@article{tunnermann_applying_2026,
	title = {Applying nephelometry for analyzing liquid yeast cultures},
	volume = {46},
	issn = {2405-5808},
	url = {https://www.sciencedirect.com/science/article/pii/S2405580826001329},
	doi = {10.1016/j.bbrep.2026.102572},
	abstract = {Saccharomyces cerevisiae is a widely used model organism for the molecular analysis of genes and proteins. Several methods have been developed to study protein function and activity through heterologous gene expression, including yeast two-hybrid and yeast complementation. Traditionally, these yeast-based assays were performed on solid agar plates. While this approach provides an easy visual readout, it is difficult to quantify the results accurately. To overcome this limitation, liquid-based methods were introduced. Most of these methods rely on the use of spectrophotometry to measure reduction in light transmission as a result of light scattering and monitor culture growth. In this study, we propose nephelometry as an additional method for performing and analyzing liquid-culture yeast complementation assays. More specifically, we compare the suitability of using nephelometry for the functional analysis of two homologous proteins using yeast complementation: The amino acid transporter homologues Arabidopsis thaliana LYSINE HISTIDINE TRANSPORTER 1 (AtLHT1) and Populus tremula L. x tremuloides Michx LYSINE HISTIDINE TRANSPORTER 1.2 (PtrLHT1.2). In previous reports, no differences in microbial growth were detected, irrespective of which homolog was used to rescue an amino acid-deficient yeast mutant strain. By using nephelometry to record yeast growth, we demonstrated that it is a robust and reproducible method. When comparing to spectrophotometric measurements of yeast cultures, it proved to be a suitable alternative. The novel approach even revealed previously undetected differences in culture growth of both homologues, highlighting nephelometry's potential to improve sensitivity in yeast-based functional assays. We present the use of nephelometry as an equal method to yeast complementation traditionally executed on solid agar medium or in liquid culture with spectrophotometric analysis.},
	urldate = {2026-04-17},
	journal = {Biochemistry and Biophysics Reports},
	author = {Tünnermann, Laura and Colou, Justine and Näsholm, Torgny and Löfstedt, Tommy and Gratz, Regina},
	month = jun,
	year = {2026},
	keywords = {Lag time, Lysine histidine transporter 1 (LHT1), Maximum slope time, Nephelometry, Spectrophotometry},
	pages = {102572},
}

Saccharomyces cerevisiae is a widely used model organism for the molecular analysis of genes and proteins. Several methods have been developed to study protein function and activity through heterologous gene expression, including yeast two-hybrid and yeast complementation. Traditionally, these yeast-based assays were performed on solid agar plates. While this approach provides an easy visual readout, it is difficult to quantify the results accurately. To overcome this limitation, liquid-based methods were introduced. Most of these methods rely on the use of spectrophotometry to measure reduction in light transmission as a result of light scattering and monitor culture growth. In this study, we propose nephelometry as an additional method for performing and analyzing liquid-culture yeast complementation assays. More specifically, we compare the suitability of using nephelometry for the functional analysis of two homologous proteins using yeast complementation: The amino acid transporter homologues Arabidopsis thaliana LYSINE HISTIDINE TRANSPORTER 1 (AtLHT1) and Populus tremula L. x tremuloides Michx LYSINE HISTIDINE TRANSPORTER 1.2 (PtrLHT1.2). In previous reports, no differences in microbial growth were detected, irrespective of which homolog was used to rescue an amino acid-deficient yeast mutant strain. By using nephelometry to record yeast growth, we demonstrated that it is a robust and reproducible method. When comparing to spectrophotometric measurements of yeast cultures, it proved to be a suitable alternative. The novel approach even revealed previously undetected differences in culture growth of both homologues, highlighting nephelometry's potential to improve sensitivity in yeast-based functional assays. We present the use of nephelometry as an equal method to yeast complementation traditionally executed on solid agar medium or in liquid culture with spectrophotometric analysis.

@article{han_development_2026,
	title = {Development and application of a genotyping by target sequencing single-nucleotide polymorphism array panel in {Salix} suchowensis},
	volume = {27},
	issn = {1471-2164},
	url = {https://doi.org/10.1186/s12864-026-12690-2},
	doi = {10.1186/s12864-026-12690-2},
	abstract = {Salix suchowensis is an important species of Salix, known for its rapid growth property and wide application in environmental construction, ecological restoration, wicker production, and biomass energy production. Due to its significance as a sustainable biological resource, S. suchowensis has been the centre of intensive breeding. However, rapid improvement of growth and biomass has been hindered by a lack of genomic resources. To address this limitation, we designed a liquid-phase probe array by genotyping by target sequencing technology. Using whole-genome resequencing data, a total of 39,076 SNPs were selected for the array panel, consisting of trait-associated SNPs, intragenic SNPs, and intergenic SNPs. This panel was validated by genotyping 550 new samples, demonstrating high call rates and effective capture of the population structure. Genome-wide association analysis identified 72 SNPs associated with plant height and ground diameter. Additionally, the array panel shows a high potential for genomic selection, with high prediction accuracy for various traits. These results highlight the efficiency of this panel in capturing genomic variations that are highly valuable for future genetic research and breeding applications.},
	language = {en},
	number = {1},
	urldate = {2026-04-17},
	journal = {BMC Genomics},
	author = {Han, Yu and Gu, Shaobo and Zhu, Mingjia and Liu, Wei and Feng, Landi and Yin, Tongming and Gao, Xuemeng and Zan, Yanjun and Huang, Rui and Ji, Yan and Liu, Jianquan},
	month = mar,
	year = {2026},
	keywords = {Genome-wide association study, Genomic selection, Ground diameter, Liquid-phase probe array, Plant height},
	pages = {355},
}

Salix suchowensis is an important species of Salix, known for its rapid growth property and wide application in environmental construction, ecological restoration, wicker production, and biomass energy production. Due to its significance as a sustainable biological resource, S. suchowensis has been the centre of intensive breeding. However, rapid improvement of growth and biomass has been hindered by a lack of genomic resources. To address this limitation, we designed a liquid-phase probe array by genotyping by target sequencing technology. Using whole-genome resequencing data, a total of 39,076 SNPs were selected for the array panel, consisting of trait-associated SNPs, intragenic SNPs, and intergenic SNPs. This panel was validated by genotyping 550 new samples, demonstrating high call rates and effective capture of the population structure. Genome-wide association analysis identified 72 SNPs associated with plant height and ground diameter. Additionally, the array panel shows a high potential for genomic selection, with high prediction accuracy for various traits. These results highlight the efficiency of this panel in capturing genomic variations that are highly valuable for future genetic research and breeding applications.

@article{liu_photosynthesis-related_2026,
	title = {Photosynthesis-related genetic and transcriptomic variations contribute to adaptive trait diversity in global {Arabidopsis} thaliana populations},
	volume = {26},
	issn = {1471-2229},
	url = {https://doi.org/10.1186/s12870-026-08279-2},
	doi = {10.1186/s12870-026-08279-2},
	abstract = {Photosynthesis is the foundational process for carbon fixation in terrestrial ecosystems. Although allelic variations in photosynthesis-related genes have the potential to enhance carbon assimilation efficiency, their functional roles in local adaptation are still not well understood. In this study, we systematically examined the genetic and transcriptomic diversity among globally distributed natural accessions of Arabidopsis thaliana, focusing on 1,103 genes associated with photosynthetic pathways. By assembling chloroplast genomes from 28 representative accessions and integrating whole-genome and transcriptome sequencing data from over 1,000 accessions, we identified extensive allelic variation. Notably, 34.0\% of these genes exhibited regulatory variations through expression quantitative trait locus mapping, including key components such as Rubisco and Rubisco activase. Functional validation demonstrated that overexpression of these genes increased cotyledon size and root length. Additionally, genome-wide and transcriptome-wide association studies revealed that natural selection acting on these allelic variations significantly contributes to local environmental adaptation. Our findings elucidate the connection between genetic variation in photosynthetic pathways and their ecological significance, providing valuable insights for optimizing carbon fixation in dynamic environments.},
	language = {en},
	number = {1},
	urldate = {2026-04-10},
	journal = {BMC Plant Biology},
	author = {Liu, Wei and Hao, Ruili and Liu, Li and Hou, Jing and Lei, Mengyu and Han, Yu and Zhu, Mingjia and Liang, Lei and Yu, Le and Si, Huan and Liu, Jianquan and Zan, Yanjun and Ji, Yan},
	month = feb,
	year = {2026},
	keywords = {Arabidopsis thaliana, Local adaptation, Natural variation, Photosynthesis pathways},
	pages = {468},
}

Photosynthesis is the foundational process for carbon fixation in terrestrial ecosystems. Although allelic variations in photosynthesis-related genes have the potential to enhance carbon assimilation efficiency, their functional roles in local adaptation are still not well understood. In this study, we systematically examined the genetic and transcriptomic diversity among globally distributed natural accessions of Arabidopsis thaliana, focusing on 1,103 genes associated with photosynthetic pathways. By assembling chloroplast genomes from 28 representative accessions and integrating whole-genome and transcriptome sequencing data from over 1,000 accessions, we identified extensive allelic variation. Notably, 34.0% of these genes exhibited regulatory variations through expression quantitative trait locus mapping, including key components such as Rubisco and Rubisco activase. Functional validation demonstrated that overexpression of these genes increased cotyledon size and root length. Additionally, genome-wide and transcriptome-wide association studies revealed that natural selection acting on these allelic variations significantly contributes to local environmental adaptation. Our findings elucidate the connection between genetic variation in photosynthetic pathways and their ecological significance, providing valuable insights for optimizing carbon fixation in dynamic environments.

@article{moreno-sanguino_phloem_2026,
	title = {Phloem {Proteomics} to {Identify} {Small} {Open} {Reading} {Frame} ({sORF})-encoded {Peptides} {With} a {Putative} {Role} in the {Control} of {Flowering} {Time} in {Arabidopsis}},
	volume = {178},
	copyright = {© 2026 The Author(s). Physiologia Plantarum published by John Wiley \& Sons Ltd on behalf of Scandinavian Plant Physiology Society.},
	issn = {1399-3054},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/ppl.70860},
	doi = {10.1111/ppl.70860},
	abstract = {Phloem sap proteomic studies have previously revealed that phloem sap composition varies during development and upon floral induction. Specific proteins, lipids, messenger RNAs (mRNAs), and peptides have been shown to accumulate at different developmental stages. Peptides are of special interest since they have the potential to act as regulatory molecules controlling plant responses to environmental changes, such as salinity and water stress, plant–microbe interactions, and developmental changes. In this context, we have characterized Arabidopsis thaliana phloem exudates to identify proteins and peptides with the potential to control flowering time, acting as signals fine-tuning plant development. In this work, we present the proteomic profiles of the phloem sap samples during floral transition along with the identification of proteins and peptides that showed changes in abundance during floral transition, suggesting that they could potentially have a role in the control of flowering. Among those, we have described the abundance pattern of the sORF1511 peptide in the phloem sap, which varies upon floral induction. We show that sORF1511 overexpression affects bolting time and alters the expression of several genes involved in the control of flowering time.},
	language = {en},
	number = {2},
	urldate = {2026-04-10},
	journal = {Physiologia Plantarum},
	author = {Moreno-Sanguino, Irene and Collás, Lucía Argente and Samuelsson, Göran and Wingsle, Gunnar and Benlloch, Reyes},
	year = {2026},
	note = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1111/ppl.70860},
	keywords = {flowering time, peptides, phloem proteomics, small open reading frames},
	pages = {e70860},
}

Phloem sap proteomic studies have previously revealed that phloem sap composition varies during development and upon floral induction. Specific proteins, lipids, messenger RNAs (mRNAs), and peptides have been shown to accumulate at different developmental stages. Peptides are of special interest since they have the potential to act as regulatory molecules controlling plant responses to environmental changes, such as salinity and water stress, plant–microbe interactions, and developmental changes. In this context, we have characterized Arabidopsis thaliana phloem exudates to identify proteins and peptides with the potential to control flowering time, acting as signals fine-tuning plant development. In this work, we present the proteomic profiles of the phloem sap samples during floral transition along with the identification of proteins and peptides that showed changes in abundance during floral transition, suggesting that they could potentially have a role in the control of flowering. Among those, we have described the abundance pattern of the sORF1511 peptide in the phloem sap, which varies upon floral induction. We show that sORF1511 overexpression affects bolting time and alters the expression of several genes involved in the control of flowering time.

@article{pravdova_rapid_2026,
	title = {Rapid {Analysis} of {NAD} and {Other} {Phosphorylated} {Metabolites} in {Complex} {Biological} {Samples} by {Hydrophilic} {Interaction} {Liquid} {Chromatography} {Coupled} with {Tandem} {Mass} {Spectrometry}},
	issn = {0003-2700},
	url = {https://doi.org/10.1021/acs.analchem.6c00721},
	doi = {10.1021/acs.analchem.6c00721},
	abstract = {Nucleotides and coenzymes play critical roles in energy metabolism and cellular signaling and as building blocks of nucleic acids. This work addresses the challenges in the measurement of the phosphorylated metabolites using hydrophilic interaction liquid chromatography coupled with mass spectrometry, which facilitates the separation and detection of polar metabolites. Here, we present optimized HILIC-MS/MS methods for rapid analysis of polar metabolites including nucleotides and their derivatives in complex biological matrices, such as murine adipose, skeletal, and liver tissues, human plasma, and bacteria. The developed methodologies enable separation of key nucleotides and other phosphorylated metabolites within 6 min and cofactors such as NAD+, NADH, NADP+, and NADPH within 4 min. Validation of these methods demonstrated high accuracy, precision, and sensitivity and stresses the substantial impact of matrix effects. The applicability of the methods was also tested on 13C-labeling experiments with mouse pluripotent stem cells. Additionally, sample pretreatment techniques, such as liquid–liquid extraction and solid-phase extraction, were evaluated as a tool to decrease the negative impact of matrix effects in complex samples. This work enhances the analytical capabilities for nucleotide quantification in metabolomics, facilitating the study of metabolic pathways and disease markers.},
	urldate = {2026-04-10},
	journal = {Analytical Chemistry},
	publisher = {American Chemical Society},
	author = {Pravdova, Adela and Kleinert, Maximilian and Henderson, John and Kafkia, Eleni and Pladevall-Morera, David and Yonamine, Caio Y. and Treebak, Jonas T. and Brodiazhenko, Tetiana and Terenin, Ilya and Zylicz, Jan Jakub and Moritz, Thomas and Hodek, Ondrej},
	month = apr,
	year = {2026},
}

Nucleotides and coenzymes play critical roles in energy metabolism and cellular signaling and as building blocks of nucleic acids. This work addresses the challenges in the measurement of the phosphorylated metabolites using hydrophilic interaction liquid chromatography coupled with mass spectrometry, which facilitates the separation and detection of polar metabolites. Here, we present optimized HILIC-MS/MS methods for rapid analysis of polar metabolites including nucleotides and their derivatives in complex biological matrices, such as murine adipose, skeletal, and liver tissues, human plasma, and bacteria. The developed methodologies enable separation of key nucleotides and other phosphorylated metabolites within 6 min and cofactors such as NAD+, NADH, NADP+, and NADPH within 4 min. Validation of these methods demonstrated high accuracy, precision, and sensitivity and stresses the substantial impact of matrix effects. The applicability of the methods was also tested on 13C-labeling experiments with mouse pluripotent stem cells. Additionally, sample pretreatment techniques, such as liquid–liquid extraction and solid-phase extraction, were evaluated as a tool to decrease the negative impact of matrix effects in complex samples. This work enhances the analytical capabilities for nucleotide quantification in metabolomics, facilitating the study of metabolic pathways and disease markers.