal = {Current Biology},
	author = {Jonsson, Kristoffer and Hamant, Olivier and Bhalerao, Rishikesh P.},
	month = apr,
	year = {2022},
	pages = {R334--R340},
}

The instructive role of mechanical cues during morphogenesis is increasingly being recognized in all kingdoms. Patterns of mechanical stress depend on shape, growth and external factors. In plants, the cell wall integrates these three parameters to function as a hub for mechanical feedback. Plant cells are interconnected by cell walls that provide structural integrity and yet are flexible enough to act as both targets and transducers of mechanical cues. Such cues may act locally at the subcellular level or across entire tissues, requiring tight control of both cell-wall composition and cell–cell adhesion. Here we focus on how changes in cell-wall chemistry and mechanics act in communicating diverse cues to direct growth asymmetries required for plant morphogenesis. We explore the role of cellulose microfibrils, microtubule arrays and pectin methylesterification in the transduction of mechanical cues during morphogenesis. Plant hormones can affect the mechanochemical composition of the cell wall and, in turn, the cell wall can modulate hormone signaling pathways, as well as the tissue-level distribution of these hormones. This also leads us to revisit the position of biochemical growth factors, such as plant hormones, acting both upstream and downstream of mechanical signaling. Finally, while the structure of the cell wall is being elucidated with increasing precision, existing data clearly show that the integration of genetic, biochemical and theoretical studies will be essential for a better understanding of the role of the cell wall as a hub for the mechanical control of plant morphogenesis.

@article{domevscik_large-scale_2022,
	title = {Large-scale assessment of artificially coated seeds for forest regeneration across {Sweden}},
	issn = {1573-5095},
	url = {https://doi.org/10.1007/s11056-022-09920-2},
	doi = {10.1007/s11056-022-09920-2},
	abstract = {We report the results of two years’ field performance of Scots pine (Pinus sylvestris) seedlings regenerated using artificially coated seeds. The coated seeds were used for regeneration on 12 clearcut sites, covering a 1000 km latitudinal gradient across Sweden. The coating was either combined with arginine-phosphate fertilizer (10 mg N per seed) or had no additions. Interactions with environmental variables associated with sites were also assessed. Coated seeds were deployed in May–June 2017 and surveyed in August–September of 2018 and 2019. After two years, the mean establishment rate of seedlings from coated seeds was 56 ± 4\% across the 12 sites. The fertilizer addition did not affect survival, and the biomass response to fertilizer varied significantly between sites. Maximum precipitation and wind speed during the first six weeks after deployment were correlated with seedling survival, regardless of fertilization treatment. Establishment increased with increasing precipitation and decreased with increasing wind speed. This highlights the importance of initial weather conditions for the seeds’ establishment. Our data suggest that Scots pine regeneration using coated seeds can be practiced in boreal forests, but also that the method is sensitive to the weather conditions at the time of deployment of the seeds.},
	language = {en},
	urldate = {2022-05-20},
	journal = {New Forests},
	author = {Domevscik, Matej and Häggström, Bodil and Lim, Hyungwoo and Öhlund, Jonas and Nordin, Annika},
	month = may,
	year = {2022},
	keywords = {Boreal forest, Coated seeds, Forest regeneration, Scots pine, SeedPAD, Seeding},
}

We report the results of two years’ field performance of Scots pine (Pinus sylvestris) seedlings regenerated using artificially coated seeds. The coated seeds were used for regeneration on 12 clearcut sites, covering a 1000 km latitudinal gradient across Sweden. The coating was either combined with arginine-phosphate fertilizer (10 mg N per seed) or had no additions. Interactions with environmental variables associated with sites were also assessed. Coated seeds were deployed in May–June 2017 and surveyed in August–September of 2018 and 2019. After two years, the mean establishment rate of seedlings from coated seeds was 56 ± 4% across the 12 sites. The fertilizer addition did not affect survival, and the biomass response to fertilizer varied significantly between sites. Maximum precipitation and wind speed during the first six weeks after deployment were correlated with seedling survival, regardless of fertilization treatment. Establishment increased with increasing precipitation and decreased with increasing wind speed. This highlights the importance of initial weather conditions for the seeds’ establishment. Our data suggest that Scots pine regeneration using coated seeds can be practiced in boreal forests, but also that the method is sensitive to the weather conditions at the time of deployment of the seeds.

@incollection{anjam_rna_2022,
	address = {New York, NY},
	series = {Methods in {Molecular} {Biology}},
	title = {{RNA} {Isolation} from {Nematode}-{Induced} {Feeding} {Sites} in {Arabidopsis} {RootsRoots} {Using} {Laser} {Capture} {Microdissection}},
	isbn = {978-1-07-162297-1},
	url = {https://doi.org/10.1007/978-1-0716-2297-1_22},
	abstract = {Nematodes are diverse multicellular organisms that are most abundantly found in the soil. Most nematodes are free-living and feed on a range of organisms. Based on their feeding habits, soil nematodes can be classified into four groups: bacterial, omnivorous, fungal, and plant-feeding. Plant-parasitic nematodes (PPNs) are a serious threat to global food security, causing substantial losses to the agricultural sector. Root-knot and cyst nematodes are the most important of PPNs, significantly limiting the yield of commercial crops such as sugar beet, mustard, and cauliflower. The life cycle of these nematodes consists of four molting stages (J1–J4) that precede adulthood. Nonetheless, only second-stage juveniles (J2), which hatch from eggs, are infective worms that can parasitize the host’s roots. The freshly hatched juveniles (J2) of beet cyst nematode, Heterodera schachtii, establish a permanent feeding site inside the roots of the host plant. A cocktail of proteinaceous secretions is injected into a selected cell which later develops into a syncytium via local cell wall dissolution of several hundred neighboring cells. The formation of syncytium is accompanied by massive transcriptional, metabolic, and proteomic changes inside the host tissues. It creates a metabolic sink in which solutes are translocated to feed the nematodes throughout their life cycle. Deciphering the molecular signaling cascades during syncytium establishment is thus essential in studying the plant-nematode interactions and ensuring sustainability in agricultural practices. However, isolating RNA, protein, and metabolites from syncytial cells remains challenging. Extensive use of laser capture microdissection (LCM) in animal and human tissues has shown this approach to be a powerful technique for isolating a single cell from complex tissues. Here, we describe a simplified protocol for Arabidopsis-Heterodera schachtii infection assays, which is routinely applied in several plant-nematode laboratories. Next, we provide a detailed protocol for isolating high-quality RNA from syncytial cells induced by Heterodera schachtii in the roots of Arabidopsis thaliana plants.},
	language = {en},
	urldate = {2022-04-29},
	booktitle = {Environmental {Responses} in {Plants}: {Methods} and {Protocols}},
	publisher = {Springer US},
	author = {Anjam, Muhammad Shahzad and Siddique, Shahid and Marhavy, Peter},
	editor = {Duque, Paula and Szakonyi, Dóra},
	year = {2022},
	keywords = {Arabidopsis root dissection, Laser capture dissection, Plant-nematode infection, RNA extraction, Syncytial cell isolation},
	pages = {313--324},
}

Nematodes are diverse multicellular organisms that are most abundantly found in the soil. Most nematodes are free-living and feed on a range of organisms. Based on their feeding habits, soil nematodes can be classified into four groups: bacterial, omnivorous, fungal, and plant-feeding. Plant-parasitic nematodes (PPNs) are a serious threat to global food security, causing substantial losses to the agricultural sector. Root-knot and cyst nematodes are the most important of PPNs, significantly limiting the yield of commercial crops such as sugar beet, mustard, and cauliflower. The life cycle of these nematodes consists of four molting stages (J1–J4) that precede adulthood. Nonetheless, only second-stage juveniles (J2), which hatch from eggs, are infective worms that can parasitize the host’s roots. The freshly hatched juveniles (J2) of beet cyst nematode, Heterodera schachtii, establish a permanent feeding site inside the roots of the host plant. A cocktail of proteinaceous secretions is injected into a selected cell which later develops into a syncytium via local cell wall dissolution of several hundred neighboring cells. The formation of syncytium is accompanied by massive transcriptional, metabolic, and proteomic changes inside the host tissues. It creates a metabolic sink in which solutes are translocated to feed the nematodes throughout their life cycle. Deciphering the molecular signaling cascades during syncytium establishment is thus essential in studying the plant-nematode interactions and ensuring sustainability in agricultural practices. However, isolating RNA, protein, and metabolites from syncytial cells remains challenging. Extensive use of laser capture microdissection (LCM) in animal and human tissues has shown this approach to be a powerful technique for isolating a single cell from complex tissues. Here, we describe a simplified protocol for Arabidopsis-Heterodera schachtii infection assays, which is routinely applied in several plant-nematode laboratories. Next, we provide a detailed protocol for isolating high-quality RNA from syncytial cells induced by Heterodera schachtii in the roots of Arabidopsis thaliana plants.