@article{choudhary_nitrate_2026,
	title = {Nitrate transiently rewires transcription in developing xylem of {Populus} wood to promote cell expansion via {CRF4}},
	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 2–4 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 knock-out 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.},
	urldate = {2026-10-02},
	journal = {The Plant Cell},
	author = {Choudhary, Shruti and Renström, Anna and Kochakarn, Theerarat Fai 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 = sep,
	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 2–4 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 knock-out 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{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},
}

@article{qi_multi-omics_2026,
	title = {Multi-omics profiling identifies triciribine as a biomarker-guided antimetabolite therapy for acute lymphoblastic leukemia},
	volume = {10},
	copyright = {2026 The Author(s)},
	issn = {2397-768X},
	url = {https://www.nature.com/articles/s41698-026-01736-z},
	doi = {10.1038/s41698-026-01736-z},
	abstract = {Acute lymphoblastic leukemia (ALL) exhibits molecular and metabolic heterogeneity that limits therapeutic efficacy. Although antimetabolites remain central to ALL treatment, determinants of therapeutic sensitivity and resistance remain incompletely understood. Here, we investigated the activity and molecular response landscape of the purine analog triciribine (TCN) across diverse ALL models using integrated phosphoproteomics, thermal proteome profiling, and quantitative proteomics. TCN showed potent cytotoxicity across ALL cell lines and a drug response profile distinct from canonical PI3K–Akt–mTOR inhibitors. Early phosphoproteomics revealed no consistent suppression of Akt pathway signaling, with transient activation of several Akt-associated readouts and inhibition of cyclin-dependent kinase signaling. The monophosphorylated metabolite TCN-P was the predominant intracellular active species, and adenosine kinase (ADK) was required for TCN-P generation and cytotoxicity. Proteome Integral Solubility Alteration profiling identified candidate TCN-P interactions involving nucleotide metabolism, DNA replication, and protein synthesis, associated with impaired purine biosynthesis, DNA damage, translational stress, and cell-cycle perturbation. Across ALL cell lines and primary samples, ADK levels correlated positively with TCN sensitivity, supporting ADK-dependent metabolism as a major determinant of therapeutic response. Together, these findings identify TCN as a metabolically activated antileukemic agent with broad antimetabolite activity and nominate ADK as a potential predictive biomarker for precision therapy in ALL.},
	language = {en},
	number = {1},
	urldate = {2026-10-22},
	journal = {npj Precision Oncology},
	publisher = {Nature Publishing Group},
	author = {Qi, Xuekang and Mermelekas, Georgios and Hodek, Ondrej and Aswad, Luay and Glaziou, Quentin and Leo, Isabelle Rose and Struyf, Nona and Hormann, Femke M. and Siavelis, Ioannis and Bwanika, Henri Colyn and Hovey, Owen F. J. and Haraldsson, Martin and Rudd, Sean G. and Johansson, Annika I. and Erkers, Tom and Tamm, Katja Pokrovskaja and Lehtiö, Janne and Jafari, Rozbeh},
	month = oct,
	year = {2026},
	keywords = {Cancer, Drug discovery, Oncology},
	pages = {390},
}

Acute lymphoblastic leukemia (ALL) exhibits molecular and metabolic heterogeneity that limits therapeutic efficacy. Although antimetabolites remain central to ALL treatment, determinants of therapeutic sensitivity and resistance remain incompletely understood. Here, we investigated the activity and molecular response landscape of the purine analog triciribine (TCN) across diverse ALL models using integrated phosphoproteomics, thermal proteome profiling, and quantitative proteomics. TCN showed potent cytotoxicity across ALL cell lines and a drug response profile distinct from canonical PI3K–Akt–mTOR inhibitors. Early phosphoproteomics revealed no consistent suppression of Akt pathway signaling, with transient activation of several Akt-associated readouts and inhibition of cyclin-dependent kinase signaling. The monophosphorylated metabolite TCN-P was the predominant intracellular active species, and adenosine kinase (ADK) was required for TCN-P generation and cytotoxicity. Proteome Integral Solubility Alteration profiling identified candidate TCN-P interactions involving nucleotide metabolism, DNA replication, and protein synthesis, associated with impaired purine biosynthesis, DNA damage, translational stress, and cell-cycle perturbation. Across ALL cell lines and primary samples, ADK levels correlated positively with TCN sensitivity, supporting ADK-dependent metabolism as a major determinant of therapeutic response. Together, these findings identify TCN as a metabolically activated antileukemic agent with broad antimetabolite activity and nominate ADK as a potential predictive biomarker for precision therapy in ALL.

@article{boyka_high-resolution_2026,
	title = {High-resolution structure of monomeric photosystem {I} from {Thermosynechococcus} vestitus},
	volume = {164},
	issn = {1573-5079},
	url = {https://doi.org/10.1007/s11120-026-01237-x},
	doi = {10.1007/s11120-026-01237-x},
	abstract = {Photosystem I (PSI) exists in trimeric (tPSI) and monomeric (mPSI) forms within the thylakoid membrane of cyanobacteria. PSI functions as a light-driven electron pump, enabling the transfer of electrons from cytochrome c6 (Cyt c6) or plastocyanin to ferredoxin. Here, we have developed a novel protocol to obtain large amounts of intact, active mPSI from Thermosynechococcus vestitus (Tv) by dissociating highly purified tPSI using the detergent octaethylene glycol monododecyl ether (C12E8) at elevated temperatures. We analysed the stability of the protein-detergent complex employing a combination of spectroscopic methods, such as fluorescence at 77 K and circular dichroism (CD), and investigated the detergent’s influence on delipidation and monomerisation. We determined the structure of mPSI to a resolution of 1.8 Å using cryogenic electron microscopy (cryo-EM). This structure retains all subunits except PsaL and we identified a sulfoquinovosyl diacylglycerol (SQD) molecule and 16 n-dodecyl ß-maltoside (βDM) molecules arranged in a ring around the complex. The mPSI structure was verified in solution at physiological temperature by applying small angle neutron scattering. Comparing the cofactor inventory of mPSI to that of tPSI, we suggest the assignment of a red-shifted chlorophyll pigment and discuss the influence of detergents and lipids on stability and oligomeric state of PSI. Finally, when adding native Tv Cyt c6 under reducing conditions, additional density was observed in close proximity of the P700 pigments, which indicates the presence of a transiently bound Cyt c6.},
	language = {en},
	number = {6},
	urldate = {2026-10-22},
	journal = {Photosynthesis Research},
	author = {Boyka, Jelena and Gaullier, Guillaume and Forsman, Jack and Graça, André T. and Golub, Maksym and Croy, Nicholas and Wood, Kathleen and Duff, Anthony P. and Moir, Michael and Pieper, Jörg and Messinger, Johannes and Müh, Frank and Zouni, Athina and Blikstad, Cecilia},
	month = oct,
	year = {2026},
	keywords = {Cryo-EM, Cytochrome c6, Photosynthesis, Photosystem I, Small angle neutron scattering, Structure},
	pages = {52},
}

Photosystem I (PSI) exists in trimeric (tPSI) and monomeric (mPSI) forms within the thylakoid membrane of cyanobacteria. PSI functions as a light-driven electron pump, enabling the transfer of electrons from cytochrome c6 (Cyt c6) or plastocyanin to ferredoxin. Here, we have developed a novel protocol to obtain large amounts of intact, active mPSI from Thermosynechococcus vestitus (Tv) by dissociating highly purified tPSI using the detergent octaethylene glycol monododecyl ether (C12E8) at elevated temperatures. We analysed the stability of the protein-detergent complex employing a combination of spectroscopic methods, such as fluorescence at 77 K and circular dichroism (CD), and investigated the detergent’s influence on delipidation and monomerisation. We determined the structure of mPSI to a resolution of 1.8 Å using cryogenic electron microscopy (cryo-EM). This structure retains all subunits except PsaL and we identified a sulfoquinovosyl diacylglycerol (SQD) molecule and 16 n-dodecyl ß-maltoside (βDM) molecules arranged in a ring around the complex. The mPSI structure was verified in solution at physiological temperature by applying small angle neutron scattering. Comparing the cofactor inventory of mPSI to that of tPSI, we suggest the assignment of a red-shifted chlorophyll pigment and discuss the influence of detergents and lipids on stability and oligomeric state of PSI. Finally, when adding native Tv Cyt c6 under reducing conditions, additional density was observed in close proximity of the P700 pigments, which indicates the presence of a transiently bound Cyt c6.

@article{sivan_comparison_2026,
	title = {Comparison of synthetic and post-synthetic molecular genetic methods of reducing xylan glucuronidation in hybrid aspen for biorefinery applications},
	volume = {19},
	issn = {2731-3654},
	url = {https://doi.org/10.1186/s13068-026-02830-x},
	doi = {10.1186/s13068-026-02830-x},
	abstract = {The pattern of xylan backbone substitution by 4-O-methylglucuronic acid (mGlcA) and O-acetyl groups generated during biosynthesis in the Golgi apparatus plays a key role in molecular interactions between secondary cell wall polymers in hardwoods, thus regulating biorefinery properties of woody biomass. This study aims at comparing the effects of two different approaches to reduce xylan glucuronidation, targeting either xylan biosynthesis by RNAi suppression of GLUCURONIC SUBSTITUTION OF XYLAN1 genes (denoted Gux1RNAi) or by xylan post-synthetic modification in the secondary cell wall by apoplastic wood-specific expression of a fungal α-glucuronidase from family GH67 (denoted WP:GH67) in hybrid aspen (Populus tremula L. x tremuloides Michx.). The effects of reducing xylan glucuronidation by these two approaches on xylan acetylation and solubility, and recalcitrance of wood to enzymatic hydrolysis were compared.},
	language = {en},
	number = {1},
	urldate = {2026-10-22},
	journal = {Biotechnology for Biofuels and Bioproducts},
	author = {Sivan, Pramod and Urbancsok, János and Gandla, Madhavi L. and Donev, Evgeniy N. and Derba-Maceluch, Marta and Roach, Melissa and Jönsson, Leif J. and Vilaplana, Francisco and Mellerowicz, Ewa J.},
	month = oct,
	year = {2026},
	keywords = {GUX1, Glucuronidation, Glucuronoxylan, Populus, Saccharification, Secondary cell wall, Transgenic trees, Wood chemistry, Xylan acetylation, α-glucuronidase},
	pages = {82},
}

The pattern of xylan backbone substitution by 4-O-methylglucuronic acid (mGlcA) and O-acetyl groups generated during biosynthesis in the Golgi apparatus plays a key role in molecular interactions between secondary cell wall polymers in hardwoods, thus regulating biorefinery properties of woody biomass. This study aims at comparing the effects of two different approaches to reduce xylan glucuronidation, targeting either xylan biosynthesis by RNAi suppression of GLUCURONIC SUBSTITUTION OF XYLAN1 genes (denoted Gux1RNAi) or by xylan post-synthetic modification in the secondary cell wall by apoplastic wood-specific expression of a fungal α-glucuronidase from family GH67 (denoted WP:GH67) in hybrid aspen (Populus tremula L. x tremuloides Michx.). The effects of reducing xylan glucuronidation by these two approaches on xylan acetylation and solubility, and recalcitrance of wood to enzymatic hydrolysis were compared.