@article{kleczkowski_is_2026,
	title = {Is {Mg2}+ sensed by adenylate kinase and serving as a signal of energy status in biological systems? (a hypothesis)},
	volume = {327},
	issn = {0176-1617},
	shorttitle = {Is {Mg2}+ sensed by adenylate kinase and serving as a signal of energy status in biological systems?},
	url = {https://www.sciencedirect.com/science/article/pii/S0176161726002154},
	doi = {10.1016/j.jplph.2026.154902},
	abstract = {The contents of adenylates and free magnesium (Mg2+) are controlled by adenylate kinase (AK), which equilibrates specific Mg-bound and free adenylates. Taking into account the true substrates of AK, the reaction is described as: MgATP + AMPfree ↔ MgADP + ADPfree, and its equilibrium constant (K) does not depend on [Mg2+]. However, when the reaction is described in terms of total contents of adenylates, i.e., ATPtot + AMPtot ↔ 2 ADPtot, its apparent K (Kapp) varies from 0.3 to 1.5, depending on [Mg2+]. Here, we argue that Mg2+ is sensed by AK via the availability of its apparent substrates (total adenylates), and that changes in its Kapp affect internal [Mg2+]; the higher the Kapp (and energy status), the lower the [Mg2+], and vice versa. In this way, Mg2+ becomes a signal of true cellular energy charge. The Mg2+-signal controls myriad metabolic and developmental processes, including kinase reactions, photosynthesis, respiration, circadian rhythms, etc., integrating metabolism and development. The AK sensing of Mg2+ and its control over the Mg2+-signal may represent a robust and sensitive measure of energy charge. It may also be universal for any organism containing AK, with shifts in [Mg2+] as vital outputs of its activity and subsequent adenylate metabolism.},
	urldate = {2026-11-05},
	journal = {Journal of Plant Physiology},
	author = {Kleczkowski, Leszek A. and Igamberdiev, Abir U.},
	month = dec,
	year = {2026},
	keywords = {Adenylate energy charge, Bioenergetics, Circadian rhythms, Equilibrium constant, Mg-sensing, Mg-signaling, Riboswitch (Mg)},
	pages = {154902},
}

The contents of adenylates and free magnesium (Mg2+) are controlled by adenylate kinase (AK), which equilibrates specific Mg-bound and free adenylates. Taking into account the true substrates of AK, the reaction is described as: MgATP + AMPfree ↔ MgADP + ADPfree, and its equilibrium constant (K) does not depend on [Mg2+]. However, when the reaction is described in terms of total contents of adenylates, i.e., ATPtot + AMPtot ↔ 2 ADPtot, its apparent K (Kapp) varies from 0.3 to 1.5, depending on [Mg2+]. Here, we argue that Mg2+ is sensed by AK via the availability of its apparent substrates (total adenylates), and that changes in its Kapp affect internal [Mg2+]; the higher the Kapp (and energy status), the lower the [Mg2+], and vice versa. In this way, Mg2+ becomes a signal of true cellular energy charge. The Mg2+-signal controls myriad metabolic and developmental processes, including kinase reactions, photosynthesis, respiration, circadian rhythms, etc., integrating metabolism and development. The AK sensing of Mg2+ and its control over the Mg2+-signal may represent a robust and sensitive measure of energy charge. It may also be universal for any organism containing AK, with shifts in [Mg2+] as vital outputs of its activity and subsequent adenylate metabolism.

@article{ibragimov_expanding_2026,
	title = {Expanding the pig metabolomics {QTL} catalog},
	volume = {58},
	issn = {1297-9686},
	url = {https://doi.org/10.1186/s12711-026-01095-0},
	doi = {10.1186/s12711-026-01095-0},
	abstract = {Understanding the genetic regulation of metabolism is essential for improving animal health and productivity and for strengthening the use of pigs as translational models for human metabolic diseases. Metabolomics, when integrated with genomic data, provides a powerful framework for identifying genetic factors that influence intermediate molecular phenotypes closely linked to physiology. While large-scale metabolomics genome‑wide association studies (GWAS) have been extensively performed in humans, comparable studies in pigs remain limited. Among omics disciplines, metabolomics, the systematic study of metabolites central to physiology, represents the omics layer most closely linked to end-point phenotypes in mammals, such as health and production traits (e.g. growth rate). Metabolite levels are influenced by genetics, diet, and microbiome composition, with human studies showing high heritability and identifying numerous metabolite quantitative trait loci (mQTLs). While such findings have advanced our understanding of disease biology in humans, comparable studies in pigs remain limited.},
	language = {en},
	number = {1},
	urldate = {2026-11-05},
	journal = {Genetics Selection Evolution},
	author = {Ibragimov, Emil and Morsing, Malene Kjelin and Rydal, Martin Peter and Cai, Zexi and Stenlund, Hans and Nielsen, Jens Peter and Fredholm, Merete and Karlskov-Mortensen, Peter},
	month = oct,
	year = {2026},
	pages = {75},
}

Understanding the genetic regulation of metabolism is essential for improving animal health and productivity and for strengthening the use of pigs as translational models for human metabolic diseases. Metabolomics, when integrated with genomic data, provides a powerful framework for identifying genetic factors that influence intermediate molecular phenotypes closely linked to physiology. While large-scale metabolomics genome‑wide association studies (GWAS) have been extensively performed in humans, comparable studies in pigs remain limited. Among omics disciplines, metabolomics, the systematic study of metabolites central to physiology, represents the omics layer most closely linked to end-point phenotypes in mammals, such as health and production traits (e.g. growth rate). Metabolite levels are influenced by genetics, diet, and microbiome composition, with human studies showing high heritability and identifying numerous metabolite quantitative trait loci (mQTLs). While such findings have advanced our understanding of disease biology in humans, comparable studies in pigs remain limited.

@article{choudhary_nitrate_2026,
	title = {Nitrate transiently rewires transcription in developing xylem of {Populus} wood to promote cell expansion via {CRF4}},
	volume = {38},
	issn = {1040-4651},
	url = {https://doi.org/10.1093/plcell/koag281},
	doi = {10.1093/plcell/koag281},
	abstract = {Nitrate functions both as a nutrient and a signaling molecule, but how nitrate is perceived and translated into developmental outputs within woody tissues is unknown. Here, we show that developing xylem in hybrid aspen (Populus tremula × P. tremuloides) mounts a rapid, cell-type-specific transcriptional response to nitrate that promotes xylem cell expansion. To isolate local nitrate signaling in wood-forming tissues, we delivered nitrate directly into the xylem sap and profiled transcriptomic responses from 2 to 48 h after treatment. Bulk RNA sequencing revealed a transient response peaking within 2 to 4 h. Single-cell RNA sequencing at the peak response resolved nitrate signaling across developing xylem cell types and showed that nitrate induced cell-type-specific programs linked to nitrogen transport, cell wall remodeling, and developmental progression, while repressing lignin-biosynthetic genes. These data indicate that nitrate acts transiently in wood-forming tissues to fine-tune early xylem development. Among nitrate-responsive transcription factors, CYTOKININ RESPONSE FACTOR 4 (CRF4) emerged as a candidate regulator of this response. CRF4 overexpression in hybrid aspen stimulated xylem cell expansion, whereas simultaneous knockout of CRF4 and its paralog, CRF3, significantly attenuated the nitrate-induced expansion. Together, our findings identify a local nitrate signaling module in developing wood and establish CRF4 as a component linking nitrate sensing to xylem cell expansion.},
	number = {10},
	urldate = {2026-11-05},
	journal = {The Plant Cell},
	author = {Choudhary, Shruti and Renström, Anna and Kochakarn, Theerarat and Miskolczi, Pal and Piombo, Edoardo and Chantreau, Maxime and Jose, Jeny and Jämtgård, Sandra and Gorzsás, András and Henriksson, Johan and Tuominen, Hannele},
	month = oct,
	year = {2026},
	pages = {koag281},
}

Nitrate functions both as a nutrient and a signaling molecule, but how nitrate is perceived and translated into developmental outputs within woody tissues is unknown. Here, we show that developing xylem in hybrid aspen (Populus tremula × P. tremuloides) mounts a rapid, cell-type-specific transcriptional response to nitrate that promotes xylem cell expansion. To isolate local nitrate signaling in wood-forming tissues, we delivered nitrate directly into the xylem sap and profiled transcriptomic responses from 2 to 48 h after treatment. Bulk RNA sequencing revealed a transient response peaking within 2 to 4 h. Single-cell RNA sequencing at the peak response resolved nitrate signaling across developing xylem cell types and showed that nitrate induced cell-type-specific programs linked to nitrogen transport, cell wall remodeling, and developmental progression, while repressing lignin-biosynthetic genes. These data indicate that nitrate acts transiently in wood-forming tissues to fine-tune early xylem development. Among nitrate-responsive transcription factors, CYTOKININ RESPONSE FACTOR 4 (CRF4) emerged as a candidate regulator of this response. CRF4 overexpression in hybrid aspen stimulated xylem cell expansion, whereas simultaneous knockout of CRF4 and its paralog, CRF3, significantly attenuated the nitrate-induced expansion. Together, our findings identify a local nitrate signaling module in developing wood and establish CRF4 as a component linking nitrate sensing to xylem cell expansion.

@article{bogdziewiez_rrquant_2026,
	title = {{RRQuant}: {High}-throughput quantification of {Arabidopsis} hypocotyl epidermal integrity},
	volume = {7},
	issn = {2632-8828},
	shorttitle = {{RRQuant}},
	url = {https://www.cambridge.org/core/journals/quantitative-plant-biology/article/rrquant-highthroughput-quantification-of-arabidopsis-hypocotyl-epidermal-integrity/D4B4A188B27AD729A5BD4DBFDE9661DF},
	doi = {10.1017/qpb.2026.10053},
	abstract = {Maintaining epidermal integrity is essential for plant growth and survival, yet quantitative methods to assess defects in cell adhesion, cell integrity and cuticle function remain limited. Here, we present RRQuant, a standardised, high-throughput workflow for quantifying epidermal integrity defects in seedlings using Ruthenium Red staining. RRQuant integrates deep learning–based segmentation with automated image analysis, staining and morphological quantification, and statistical evaluation. The workflow is accompanied by a detailed user guide, and an interactive R Shiny application for data visualisation and quality control. This pipeline converts qualitative staining patterns into reproducible quantitative measurements, enabling large-scale phenotyping and comparative studies across genotypes and treatments. We demonstrate the usefulness of RRQuant by quantitatively comparing adhesion defective phenotypes and discuss its potential for adaptation to other organs, staining methods, and pigment-based assays. By providing an open and extensible platform, RRQuant bridges the gap between traditional qualitative assessments and modern quantitative phenotyping in plant biology.},
	language = {en},
	urldate = {2026-11-05},
	journal = {Quantitative Plant Biology},
	author = {Bogdziewiez, Léa and Lisica, Lucija and Baba, Abu Imran and Erguvan, Özer and Heymans, Adrien and Atakhani, Asal and Sjölander, Johan and Demes-Causse, Elsa and Rigaud, Audrey and Verger, Stéphane},
	month = jan,
	year = {2026},
	keywords = {Arabidopsis, adhesion, cuticle, deep learning, epidermis, hypocotyl, image analysis, plant},
	pages = {e19},
}

Maintaining epidermal integrity is essential for plant growth and survival, yet quantitative methods to assess defects in cell adhesion, cell integrity and cuticle function remain limited. Here, we present RRQuant, a standardised, high-throughput workflow for quantifying epidermal integrity defects in seedlings using Ruthenium Red staining. RRQuant integrates deep learning–based segmentation with automated image analysis, staining and morphological quantification, and statistical evaluation. The workflow is accompanied by a detailed user guide, and an interactive R Shiny application for data visualisation and quality control. This pipeline converts qualitative staining patterns into reproducible quantitative measurements, enabling large-scale phenotyping and comparative studies across genotypes and treatments. We demonstrate the usefulness of RRQuant by quantitatively comparing adhesion defective phenotypes and discuss its potential for adaptation to other organs, staining methods, and pigment-based assays. By providing an open and extensible platform, RRQuant bridges the gap between traditional qualitative assessments and modern quantitative phenotyping in plant biology.

@article{postel_evolutionary_2026,
	title = {Evolutionary consequences of repeated loss of distyly in {Linum}},
	journal = {Genome Biology and Evolution},
	author = {Postel, Zoé and Zervakis, Panagiotis-Ioannis and Fracassetti, Marco and Losvik, Aleksandra and Wanntorp, Matias and Soler, Lucile and Churcher, Allison and Humphreys, Aelys M and Slotte, Tanja},
	year = {2026},
}