Publications 2024
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2024
(19)
S1 basic leucine zipper transcription factors shape plant architecture by controlling C/N partitioning to apical and lateral organs.
Kreisz, P., Hellens, A. M., Fröschel, C., Krischke, M., Maag, D., Feil, R., Wildenhain, T., Draken, J., Braune, G., Erdelitsch, L., Cecchino, L., Wagner, T. C., Ache, P., Mueller, M. J., Becker, D., Lunn, J. E., Hanson, J., Beveridge, C. A., Fichtner, F., Barbier, F. F., & Weiste, C.
Proceedings of the National Academy of Sciences, 121(7): e2313343121. February 2024.
Publisher: Proceedings of the National Academy of Sciences
Paper doi link bibtex abstract
Paper doi link bibtex abstract
@article{kreisz_s1_2024, title = {S1 basic leucine zipper transcription factors shape plant architecture by controlling {C}/{N} partitioning to apical and lateral organs}, volume = {121}, url = {https://www.pnas.org/doi/10.1073/pnas.2313343121}, doi = {10.1073/pnas.2313343121}, abstract = {Plants tightly control growth of their lateral organs, which led to the concept of apical dominance. However, outgrowth of the dormant lateral primordia is sensitive to the plant’s nutritional status, resulting in an immense plasticity in plant architecture. While the impact of hormonal regulation on apical dominance is well characterized, the prime importance of sugar signaling to unleash lateral organ formation has just recently emerged. Here, we aimed to identify transcriptional regulators, which control the trade-off between growth of apical versus lateral organs. Making use of locally inducible gain-of-function as well as single and higher-order loss-of-function approaches of the sugar-responsive S1-basic-leucine-zipper (S1-bZIP) transcription factors, we disclosed their largely redundant function in establishing apical growth dominance. Consistently, comprehensive phenotypical and analytical studies of S1-bZIP mutants show a clear shift of sugar and organic nitrogen (N) allocation from apical to lateral organs, coinciding with strong lateral organ outgrowth. Tissue-specific transcriptomics reveal specific clade III SWEET sugar transporters, crucial for long-distance sugar transport to apical sinks and the glutaminase GLUTAMINE AMIDO-TRANSFERASE 1\_2.1, involved in N homeostasis, as direct S1-bZIP targets, linking the architectural and metabolic mutant phenotypes to downstream gene regulation. Based on these results, we propose that S1-bZIPs control carbohydrate (C) partitioning from source leaves to apical organs and tune systemic N supply to restrict lateral organ formation by C/N depletion. Knowledge of the underlying mechanisms controlling plant C/N partitioning is of pivotal importance for breeding strategies to generate plants with desired architectural and nutritional characteristics.}, number = {7}, urldate = {2024-03-18}, journal = {Proceedings of the National Academy of Sciences}, author = {Kreisz, Philipp and Hellens, Alicia M. and Fröschel, Christian and Krischke, Markus and Maag, Daniel and Feil, Regina and Wildenhain, Theresa and Draken, Jan and Braune, Gabriel and Erdelitsch, Leon and Cecchino, Laura and Wagner, Tobias C. and Ache, Peter and Mueller, Martin J. and Becker, Dirk and Lunn, John E. and Hanson, Johannes and Beveridge, Christine A. and Fichtner, Franziska and Barbier, Francois F. and Weiste, Christoph}, month = feb, year = {2024}, note = {Publisher: Proceedings of the National Academy of Sciences}, pages = {e2313343121}, }
Plants tightly control growth of their lateral organs, which led to the concept of apical dominance. However, outgrowth of the dormant lateral primordia is sensitive to the plant’s nutritional status, resulting in an immense plasticity in plant architecture. While the impact of hormonal regulation on apical dominance is well characterized, the prime importance of sugar signaling to unleash lateral organ formation has just recently emerged. Here, we aimed to identify transcriptional regulators, which control the trade-off between growth of apical versus lateral organs. Making use of locally inducible gain-of-function as well as single and higher-order loss-of-function approaches of the sugar-responsive S1-basic-leucine-zipper (S1-bZIP) transcription factors, we disclosed their largely redundant function in establishing apical growth dominance. Consistently, comprehensive phenotypical and analytical studies of S1-bZIP mutants show a clear shift of sugar and organic nitrogen (N) allocation from apical to lateral organs, coinciding with strong lateral organ outgrowth. Tissue-specific transcriptomics reveal specific clade III SWEET sugar transporters, crucial for long-distance sugar transport to apical sinks and the glutaminase GLUTAMINE AMIDO-TRANSFERASE 1_2.1, involved in N homeostasis, as direct S1-bZIP targets, linking the architectural and metabolic mutant phenotypes to downstream gene regulation. Based on these results, we propose that S1-bZIPs control carbohydrate (C) partitioning from source leaves to apical organs and tune systemic N supply to restrict lateral organ formation by C/N depletion. Knowledge of the underlying mechanisms controlling plant C/N partitioning is of pivotal importance for breeding strategies to generate plants with desired architectural and nutritional characteristics.
Fungal-Bacterial Combinations in Plant Health under Stress: Physiological and Biochemical Characteristics of the Filamentous Fungus Serendipita indica and the Actinobacterium Zhihengliuella sp. ISTPL4 under In Vitro Arsenic Stress.
Sharma, N., Koul, M., Joshi, N. C., Dufossé, L., & Mishra, A.
Microorganisms, 12(2): 405. February 2024.
Number: 2 Publisher: Multidisciplinary Digital Publishing Institute
Paper doi link bibtex abstract
Paper doi link bibtex abstract
@article{sharma_fungal-bacterial_2024, title = {Fungal-{Bacterial} {Combinations} in {Plant} {Health} under {Stress}: {Physiological} and {Biochemical} {Characteristics} of the {Filamentous} {Fungus} {Serendipita} indica and the {Actinobacterium} {Zhihengliuella} sp. {ISTPL4} under {In} {Vitro} {Arsenic} {Stress}}, volume = {12}, copyright = {http://creativecommons.org/licenses/by/3.0/}, issn = {2076-2607}, shorttitle = {Fungal-{Bacterial} {Combinations} in {Plant} {Health} under {Stress}}, url = {https://www.mdpi.com/2076-2607/12/2/405}, doi = {10.3390/microorganisms12020405}, abstract = {Fungal-bacterial combinations have a significant role in increasing and improving plant health under various stress conditions. Metabolites secreted by fungi and bacteria play an important role in this process. Our study emphasizes the significance of secondary metabolites secreted by the fungus Serendipita indica alone and by an actinobacterium Zhihengliuella sp. ISTPL4 under normal growth conditions and arsenic (As) stress condition. Here, we evaluated the arsenic tolerance ability of S. indica alone and in combination with Z. sp. ISTPL4 under in vitro conditions. The growth of S. indica and Z. sp. ISTPL4 was measured in varying concentrations of arsenic and the effect of arsenic on spore size and morphology of S. indica was determined using confocal microscopy and scanning electron microscopy. The metabolomics study indicated that S. indica alone in normal growth conditions and under As stress released pentadecanoic acid, glycerol tricaprylate, L-proline and cyclo(L-prolyl-L-valine). Similarly, d-Ribose, 2-deoxy-bis(thioheptyl)-dithioacetal were secreted by a combination of S. indica and Z. sp. ISTPL4. Confocal studies revealed that spore size of S. indica decreased by 18\% at 1.9 mM and by 15\% when in combination with Z. sp. ISTPL4 at a 2.4 mM concentration of As. Arsenic above this concentration resulted in spore degeneration and hyphae fragmentation. Scanning electron microscopy (SEM) results indicated an increased spore size of S. indica in the presence of Z. sp. ISTPL4 (18 ± 0.75 µm) compared to S. indica alone (14 ± 0.24 µm) under normal growth conditions. Our study concluded that the suggested combination of microbial consortium can be used to increase sustainable agriculture by combating biotic as well as abiotic stress. This is because the metabolites released by the microbial combination display antifungal and antibacterial properties. The metabolites, besides evading stress, also confer other survival strategies. Therefore, the choice of consortia and combination partners is important and can help in developing strategies for coping with As stress.}, language = {en}, number = {2}, urldate = {2024-03-18}, journal = {Microorganisms}, author = {Sharma, Neha and Koul, Monika and Joshi, Naveen Chandra and Dufossé, Laurent and Mishra, Arti}, month = feb, year = {2024}, note = {Number: 2 Publisher: Multidisciplinary Digital Publishing Institute}, keywords = {\textit{Oryza sativa}, \textit{Serendipita indica}, arsenic, heavy metal stress, secondary metabolites}, pages = {405}, }
Fungal-bacterial combinations have a significant role in increasing and improving plant health under various stress conditions. Metabolites secreted by fungi and bacteria play an important role in this process. Our study emphasizes the significance of secondary metabolites secreted by the fungus Serendipita indica alone and by an actinobacterium Zhihengliuella sp. ISTPL4 under normal growth conditions and arsenic (As) stress condition. Here, we evaluated the arsenic tolerance ability of S. indica alone and in combination with Z. sp. ISTPL4 under in vitro conditions. The growth of S. indica and Z. sp. ISTPL4 was measured in varying concentrations of arsenic and the effect of arsenic on spore size and morphology of S. indica was determined using confocal microscopy and scanning electron microscopy. The metabolomics study indicated that S. indica alone in normal growth conditions and under As stress released pentadecanoic acid, glycerol tricaprylate, L-proline and cyclo(L-prolyl-L-valine). Similarly, d-Ribose, 2-deoxy-bis(thioheptyl)-dithioacetal were secreted by a combination of S. indica and Z. sp. ISTPL4. Confocal studies revealed that spore size of S. indica decreased by 18% at 1.9 mM and by 15% when in combination with Z. sp. ISTPL4 at a 2.4 mM concentration of As. Arsenic above this concentration resulted in spore degeneration and hyphae fragmentation. Scanning electron microscopy (SEM) results indicated an increased spore size of S. indica in the presence of Z. sp. ISTPL4 (18 ± 0.75 µm) compared to S. indica alone (14 ± 0.24 µm) under normal growth conditions. Our study concluded that the suggested combination of microbial consortium can be used to increase sustainable agriculture by combating biotic as well as abiotic stress. This is because the metabolites released by the microbial combination display antifungal and antibacterial properties. The metabolites, besides evading stress, also confer other survival strategies. Therefore, the choice of consortia and combination partners is important and can help in developing strategies for coping with As stress.
Biohybrid Energy Storage Circuits Based on Electronically Functionalized Plant Roots.
Parker, D., Dar, A. M., Armada-Moreira, A., Bernacka Wojcik, I., Rai, R., Mantione, D., & Stavrinidou, E.
ACS Applied Materials & Interfaces. March 2024.
Publisher: American Chemical Society
Paper doi link bibtex abstract
Paper doi link bibtex abstract
@article{parker_biohybrid_2024, title = {Biohybrid {Energy} {Storage} {Circuits} {Based} on {Electronically} {Functionalized} {Plant} {Roots}}, issn = {1944-8244}, url = {https://doi.org/10.1021/acsami.3c16861}, doi = {10.1021/acsami.3c16861}, abstract = {Biohybrid systems based on plants integrate plant structures and processes into technological components targeting more sustainable solutions. Plants’ biocatalytic machinery, for example, has been leveraged for the organization of electronic materials directly in the vasculature and roots of living plants, resulting in biohybrid electrochemical devices. Among other applications, energy storage devices were demonstrated where the charge storage electrodes were seamlessly integrated into the plant tissue. However, the capacitance and the voltage output of a single biohybrid supercapacitor are limited. Here, we developed biohybrid circuits based on functionalized conducting roots, extending the performance of plant based biohybrid energy storage systems. We show that root-supercapacitors can be combined in series and in parallel configuration, achieving up to 1.5 V voltage output or up to 11 mF capacitance, respectively. We further demonstrate that the supercapacitors circuit can be charged with an organic photovoltaic cell, and that the stored charge can be used to power an electrochromic display or a bioelectronic device. Furthermore, the functionalized roots degrade in composting similarly to native roots. The proof-of-concept demonstrations illustrate the potential of this technology to achieve more sustainable solutions for powering low consumption devices such as bioelectronics for agriculture or IoT applications.}, urldate = {2024-03-08}, journal = {ACS Applied Materials \& Interfaces}, author = {Parker, Daniela and Dar, Abdul Manan and Armada-Moreira, Adam and Bernacka Wojcik, Iwona and Rai, Rajat and Mantione, Daniele and Stavrinidou, Eleni}, month = mar, year = {2024}, note = {Publisher: American Chemical Society}, }
Biohybrid systems based on plants integrate plant structures and processes into technological components targeting more sustainable solutions. Plants’ biocatalytic machinery, for example, has been leveraged for the organization of electronic materials directly in the vasculature and roots of living plants, resulting in biohybrid electrochemical devices. Among other applications, energy storage devices were demonstrated where the charge storage electrodes were seamlessly integrated into the plant tissue. However, the capacitance and the voltage output of a single biohybrid supercapacitor are limited. Here, we developed biohybrid circuits based on functionalized conducting roots, extending the performance of plant based biohybrid energy storage systems. We show that root-supercapacitors can be combined in series and in parallel configuration, achieving up to 1.5 V voltage output or up to 11 mF capacitance, respectively. We further demonstrate that the supercapacitors circuit can be charged with an organic photovoltaic cell, and that the stored charge can be used to power an electrochromic display or a bioelectronic device. Furthermore, the functionalized roots degrade in composting similarly to native roots. The proof-of-concept demonstrations illustrate the potential of this technology to achieve more sustainable solutions for powering low consumption devices such as bioelectronics for agriculture or IoT applications.
A proxitome-RNA-capture approach reveals that processing bodies repress coregulated hub genes.
Liu, C., Mentzelopoulou, A., Hatzianestis, I. H, Tzagkarakis, E., Skaltsogiannis, V., Ma, X., Michalopoulou, V. A, Romero-Campero, F. J, Romero-Losada, A. B, Sarris, P. F, Marhavy, P., Bölter, B., Kanterakis, A., Gutierrez-Beltran, E., & Moschou, P. N
The Plant Cell, 36(3): 559–584. March 2024.
Paper doi link bibtex abstract
Paper doi link bibtex abstract
@article{liu_proxitome-rna-capture_2024, title = {A proxitome-{RNA}-capture approach reveals that processing bodies repress coregulated hub genes}, volume = {36}, issn = {1040-4651}, url = {https://doi.org/10.1093/plcell/koad288}, doi = {10.1093/plcell/koad288}, abstract = {Cellular condensates are usually ribonucleoprotein assemblies with liquid- or solid-like properties. Because these subcellular structures lack a delineating membrane, determining their compositions is difficult. Here we describe a proximity-biotinylation approach for capturing the RNAs of the condensates known as processing bodies (PBs) in Arabidopsis (Arabidopsis thaliana). By combining this approach with RNA detection, in silico, and high-resolution imaging approaches, we studied PBs under normal conditions and heat stress. PBs showed a much more dynamic RNA composition than the total transcriptome. RNAs involved in cell wall development and regeneration, plant hormonal signaling, secondary metabolism/defense, and RNA metabolism were enriched in PBs. RNA-binding proteins and the liquidity of PBs modulated RNA recruitment, while RNAs were frequently recruited together with their encoded proteins. In PBs, RNAs follow distinct fates: in small liquid-like PBs, RNAs get degraded while in more solid-like larger ones, they are stored. PB properties can be regulated by the actin-polymerizing SCAR (suppressor of the cyclic AMP)-WAVE (WASP family verprolin homologous) complex. SCAR/WAVE modulates the shuttling of RNAs between PBs and the translational machinery, thereby adjusting ethylene signaling. In summary, we provide an approach to identify RNAs in condensates that allowed us to reveal a mechanism for regulating RNA fate.}, number = {3}, urldate = {2024-03-01}, journal = {The Plant Cell}, author = {Liu, Chen and Mentzelopoulou, Andriani and Hatzianestis, Ioannis H and Tzagkarakis, Epameinondas and Skaltsogiannis, Vasileios and Ma, Xuemin and Michalopoulou, Vassiliki A and Romero-Campero, Francisco J and Romero-Losada, Ana B and Sarris, Panagiotis F and Marhavy, Peter and Bölter, Bettina and Kanterakis, Alexandros and Gutierrez-Beltran, Emilio and Moschou, Panagiotis N}, month = mar, year = {2024}, pages = {559--584}, }
Cellular condensates are usually ribonucleoprotein assemblies with liquid- or solid-like properties. Because these subcellular structures lack a delineating membrane, determining their compositions is difficult. Here we describe a proximity-biotinylation approach for capturing the RNAs of the condensates known as processing bodies (PBs) in Arabidopsis (Arabidopsis thaliana). By combining this approach with RNA detection, in silico, and high-resolution imaging approaches, we studied PBs under normal conditions and heat stress. PBs showed a much more dynamic RNA composition than the total transcriptome. RNAs involved in cell wall development and regeneration, plant hormonal signaling, secondary metabolism/defense, and RNA metabolism were enriched in PBs. RNA-binding proteins and the liquidity of PBs modulated RNA recruitment, while RNAs were frequently recruited together with their encoded proteins. In PBs, RNAs follow distinct fates: in small liquid-like PBs, RNAs get degraded while in more solid-like larger ones, they are stored. PB properties can be regulated by the actin-polymerizing SCAR (suppressor of the cyclic AMP)-WAVE (WASP family verprolin homologous) complex. SCAR/WAVE modulates the shuttling of RNAs between PBs and the translational machinery, thereby adjusting ethylene signaling. In summary, we provide an approach to identify RNAs in condensates that allowed us to reveal a mechanism for regulating RNA fate.
High-quality genome assembly enables prediction of allele-specific gene expression in hybrid poplar.
Shi, T., Jia, K., Bao, Y., Nie, S., Tian, X., Yan, X., Chen, Z., Li, Z., Zhao, S., Ma, H., Zhao, Y., Li, X., Zhang, R., Guo, J., Zhao, W., El-Kassaby, Y. A., Müller, N., Van de Peer, Y., Wang, X., Street, N. R., Porth, I., An, X., & Mao, J.
Plant Physiology,kiae078. February 2024.
Paper doi link bibtex abstract
Paper doi link bibtex abstract
@article{shi_high-quality_2024, title = {High-quality genome assembly enables prediction of allele-specific gene expression in hybrid poplar}, issn = {0032-0889}, url = {https://doi.org/10.1093/plphys/kiae078}, doi = {10.1093/plphys/kiae078}, abstract = {Poplar (Populus) is a well-established model system for tree genomics and molecular breeding, and hybrid poplar is widely used in forest plantations. However, distinguishing its diploid homologous chromosomes is difficult, complicating advanced functional studies on specific alleles. In this study, we applied a trio-binning design and PacBio High-Fidelity long-read sequencing to obtain haplotype-phased telomere-to-telomere genome assemblies for the two parents of the well-studied F1 hybrid “84K” (Populus alba × P. tremula var. glandulosa). Almost all chromosomes, including the telomeres and centromeres, were completely assembled for each haplotype subgenome apart from two small gaps on one chromosome. By incorporating information from these haplotype assemblies and extensive RNA-seq data, we analyzed gene expression patterns between the two subgenomes and alleles. Transcription bias at the subgenome level was not uncovered, but extensive expression differences were detected between alleles. We developed machine-learning (ML) models to predict allele-specific expression (ASE) with high accuracy and identified underlying genome features most highly influencing ASE. One of our models with 15 predictor variables achieved 77\% accuracy on the training set and 74\% accuracy on the testing set. ML models identified gene body CHG methylation, sequence divergence, and transposon occupancy both upstream and downstream of alleles as important factors for ASE. Our haplotype-phased genome assemblies and ML strategy highlight an avenue for functional studies in Populus and provide additional tools for studying ASE and heterosis in hybrids.}, urldate = {2024-03-01}, journal = {Plant Physiology}, author = {Shi, Tian-Le and Jia, Kai-Hua and Bao, Yu-Tao and Nie, Shuai and Tian, Xue-Chan and Yan, Xue-Mei and Chen, Zhao-Yang and Li, Zhi-Chao and Zhao, Shi-Wei and Ma, Hai-Yao and Zhao, Ye and Li, Xiang and Zhang, Ren-Gang and Guo, Jing and Zhao, Wei and El-Kassaby, Yousry Aly and Müller, Niels and Van de Peer, Yves and Wang, Xiao-Ru and Street, Nathaniel Robert and Porth, Ilga and An, Xinmin and Mao, Jian-Feng}, month = feb, year = {2024}, pages = {kiae078}, }
Poplar (Populus) is a well-established model system for tree genomics and molecular breeding, and hybrid poplar is widely used in forest plantations. However, distinguishing its diploid homologous chromosomes is difficult, complicating advanced functional studies on specific alleles. In this study, we applied a trio-binning design and PacBio High-Fidelity long-read sequencing to obtain haplotype-phased telomere-to-telomere genome assemblies for the two parents of the well-studied F1 hybrid “84K” (Populus alba × P. tremula var. glandulosa). Almost all chromosomes, including the telomeres and centromeres, were completely assembled for each haplotype subgenome apart from two small gaps on one chromosome. By incorporating information from these haplotype assemblies and extensive RNA-seq data, we analyzed gene expression patterns between the two subgenomes and alleles. Transcription bias at the subgenome level was not uncovered, but extensive expression differences were detected between alleles. We developed machine-learning (ML) models to predict allele-specific expression (ASE) with high accuracy and identified underlying genome features most highly influencing ASE. One of our models with 15 predictor variables achieved 77% accuracy on the training set and 74% accuracy on the testing set. ML models identified gene body CHG methylation, sequence divergence, and transposon occupancy both upstream and downstream of alleles as important factors for ASE. Our haplotype-phased genome assemblies and ML strategy highlight an avenue for functional studies in Populus and provide additional tools for studying ASE and heterosis in hybrids.
Gene co-expression network analysis reveal core responsive genes in Parascaris univalens tissues following ivermectin exposure.
Dube, F., Delhomme, N., Martin, F., Hinas, A., Åbrink, M., Svärd, S., & Tydén, E.
PLOS ONE, 19(2): e0298039. February 2024.
Publisher: Public Library of Science
Paper doi link bibtex abstract
Paper doi link bibtex abstract
@article{dube_gene_2024, title = {Gene co-expression network analysis reveal core responsive genes in {Parascaris} univalens tissues following ivermectin exposure}, volume = {19}, issn = {1932-6203}, url = {https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0298039}, doi = {10.1371/journal.pone.0298039}, abstract = {Anthelmintic resistance in equine parasite Parascaris univalens, compromises ivermectin (IVM) effectiveness and necessitates an in-depth understanding of its resistance mechanisms. Most research, primarily focused on holistic gene expression analyses, may overlook vital tissue-specific responses and often limit the scope of novel genes. This study leveraged gene co-expression network analysis to elucidate tissue-specific transcriptional responses and to identify core genes implicated in the IVM response in P. univalens. Adult worms (n = 28) were exposed to 10−11 M and 10−9 M IVM in vitro for 24 hours. RNA-sequencing examined transcriptional changes in the anterior end and intestine. Differential expression analysis revealed pronounced tissue differences, with the intestine exhibiting substantially more IVM-induced transcriptional activity. Gene co-expression network analysis identified seven modules significantly associated with the response to IVM. Within these, 219 core genes were detected, largely expressed in the intestinal tissue and spanning diverse biological processes with unspecific patterns. After 10−11 M IVM, intestinal tissue core genes showed transcriptional suppression, cell cycle inhibition, and ribosomal alterations. Interestingly, genes PgR028\_g047 (sorb-1), PgB01\_g200 (gmap-1) and PgR046\_g017 (col-37 \& col-102) switched from downregulation at 10−11 M to upregulation at 10−9 M IVM. The 10−9 M concentration induced expression of cuticle and membrane integrity core genes in the intestinal tissue. No clear core gene patterns were visible in the anterior end after 10−11 M IVM. However, after 10−9 M IVM, the anterior end mostly displayed downregulation, indicating disrupted transcriptional regulation. One interesting finding was the non-modular calcium-signaling gene, PgR047\_g066 (gegf-1), which uniquely connected 71 genes across four modules. These genes were enriched for transmembrane signaling activity, suggesting that PgR047\_g066 (gegf-1) could have a key signaling role. By unveiling tissue-specific expression patterns and highlighting biological processes through unbiased core gene detection, this study reveals intricate IVM responses in P. univalens. These findings suggest alternative drug uptake of IVM and can guide functional validations to further IVM resistance mechanism understanding.}, language = {en}, number = {2}, urldate = {2024-02-23}, journal = {PLOS ONE}, author = {Dube, Faruk and Delhomme, Nicolas and Martin, Frida and Hinas, Andrea and Åbrink, Magnus and Svärd, Staffan and Tydén, Eva}, month = feb, year = {2024}, note = {Publisher: Public Library of Science}, keywords = {Cellular structures and organelles, Gastrointestinal tract, Gene expression, Gene ontologies, Gene regulatory networks, Genetic networks, Nematode infections, Signal transduction}, pages = {e0298039}, }
Anthelmintic resistance in equine parasite Parascaris univalens, compromises ivermectin (IVM) effectiveness and necessitates an in-depth understanding of its resistance mechanisms. Most research, primarily focused on holistic gene expression analyses, may overlook vital tissue-specific responses and often limit the scope of novel genes. This study leveraged gene co-expression network analysis to elucidate tissue-specific transcriptional responses and to identify core genes implicated in the IVM response in P. univalens. Adult worms (n = 28) were exposed to 10−11 M and 10−9 M IVM in vitro for 24 hours. RNA-sequencing examined transcriptional changes in the anterior end and intestine. Differential expression analysis revealed pronounced tissue differences, with the intestine exhibiting substantially more IVM-induced transcriptional activity. Gene co-expression network analysis identified seven modules significantly associated with the response to IVM. Within these, 219 core genes were detected, largely expressed in the intestinal tissue and spanning diverse biological processes with unspecific patterns. After 10−11 M IVM, intestinal tissue core genes showed transcriptional suppression, cell cycle inhibition, and ribosomal alterations. Interestingly, genes PgR028_g047 (sorb-1), PgB01_g200 (gmap-1) and PgR046_g017 (col-37 & col-102) switched from downregulation at 10−11 M to upregulation at 10−9 M IVM. The 10−9 M concentration induced expression of cuticle and membrane integrity core genes in the intestinal tissue. No clear core gene patterns were visible in the anterior end after 10−11 M IVM. However, after 10−9 M IVM, the anterior end mostly displayed downregulation, indicating disrupted transcriptional regulation. One interesting finding was the non-modular calcium-signaling gene, PgR047_g066 (gegf-1), which uniquely connected 71 genes across four modules. These genes were enriched for transmembrane signaling activity, suggesting that PgR047_g066 (gegf-1) could have a key signaling role. By unveiling tissue-specific expression patterns and highlighting biological processes through unbiased core gene detection, this study reveals intricate IVM responses in P. univalens. These findings suggest alternative drug uptake of IVM and can guide functional validations to further IVM resistance mechanism understanding.
In situ seasonal patterns of root auxin concentrations and meristem length in an arctic sedge.
Blume-Werry, G., Semenchuk, P., Ljung, K., Milbau, A., Novak, O., Olofsson, J., & Brunoni, F.
New Phytologist. February 2024.
_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1111/nph.19616
Paper doi link bibtex abstract
Paper doi link bibtex abstract
@article{blume-werry_situ_2024, title = {In situ seasonal patterns of root auxin concentrations and meristem length in an arctic sedge}, copyright = {© 2024 The Authors. New Phytologist © 2024 New Phytologist Foundation}, issn = {1469-8137}, url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/nph.19616}, doi = {10.1111/nph.19616}, abstract = {Seasonal dynamics of root growth play an important role in large-scale ecosystem processes; they are largely governed by growth regulatory compounds and influenced by environmental conditions. Yet, our knowledge about physiological drivers of root growth is mostly limited to laboratory-based studies on model plant species. We sampled root tips of Eriophorum vaginatum and analyzed their auxin concentrations and meristem lengths biweekly over a growing season in situ in a subarctic peatland, both in surface soil and at the permafrost thawfront. Auxin concentrations were almost five times higher in surface than in thawfront soils and increased over the season, especially at the thawfront. Surprisingly, meristem length showed an opposite pattern and was almost double in thawfront compared with surface soils. Meristem length increased from peak to late season in the surface soils but decreased at the thawfront. Our study of in situ seasonal dynamics in root physiological parameters illustrates the potential for physiological methods to be applied in ecological studies and emphasizes the importance of in situ measurements. The strong effect of root location and the unexpected opposite patterns of meristem length and auxin concentrations likely show that auxin actively governs root growth to ensure a high potential for nutrient uptake at the thawfront.}, language = {en}, urldate = {2024-02-23}, journal = {New Phytologist}, author = {Blume-Werry, Gesche and Semenchuk, Philipp and Ljung, Karin and Milbau, Ann and Novak, Ondrej and Olofsson, Johan and Brunoni, Federica}, month = feb, year = {2024}, note = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1111/nph.19616}, keywords = {Eriophorum vaginatum, auxin, meristem length, permafrost, root growth, root phenology}, }
Seasonal dynamics of root growth play an important role in large-scale ecosystem processes; they are largely governed by growth regulatory compounds and influenced by environmental conditions. Yet, our knowledge about physiological drivers of root growth is mostly limited to laboratory-based studies on model plant species. We sampled root tips of Eriophorum vaginatum and analyzed their auxin concentrations and meristem lengths biweekly over a growing season in situ in a subarctic peatland, both in surface soil and at the permafrost thawfront. Auxin concentrations were almost five times higher in surface than in thawfront soils and increased over the season, especially at the thawfront. Surprisingly, meristem length showed an opposite pattern and was almost double in thawfront compared with surface soils. Meristem length increased from peak to late season in the surface soils but decreased at the thawfront. Our study of in situ seasonal dynamics in root physiological parameters illustrates the potential for physiological methods to be applied in ecological studies and emphasizes the importance of in situ measurements. The strong effect of root location and the unexpected opposite patterns of meristem length and auxin concentrations likely show that auxin actively governs root growth to ensure a high potential for nutrient uptake at the thawfront.
The effect of nitrogen source and levels on hybrid aspen tree physiology and wood formation.
Renström, A., Choudhary, S., Gandla, M. L., Jönsson, L. J., Hedenström, M., Jämtgård, S., & Tuominen, H.
Physiologia Plantarum, 176(1): e14219. February 2024.
_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1111/ppl.14219
Paper doi link bibtex abstract
Paper doi link bibtex abstract
@article{renstrom_effect_2024, title = {The effect of nitrogen source and levels on hybrid aspen tree physiology and wood formation}, volume = {176}, copyright = {© 2024 The Authors. 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.14219}, doi = {10.1111/ppl.14219}, abstract = {Nitrogen can be taken up by trees in the form of nitrate, ammonium and amino acids, but the influence of the different forms on tree growth and development is poorly understood in angiosperm species like Populus. We studied the effects of both organic and inorganic forms of nitrogen on growth and wood formation of hybrid aspen trees in experimental conditions that allowed growth under four distinct steady-state nitrogen levels. Increased nitrogen availability had a positive influence on biomass accumulation and the radial dimensions of both xylem vessels and fibers, and a negative influence on wood density. An optimal level of nitrogen availability was identified where increases in biomass accumulation outweighed decreases in wood density. None of these responses depended on the source of nitrogen except for shoot biomass accumulation, which was stimulated more by treatments complemented with nitrate than by ammonium alone or the organic source arginine. The most striking difference between the nitrogen sources was the effect on lignin composition, whereby the abundance of H-type lignin increased only in the presence of nitrate. The differential effect of nitrate is possibly related to the well-known role of nitrate as a signaling compound. RNA-sequencing revealed that while the lignin-biosynthetic genes did not significantly (FDR {\textless}0.01) respond to added NO3−, the expression of several laccases, catalysing lignin polymerization, was dependent on N-availability. These results reveal a unique role of nitrate in wood formation and contribute to the knowledge basis for decision-making in utilizing hybrid aspen as a bioresource.}, language = {en}, number = {1}, urldate = {2024-02-23}, journal = {Physiologia Plantarum}, author = {Renström, Anna and Choudhary, Shruti and Gandla, Madhavi Latha and Jönsson, Leif J. and Hedenström, Mattias and Jämtgård, Sandra and Tuominen, Hannele}, month = feb, year = {2024}, note = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1111/ppl.14219}, keywords = {H-type lignin, N-nutrition, Populus tremula x P. tremuloides, Pyrolysis-GC/MS, lignin composition, organic vs. inorganic N, xylogenesis}, pages = {e14219}, }
Nitrogen can be taken up by trees in the form of nitrate, ammonium and amino acids, but the influence of the different forms on tree growth and development is poorly understood in angiosperm species like Populus. We studied the effects of both organic and inorganic forms of nitrogen on growth and wood formation of hybrid aspen trees in experimental conditions that allowed growth under four distinct steady-state nitrogen levels. Increased nitrogen availability had a positive influence on biomass accumulation and the radial dimensions of both xylem vessels and fibers, and a negative influence on wood density. An optimal level of nitrogen availability was identified where increases in biomass accumulation outweighed decreases in wood density. None of these responses depended on the source of nitrogen except for shoot biomass accumulation, which was stimulated more by treatments complemented with nitrate than by ammonium alone or the organic source arginine. The most striking difference between the nitrogen sources was the effect on lignin composition, whereby the abundance of H-type lignin increased only in the presence of nitrate. The differential effect of nitrate is possibly related to the well-known role of nitrate as a signaling compound. RNA-sequencing revealed that while the lignin-biosynthetic genes did not significantly (FDR \textless0.01) respond to added NO3−, the expression of several laccases, catalysing lignin polymerization, was dependent on N-availability. These results reveal a unique role of nitrate in wood formation and contribute to the knowledge basis for decision-making in utilizing hybrid aspen as a bioresource.
Progress in phylogenetics, multi-omics and flower coloration studies in Rhododendron.
Nie, S., Ma, H., Shi, T., Tian, X., El-Kassaby, Y. A., Porth, I., Yang, F., Mao, J., Nie, S., Ma, H., Shi, T., Tian, X., El-Kassaby, Y. A., Porth, I., Yang, F., & Mao, J.
Ornamental Plant Research, 4(1). January 2024.
Bandiera_abtest: a Cc_license_type: cc_by Cg_type: Maximum Academic Press Number: opr-0024-0001 Primary_atype: Ornamental Plant Research Publisher: Maximum Academic Press Subject_term: REVIEW Subject_term_id: REVIEW
Paper doi link bibtex abstract
Paper doi link bibtex abstract
@article{nie_progress_2024, title = {Progress in phylogenetics, multi-omics and flower coloration studies in \textit{{Rhododendron}}}, volume = {4}, copyright = {2024 The Author(s)}, issn = {2769-2094}, url = {https://www.maxapress.com/rticle/doi/10.48130/opr-0024-0001}, doi = {10.48130/opr-0024-0001}, abstract = {{\textless}p{\textgreater}The genus {\textless}italic{\textgreater}Rhododendron{\textless}/italic{\textgreater} exhibits an immense diversity of flower colors and represents one of the largest groups of woody plants, which is of great importance for ornamental plant research. This review summarizes recent progress in deciphering the genetic basis for flower coloration in {\textless}italic{\textgreater}Rhododendron{\textless}/italic{\textgreater}. We describe advances in phylogenetic reconstruction and genome sequencing of {\textless}italic{\textgreater}Rhododendron{\textless}/italic{\textgreater} species. The metabolic pathways of flower color are outlined, focusing on key structural and regulatory genes involved in pigment synthesis. Gene duplications and losses associated with color diversification are discussed. In addition, the application of multi-omics approaches and analysis of gene co-expression networks to elucidate complex gene regulatory mechanisms is emphasized. This synthesis of current knowledge provides a foundation for future research on the evolution of flower color diversity within the {\textless}italic{\textgreater}Rhododendron{\textless}/italic{\textgreater} lineage. Ultimately, these discoveries will support breeding endeavors aimed at harnessing the genetics of flower coloration and developing novel cultivars that exhibit desired floral traits.{\textless}/p{\textgreater}}, language = {en}, number = {1}, urldate = {2024-02-23}, journal = {Ornamental Plant Research}, author = {Nie, Shuai and Ma, Hai-Yao and Shi, Tian-Le and Tian, Xue-Chan and El-Kassaby, Yousry A. and Porth, Ilga and Yang, Fu-Sheng and Mao, Jian-Feng and Nie, Shuai and Ma, Hai-Yao and Shi, Tian-Le and Tian, Xue-Chan and El-Kassaby, Yousry A. and Porth, Ilga and Yang, Fu-Sheng and Mao, Jian-Feng}, month = jan, year = {2024}, note = {Bandiera\_abtest: a Cc\_license\_type: cc\_by Cg\_type: Maximum Academic Press Number: opr-0024-0001 Primary\_atype: Ornamental Plant Research Publisher: Maximum Academic Press Subject\_term: REVIEW Subject\_term\_id: REVIEW}, }
\textlessp\textgreaterThe genus \textlessitalic\textgreaterRhododendron\textless/italic\textgreater exhibits an immense diversity of flower colors and represents one of the largest groups of woody plants, which is of great importance for ornamental plant research. This review summarizes recent progress in deciphering the genetic basis for flower coloration in \textlessitalic\textgreaterRhododendron\textless/italic\textgreater. We describe advances in phylogenetic reconstruction and genome sequencing of \textlessitalic\textgreaterRhododendron\textless/italic\textgreater species. The metabolic pathways of flower color are outlined, focusing on key structural and regulatory genes involved in pigment synthesis. Gene duplications and losses associated with color diversification are discussed. In addition, the application of multi-omics approaches and analysis of gene co-expression networks to elucidate complex gene regulatory mechanisms is emphasized. This synthesis of current knowledge provides a foundation for future research on the evolution of flower color diversity within the \textlessitalic\textgreaterRhododendron\textless/italic\textgreater lineage. Ultimately, these discoveries will support breeding endeavors aimed at harnessing the genetics of flower coloration and developing novel cultivars that exhibit desired floral traits.\textless/p\textgreater
Shifts in microbial community composition and metabolism correspond with rapid soil carbon accumulation in response to 20 years of simulated nitrogen deposition.
Forsmark, B., Bizjak, T., Nordin, A., Rosenstock, N., Wallander, H., & Gundale, M.
Science of the Total Environment, 918(170741). February 2024.
doi link bibtex abstract
doi link bibtex abstract
@article{forsmark_shifts_2024, title = {Shifts in microbial community composition and metabolism correspond with rapid soil carbon accumulation in response to 20 years of simulated nitrogen deposition}, volume = {918}, issn = {0048-9697}, doi = {10.1016/j.scitotenv.2024.170741}, abstract = {Anthropogenic nitrogen (N) deposition and fertilization in boreal forests frequently reduces decomposition and soil respiration and enhances C storage in the topsoil. This enhancement of the C sink can be as strong as the aboveground biomass response to N additions and has implications for the global C cycle, but the mechanisms remain elusive. We hypothesized that this effect would be associated with a shift in the microbial community and its activity, and particularly by fungal taxa reported to be capable of lignin degradation and organic N acquisition. We sampled the organic layer below the intact litter of a Norway spruce (Picea abies (L.) Karst) forest in northern Sweden after 20 years of annual N additions at low (12.5 kg N ha−1 yr−1) and high (50 kg N ha−1 yr−1) rates. We measured microbial biomass using phospholipid fatty-acid analysis (PLFA) and ergosterol measurements and used ITS metagenomics to profile the fungal community of soil and fine-roots. We probed the metabolic activity of the soil community by measuring the activity of extracellular enzymes and evaluated its relationships with the most N responsive soil fungal species. Nitrogen addition decreased the abundance of fungal PLFA markers and changed the fungal community in humus and fine-roots. Specifically, the humus community changed in part due to a shift from Oidiodendron pilicola, Cenococcum geophilum, and Cortinarius caperatus to Tylospora fibrillosa and Russula griseascens. These microbial community changes were associated with decreased activity of Mn-peroxidase and peptidase, and an increase in the activity of C acquiring enzymes. Our results show that the rapid accumulation of C in the humus layer frequently observed in areas with high N deposition is consistent with a shift in microbial metabolism, where decomposition associated with organic N acquisition is downregulated when inorganic N forms are readily available. © 2024 The Authors}, language = {English}, number = {170741}, journal = {Science of the Total Environment}, author = {Forsmark, B. and Bizjak, T. and Nordin, A. and Rosenstock, N.P. and Wallander, H. and Gundale, M.J.}, month = feb, year = {2024}, keywords = {Boreal forest, Carbon sequestration, Ectomycorrhizal fungi, Extracellular enzymes, Microbial community, Nitrogen deposition}, }
Anthropogenic nitrogen (N) deposition and fertilization in boreal forests frequently reduces decomposition and soil respiration and enhances C storage in the topsoil. This enhancement of the C sink can be as strong as the aboveground biomass response to N additions and has implications for the global C cycle, but the mechanisms remain elusive. We hypothesized that this effect would be associated with a shift in the microbial community and its activity, and particularly by fungal taxa reported to be capable of lignin degradation and organic N acquisition. We sampled the organic layer below the intact litter of a Norway spruce (Picea abies (L.) Karst) forest in northern Sweden after 20 years of annual N additions at low (12.5 kg N ha−1 yr−1) and high (50 kg N ha−1 yr−1) rates. We measured microbial biomass using phospholipid fatty-acid analysis (PLFA) and ergosterol measurements and used ITS metagenomics to profile the fungal community of soil and fine-roots. We probed the metabolic activity of the soil community by measuring the activity of extracellular enzymes and evaluated its relationships with the most N responsive soil fungal species. Nitrogen addition decreased the abundance of fungal PLFA markers and changed the fungal community in humus and fine-roots. Specifically, the humus community changed in part due to a shift from Oidiodendron pilicola, Cenococcum geophilum, and Cortinarius caperatus to Tylospora fibrillosa and Russula griseascens. These microbial community changes were associated with decreased activity of Mn-peroxidase and peptidase, and an increase in the activity of C acquiring enzymes. Our results show that the rapid accumulation of C in the humus layer frequently observed in areas with high N deposition is consistent with a shift in microbial metabolism, where decomposition associated with organic N acquisition is downregulated when inorganic N forms are readily available. © 2024 The Authors
Differential gene expression and potential regulatory network of fatty acid biosynthesis during fruit and leaf development in yellowhorn (Xanthoceras sorbifolium), an oil-producing tree with significant deployment values.
Shi, T., Ma, H., Wang, X., Liu, H., Yan, X., Tian, X., Li, Z., Bao, Y., Chen, Z., Zhao, S., Xiang, Q., Jia, K., Nie, S., Guan, W., & Mao, J.
Frontiers in Plant Science, 14. January 2024.
Paper link bibtex abstract
Paper link bibtex abstract
@article{shi_differential_2024, title = {Differential gene expression and potential regulatory network of fatty acid biosynthesis during fruit and leaf development in yellowhorn ({Xanthoceras} sorbifolium), an oil-producing tree with significant deployment values}, volume = {14}, issn = {1664-462X}, url = {https://www.frontiersin.org/journals/plant-science/articles/10.3389/fpls.2023.1297817}, abstract = {Xanthoceras sorbifolium (yellowhorn) is a woody oil plant with super stress resistance and excellent oil characteristics. The yellowhorn oil can be used as biofuel and edible oil with high nutritional and medicinal value. However, genetic studies on yellowhorn are just in the beginning, and fundamental biological questions regarding its very long-chain fatty acid (VLCFA) biosynthesis pathway remain largely unknown. In this study, we reconstructed the VLCFA biosynthesis pathway and annotated 137 genes encoding relevant enzymes. We identified four oleosin genes that package triacylglycerols (TAGs) and are specifically expressed in fruits, likely playing key roles in yellowhorn oil production. Especially, by examining time-ordered gene co-expression network (TO-GCN) constructed from fruit and leaf developments, we identified key enzymatic genes and potential regulatory transcription factors involved in VLCFA synthesis. In fruits, we further inferred a hierarchical regulatory network with MYB-related (XS03G0296800) and B3 (XS02G0057600) transcription factors as top-tier regulators, providing clues into factors controlling carbon flux into fatty acids. Our results offer new insights into key genes and transcriptional regulators governing fatty acid production in yellowhorn, laying the foundation for efforts to optimize oil content and fatty acid composition. Moreover, the gene expression patterns and putative regulatory relationships identified here will inform metabolic engineering and molecular breeding approaches tailored to meet biofuel and bioproduct demands.}, urldate = {2024-02-16}, journal = {Frontiers in Plant Science}, author = {Shi, Tian-Le and Ma, Hai-Yao and Wang, Xinrui and Liu, Hui and Yan, Xue-Mei and Tian, Xue-Chan and Li, Zhi-Chao and Bao, Yu-Tao and Chen, Zhao-Yang and Zhao, Shi-Wei and Xiang, Qiuhong and Jia, Kai-Hua and Nie, Shuai and Guan, Wenbin and Mao, Jian-Feng}, month = jan, year = {2024}, keywords = {⛔ No DOI found}, }
Xanthoceras sorbifolium (yellowhorn) is a woody oil plant with super stress resistance and excellent oil characteristics. The yellowhorn oil can be used as biofuel and edible oil with high nutritional and medicinal value. However, genetic studies on yellowhorn are just in the beginning, and fundamental biological questions regarding its very long-chain fatty acid (VLCFA) biosynthesis pathway remain largely unknown. In this study, we reconstructed the VLCFA biosynthesis pathway and annotated 137 genes encoding relevant enzymes. We identified four oleosin genes that package triacylglycerols (TAGs) and are specifically expressed in fruits, likely playing key roles in yellowhorn oil production. Especially, by examining time-ordered gene co-expression network (TO-GCN) constructed from fruit and leaf developments, we identified key enzymatic genes and potential regulatory transcription factors involved in VLCFA synthesis. In fruits, we further inferred a hierarchical regulatory network with MYB-related (XS03G0296800) and B3 (XS02G0057600) transcription factors as top-tier regulators, providing clues into factors controlling carbon flux into fatty acids. Our results offer new insights into key genes and transcriptional regulators governing fatty acid production in yellowhorn, laying the foundation for efforts to optimize oil content and fatty acid composition. Moreover, the gene expression patterns and putative regulatory relationships identified here will inform metabolic engineering and molecular breeding approaches tailored to meet biofuel and bioproduct demands.
Unveiling Molecular Signatures in Light-Induced Seed Germination: Insights from PIN3, PIN7, and AUX1 in Arabidopsis thaliana.
Tognacca, R. S., Ljung, K., & Botto, J. F.
Plants, 13(3): 408. January 2024.
Number: 3 Publisher: Multidisciplinary Digital Publishing Institute
Paper doi link bibtex abstract
Paper doi link bibtex abstract
@article{tognacca_unveiling_2024, title = {Unveiling {Molecular} {Signatures} in {Light}-{Induced} {Seed} {Germination}: {Insights} from {PIN3}, {PIN7}, and {AUX1} in {Arabidopsis} thaliana}, volume = {13}, copyright = {http://creativecommons.org/licenses/by/3.0/}, issn = {2223-7747}, shorttitle = {Unveiling {Molecular} {Signatures} in {Light}-{Induced} {Seed} {Germination}}, url = {https://www.mdpi.com/2223-7747/13/3/408}, doi = {10.3390/plants13030408}, abstract = {Light provides seeds with information that is essential for the adjustment of their germination to the conditions that are most favorable for the successful establishment of the future seedling. The promotion of germination depends mainly on environmental factors, like temperature and light, as well as internal factors associated with the hormonal balance between gibberellins (GA) and abscisic acid (ABA), although other hormones such as auxins may act secondarily. While transcriptomic studies of light-germinating Arabidopsis thaliana seeds suggest that auxins and auxin transporters are necessary, there are still no functional studies connecting the activity of the auxin transporters in light-induced seed germination. In this study, we investigated the roles of two auxin efflux carrier (PIN3 and PIN7) proteins and one auxin influx (AUX1) carrier protein during Arabidopsis thaliana seed germination. By using next-generation sequencing (RNAseq), gene expression analyses, hormonal sensitivity assays, and the quantification of indole-3-acetic acid (IAA) levels, we assessed the functional roles of PIN3, PIN7, and AUX1 during light-induced seed germination. We showed that auxin levels are increased 24 h after a red-pulse (Rp). Additionally, we evaluated the germination responses of pin3, pin7, and aux1 mutant seeds and showed that PIN3, PIN7, and AUX1 auxin carriers are important players in the regulation of seed germination. By using gene expression analysis in water, fluridone (F), and ABA+F treated seeds, we confirmed that Rp-induced seed germination is associated with auxin transport, and ABA controls the function of PIN3, PIN7, and AUX1 during this process. Overall, our results highlight the relevant and positive role of auxin transporters in germinating the seeds of Arabidopsis thaliana.}, language = {en}, number = {3}, urldate = {2024-02-16}, journal = {Plants}, author = {Tognacca, Rocío Soledad and Ljung, Karin and Botto, Javier Francisco}, month = jan, year = {2024}, note = {Number: 3 Publisher: Multidisciplinary Digital Publishing Institute}, keywords = {\textit{Arabidopsis thaliana}, ABA, AUX1, PIN3, PIN7, auxin, hormonal crosstalk, molecular regulation, seed germination}, pages = {408}, }
Light provides seeds with information that is essential for the adjustment of their germination to the conditions that are most favorable for the successful establishment of the future seedling. The promotion of germination depends mainly on environmental factors, like temperature and light, as well as internal factors associated with the hormonal balance between gibberellins (GA) and abscisic acid (ABA), although other hormones such as auxins may act secondarily. While transcriptomic studies of light-germinating Arabidopsis thaliana seeds suggest that auxins and auxin transporters are necessary, there are still no functional studies connecting the activity of the auxin transporters in light-induced seed germination. In this study, we investigated the roles of two auxin efflux carrier (PIN3 and PIN7) proteins and one auxin influx (AUX1) carrier protein during Arabidopsis thaliana seed germination. By using next-generation sequencing (RNAseq), gene expression analyses, hormonal sensitivity assays, and the quantification of indole-3-acetic acid (IAA) levels, we assessed the functional roles of PIN3, PIN7, and AUX1 during light-induced seed germination. We showed that auxin levels are increased 24 h after a red-pulse (Rp). Additionally, we evaluated the germination responses of pin3, pin7, and aux1 mutant seeds and showed that PIN3, PIN7, and AUX1 auxin carriers are important players in the regulation of seed germination. By using gene expression analysis in water, fluridone (F), and ABA+F treated seeds, we confirmed that Rp-induced seed germination is associated with auxin transport, and ABA controls the function of PIN3, PIN7, and AUX1 during this process. Overall, our results highlight the relevant and positive role of auxin transporters in germinating the seeds of Arabidopsis thaliana.
Scots pine – panmixia and the elusive signal of genetic adaptation.
Bruxaux, J., Zhao, W., Hall, D., Curtu, A. L., Androsiuk, P., Drouzas, A. D., Gailing, O., Konrad, H., Sullivan, A. R., Semerikov, V., & Wang, X.
New Phytologist. February 2024.
_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1111/nph.19563
Paper doi link bibtex abstract
Paper doi link bibtex abstract
@article{bruxaux_scots_2024, title = {Scots pine – panmixia and the elusive signal of genetic adaptation}, copyright = {© 2024 The Authors. New Phytologist © 2024 New Phytologist Foundation}, issn = {1469-8137}, url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/nph.19563}, doi = {10.1111/nph.19563}, abstract = {Scots pine is the foundation species of diverse forested ecosystems across Eurasia and displays remarkable ecological breadth, occurring in environments ranging from temperate rainforests to arid tundra margins. Such expansive distributions can be favored by various demographic and adaptive processes and the interactions between them. To understand the impact of neutral and selective forces on genetic structure in Scots pine, we conducted range-wide population genetic analyses on 2321 trees from 202 populations using genotyping-by-sequencing, reconstructed the recent demography of the species and examined signals of genetic adaptation. We found a high and uniform genetic diversity across the entire range (global FST 0.048), no increased genetic load in expanding populations and minor impact of the last glacial maximum on historical population sizes. Genetic-environmental associations identified only a handful of single-nucleotide polymorphisms significantly linked to environmental gradients. The results suggest that extensive gene flow is predominantly responsible for the observed genetic patterns in Scots pine. The apparent missing signal of genetic adaptation is likely attributed to the intricate genetic architecture controlling adaptation to multi-dimensional environments. The panmixia metapopulation of Scots pine offers a good study system for further exploration into how genetic adaptation and plasticity evolve under gene flow and changing environment.}, language = {en}, urldate = {2024-02-09}, journal = {New Phytologist}, author = {Bruxaux, Jade and Zhao, Wei and Hall, David and Curtu, Alexandru Lucian and Androsiuk, Piotr and Drouzas, Andreas D. and Gailing, Oliver and Konrad, Heino and Sullivan, Alexis R. and Semerikov, Vladimir and Wang, Xiao-Ru}, month = feb, year = {2024}, note = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1111/nph.19563}, keywords = {Pinus sylvestris, conifer, demography, gene flow, genetic diversity, genetic-environmental association, population structure}, }
Scots pine is the foundation species of diverse forested ecosystems across Eurasia and displays remarkable ecological breadth, occurring in environments ranging from temperate rainforests to arid tundra margins. Such expansive distributions can be favored by various demographic and adaptive processes and the interactions between them. To understand the impact of neutral and selective forces on genetic structure in Scots pine, we conducted range-wide population genetic analyses on 2321 trees from 202 populations using genotyping-by-sequencing, reconstructed the recent demography of the species and examined signals of genetic adaptation. We found a high and uniform genetic diversity across the entire range (global FST 0.048), no increased genetic load in expanding populations and minor impact of the last glacial maximum on historical population sizes. Genetic-environmental associations identified only a handful of single-nucleotide polymorphisms significantly linked to environmental gradients. The results suggest that extensive gene flow is predominantly responsible for the observed genetic patterns in Scots pine. The apparent missing signal of genetic adaptation is likely attributed to the intricate genetic architecture controlling adaptation to multi-dimensional environments. The panmixia metapopulation of Scots pine offers a good study system for further exploration into how genetic adaptation and plasticity evolve under gene flow and changing environment.
S1 basic leucine zipper transcription factors shape plant architecture by controlling C/N partitioning to apical and lateral organs.
Kreisz, P., Hellens, A. M., Fröschel, C., Krischke, M., Maag, D., Feil, R., Wildenhain, T., Draken, J., Braune, G., Erdelitsch, L., Cecchino, L., Wagner, T. C., Ache, P., Mueller, M. J., Becker, D., Lunn, J. E., Hanson, J., Beveridge, C. A., Fichtner, F., Barbier, F. F., & Weiste, C.
Proceedings of the National Academy of Sciences, 121(7): e2313343121. February 2024.
Publisher: Proceedings of the National Academy of Sciences
Paper doi link bibtex abstract
Paper doi link bibtex abstract
@article{kreisz_s1_2024-1, title = {S1 basic leucine zipper transcription factors shape plant architecture by controlling {C}/{N} partitioning to apical and lateral organs}, volume = {121}, url = {https://www.pnas.org/doi/10.1073/pnas.2313343121}, doi = {10.1073/pnas.2313343121}, abstract = {Plants tightly control growth of their lateral organs, which led to the concept of apical dominance. However, outgrowth of the dormant lateral primordia is sensitive to the plant’s nutritional status, resulting in an immense plasticity in plant architecture. While the impact of hormonal regulation on apical dominance is well characterized, the prime importance of sugar signaling to unleash lateral organ formation has just recently emerged. Here, we aimed to identify transcriptional regulators, which control the trade-off between growth of apical versus lateral organs. Making use of locally inducible gain-of-function as well as single and higher-order loss-of-function approaches of the sugar-responsive S1-basic-leucine-zipper (S1-bZIP) transcription factors, we disclosed their largely redundant function in establishing apical growth dominance. Consistently, comprehensive phenotypical and analytical studies of S1-bZIP mutants show a clear shift of sugar and organic nitrogen (N) allocation from apical to lateral organs, coinciding with strong lateral organ outgrowth. Tissue-specific transcriptomics reveal specific clade III SWEET sugar transporters, crucial for long-distance sugar transport to apical sinks and the glutaminase GLUTAMINE AMIDO-TRANSFERASE 1\_2.1, involved in N homeostasis, as direct S1-bZIP targets, linking the architectural and metabolic mutant phenotypes to downstream gene regulation. Based on these results, we propose that S1-bZIPs control carbohydrate (C) partitioning from source leaves to apical organs and tune systemic N supply to restrict lateral organ formation by C/N depletion. Knowledge of the underlying mechanisms controlling plant C/N partitioning is of pivotal importance for breeding strategies to generate plants with desired architectural and nutritional characteristics.}, number = {7}, urldate = {2024-02-09}, journal = {Proceedings of the National Academy of Sciences}, author = {Kreisz, Philipp and Hellens, Alicia M. and Fröschel, Christian and Krischke, Markus and Maag, Daniel and Feil, Regina and Wildenhain, Theresa and Draken, Jan and Braune, Gabriel and Erdelitsch, Leon and Cecchino, Laura and Wagner, Tobias C. and Ache, Peter and Mueller, Martin J. and Becker, Dirk and Lunn, John E. and Hanson, Johannes and Beveridge, Christine A. and Fichtner, Franziska and Barbier, Francois F. and Weiste, Christoph}, month = feb, year = {2024}, note = {Publisher: Proceedings of the National Academy of Sciences}, pages = {e2313343121}, }
Plants tightly control growth of their lateral organs, which led to the concept of apical dominance. However, outgrowth of the dormant lateral primordia is sensitive to the plant’s nutritional status, resulting in an immense plasticity in plant architecture. While the impact of hormonal regulation on apical dominance is well characterized, the prime importance of sugar signaling to unleash lateral organ formation has just recently emerged. Here, we aimed to identify transcriptional regulators, which control the trade-off between growth of apical versus lateral organs. Making use of locally inducible gain-of-function as well as single and higher-order loss-of-function approaches of the sugar-responsive S1-basic-leucine-zipper (S1-bZIP) transcription factors, we disclosed their largely redundant function in establishing apical growth dominance. Consistently, comprehensive phenotypical and analytical studies of S1-bZIP mutants show a clear shift of sugar and organic nitrogen (N) allocation from apical to lateral organs, coinciding with strong lateral organ outgrowth. Tissue-specific transcriptomics reveal specific clade III SWEET sugar transporters, crucial for long-distance sugar transport to apical sinks and the glutaminase GLUTAMINE AMIDO-TRANSFERASE 1_2.1, involved in N homeostasis, as direct S1-bZIP targets, linking the architectural and metabolic mutant phenotypes to downstream gene regulation. Based on these results, we propose that S1-bZIPs control carbohydrate (C) partitioning from source leaves to apical organs and tune systemic N supply to restrict lateral organ formation by C/N depletion. Knowledge of the underlying mechanisms controlling plant C/N partitioning is of pivotal importance for breeding strategies to generate plants with desired architectural and nutritional characteristics.
PLANT UNCOUPLING MITOCHONDRIAL PROTEIN 2 localizes to the Golgi.
Fuchs, P., Feixes-Prats, E., Arruda, P., Feitosa-Araújo, E., Fernie, A. R, Grefen, C., Lichtenauer, S., Linka, N., de Godoy Maia, I., Meyer, A. J, Schilasky, S., Sweetlove, L. J, Wege, S., Weber, A. P M, Millar, A H., Keech, O., Florez-Sarasa, I., Barreto, P., & Schwarzländer, M.
Plant Physiology, 194(2): 623–628. February 2024.
Paper doi link bibtex abstract
Paper doi link bibtex abstract
@article{fuchs_plant_2024, title = {{PLANT} {UNCOUPLING} {MITOCHONDRIAL} {PROTEIN} 2 localizes to the {Golgi}}, volume = {194}, issn = {0032-0889}, url = {https://doi.org/10.1093/plphys/kiad540}, doi = {10.1093/plphys/kiad540}, abstract = {Mitochondria act as cellular hubs of energy transformation and metabolite conversion in most eukaryotes. Plant mitochondrial electron transport chains are particularly flexible, featuring components that can bypass proton translocation steps, such as ALTERNATIVE NAD(P)H DEHYDROGENASES and ALTERNATIVE OXIDASES (AOXs). PLANT UNCOUPLING MITOCHONDRIAL PROTEINS (PUMPs or plant UNCOUPLING PROTEINS [UCPs]) have been identified in plants as homologs of mammalian UCPs, and their physiological roles have been investigated in the context of mitochondrial energy metabolism. To dissect UCP function in Arabidopsis (Arabidopsis thaliana), the 2 most conserved family members, UCP1 and UCP2, have been genetically ablated assuming that they both reside in the inner mitochondrial membrane. Yet, contradicting results have been reported on plant UCP2 localization. After UCP1 (Maia et al. 1998) and UCP2 (Watanabe et al. 1999) were identified as plant homologs of mammalian UCP1, 6 Arabidopsis isogenes were named PUMP1 to PUMP6 (Borecký et al. 2006). However, PUMP4 to PUMP6 exhibit properties typical of the phylogenetically related mitochondrial dicarboxylate carrier (DIC) proteins (Palmieri et al. 2008). Accordingly, PUMPs were regrouped into plant UCP1 to UCP3 and plant DIC1 to DIC3 (Supplemental Fig. S1) (Palmieri et al. 2008). UCP1 and UCP2 are highly similar in sequence and share 72\% amino acid identity (Supplemental Fig. S2A) (Monné et al. 2018). We provide evidence that UCP2 localizes to the Golgi unlike UCP1, which localizes to the mitochondria, and we provide perspectives on UCP protein function, Golgi membrane transport, and subcellular targeting principles of membrane proteins.}, number = {2}, urldate = {2024-02-02}, journal = {Plant Physiology}, author = {Fuchs, Philippe and Feixes-Prats, Elisenda and Arruda, Paulo and Feitosa-Araújo, Elias and Fernie, Alisdair R and Grefen, Christopher and Lichtenauer, Sophie and Linka, Nicole and de Godoy Maia, Ivan and Meyer, Andreas J and Schilasky, Sören and Sweetlove, Lee J and Wege, Stefanie and Weber, Andreas P M and Millar, A Harvey and Keech, Olivier and Florez-Sarasa, Igor and Barreto, Pedro and Schwarzländer, Markus}, month = feb, year = {2024}, pages = {623--628}, }
Mitochondria act as cellular hubs of energy transformation and metabolite conversion in most eukaryotes. Plant mitochondrial electron transport chains are particularly flexible, featuring components that can bypass proton translocation steps, such as ALTERNATIVE NAD(P)H DEHYDROGENASES and ALTERNATIVE OXIDASES (AOXs). PLANT UNCOUPLING MITOCHONDRIAL PROTEINS (PUMPs or plant UNCOUPLING PROTEINS [UCPs]) have been identified in plants as homologs of mammalian UCPs, and their physiological roles have been investigated in the context of mitochondrial energy metabolism. To dissect UCP function in Arabidopsis (Arabidopsis thaliana), the 2 most conserved family members, UCP1 and UCP2, have been genetically ablated assuming that they both reside in the inner mitochondrial membrane. Yet, contradicting results have been reported on plant UCP2 localization. After UCP1 (Maia et al. 1998) and UCP2 (Watanabe et al. 1999) were identified as plant homologs of mammalian UCP1, 6 Arabidopsis isogenes were named PUMP1 to PUMP6 (Borecký et al. 2006). However, PUMP4 to PUMP6 exhibit properties typical of the phylogenetically related mitochondrial dicarboxylate carrier (DIC) proteins (Palmieri et al. 2008). Accordingly, PUMPs were regrouped into plant UCP1 to UCP3 and plant DIC1 to DIC3 (Supplemental Fig. S1) (Palmieri et al. 2008). UCP1 and UCP2 are highly similar in sequence and share 72% amino acid identity (Supplemental Fig. S2A) (Monné et al. 2018). We provide evidence that UCP2 localizes to the Golgi unlike UCP1, which localizes to the mitochondria, and we provide perspectives on UCP protein function, Golgi membrane transport, and subcellular targeting principles of membrane proteins.
Whole-genome resequencing facilitates the development of a 50K single nucleotide polymorphism genotyping array for Scots pine (Pinus sylvestris L.) and its transferability to other pine species.
Estravis Barcala, M., van der Valk, T., Chen, Z., Funda, T., Chaudhary, R., Klingberg, A., Fundova, I., Suontama, M., Hallingbäck, H., Bernhardsson, C., Nystedt, B., Ingvarsson, P. K., Sherwood, E., Street, N., Gyllensten, U., Nilsson, O., & Wu, H. X.
The Plant Journal, 117(3): 944–955. 2024.
_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1111/tpj.16535
Paper doi link bibtex abstract
Paper doi link bibtex abstract
@article{estravis_barcala_whole-genome_2024, title = {Whole-genome resequencing facilitates the development of a {50K} single nucleotide polymorphism genotyping array for {Scots} pine ({Pinus} sylvestris {L}.) and its transferability to other pine species}, volume = {117}, copyright = {© 2023 The Authors. The Plant Journal published by Society for Experimental Biology and John Wiley \& Sons Ltd.}, issn = {1365-313X}, url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/tpj.16535}, doi = {10.1111/tpj.16535}, abstract = {Scots pine (Pinus sylvestris L.) is one of the most widespread and economically important conifer species in the world. Applications like genomic selection and association studies, which could help accelerate breeding cycles, are challenging in Scots pine because of its large and repetitive genome. For this reason, genotyping tools for conifer species, and in particular for Scots pine, are commonly based on transcribed regions of the genome. In this article, we present the Axiom Psyl50K array, the first single nucleotide polymorphism (SNP) genotyping array for Scots pine based on whole-genome resequencing, that represents both genic and intergenic regions. This array was designed following a two-step procedure: first, 192 trees were sequenced, and a 430K SNP screening array was constructed. Then, 480 samples, including haploid megagametophytes, full-sib family trios, breeding population, and range-wide individuals from across Eurasia were genotyped with the screening array. The best 50K SNPs were selected based on quality, replicability, distribution across the draft genome assembly, balance between genic and intergenic regions, and genotype–environment and genotype–phenotype associations. Of the final 49 877 probes tiled in the array, 20 372 (40.84\%) occur inside gene models, while the rest lie in intergenic regions. We also show that the Psyl50K array can yield enough high-confidence SNPs for genetic studies in pine species from North America and Eurasia. This new genotyping tool will be a valuable resource for high-throughput fundamental and applied research of Scots pine and other pine species.}, language = {en}, number = {3}, urldate = {2024-02-02}, journal = {The Plant Journal}, author = {Estravis Barcala, Maximiliano and van der Valk, Tom and Chen, Zhiqiang and Funda, Tomas and Chaudhary, Rajiv and Klingberg, Adam and Fundova, Irena and Suontama, Mari and Hallingbäck, Henrik and Bernhardsson, Carolina and Nystedt, Björn and Ingvarsson, Pär K. and Sherwood, Ellen and Street, Nathaniel and Gyllensten, Ulf and Nilsson, Ove and Wu, Harry X.}, year = {2024}, note = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1111/tpj.16535}, keywords = {Pinus sylvestris, SNP array, genome resequencing, genome-wide association studies, genomic selection, pines}, pages = {944--955}, }
Scots pine (Pinus sylvestris L.) is one of the most widespread and economically important conifer species in the world. Applications like genomic selection and association studies, which could help accelerate breeding cycles, are challenging in Scots pine because of its large and repetitive genome. For this reason, genotyping tools for conifer species, and in particular for Scots pine, are commonly based on transcribed regions of the genome. In this article, we present the Axiom Psyl50K array, the first single nucleotide polymorphism (SNP) genotyping array for Scots pine based on whole-genome resequencing, that represents both genic and intergenic regions. This array was designed following a two-step procedure: first, 192 trees were sequenced, and a 430K SNP screening array was constructed. Then, 480 samples, including haploid megagametophytes, full-sib family trios, breeding population, and range-wide individuals from across Eurasia were genotyped with the screening array. The best 50K SNPs were selected based on quality, replicability, distribution across the draft genome assembly, balance between genic and intergenic regions, and genotype–environment and genotype–phenotype associations. Of the final 49 877 probes tiled in the array, 20 372 (40.84%) occur inside gene models, while the rest lie in intergenic regions. We also show that the Psyl50K array can yield enough high-confidence SNPs for genetic studies in pine species from North America and Eurasia. This new genotyping tool will be a valuable resource for high-throughput fundamental and applied research of Scots pine and other pine species.
Genomic basis of seed colour in quinoa inferred from variant patterns using extreme gradient boosting.
Sandell, F. L., Holzweber, T., Street, N. R., Dohm, J. C., & Himmelbauer, H.
Plant Biotechnology Journal. January 2024.
_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1111/pbi.14267
Paper doi link bibtex abstract
Paper doi link bibtex abstract
@article{sandell_genomic_2024, title = {Genomic basis of seed colour in quinoa inferred from variant patterns using extreme gradient boosting}, copyright = {© 2024 The Authors. Plant Biotechnology Journal published by Society for Experimental Biology and The Association of Applied Biologists and John Wiley \& Sons Ltd.}, issn = {1467-7652}, url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/pbi.14267}, doi = {10.1111/pbi.14267}, abstract = {Quinoa is an agriculturally important crop species originally domesticated in the Andes of central South America. One of its most important phenotypic traits is seed colour. Seed colour variation is determined by contrasting abundance of betalains, a class of strong antioxidant and free radicals scavenging colour pigments only found in plants of the order Caryophyllales. However, the genetic basis for these pigments in seeds remains to be identified. Here we demonstrate the application of machine learning (extreme gradient boosting) to identify genetic variants predictive of seed colour. We show that extreme gradient boosting outperforms the classical genome-wide association approach. We provide re-sequencing and phenotypic data for 156 South American quinoa accessions and identify candidate genes potentially controlling betalain content in quinoa seeds. Genes identified include novel cytochrome P450 genes and known members of the betalain synthesis pathway, as well as genes annotated as being involved in seed development. Our work showcases the power of modern machine learning methods to extract biologically meaningful information from large sequencing data sets.}, language = {en}, urldate = {2024-01-19}, journal = {Plant Biotechnology Journal}, author = {Sandell, Felix L. and Holzweber, Thomas and Street, Nathaniel R. and Dohm, Juliane C. and Himmelbauer, Heinz}, month = jan, year = {2024}, note = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1111/pbi.14267}, keywords = {betalain synthesis pathway, genome sequencing, genotype-phenotype relationships, machine learning, quinoa, seed colour}, }
Quinoa is an agriculturally important crop species originally domesticated in the Andes of central South America. One of its most important phenotypic traits is seed colour. Seed colour variation is determined by contrasting abundance of betalains, a class of strong antioxidant and free radicals scavenging colour pigments only found in plants of the order Caryophyllales. However, the genetic basis for these pigments in seeds remains to be identified. Here we demonstrate the application of machine learning (extreme gradient boosting) to identify genetic variants predictive of seed colour. We show that extreme gradient boosting outperforms the classical genome-wide association approach. We provide re-sequencing and phenotypic data for 156 South American quinoa accessions and identify candidate genes potentially controlling betalain content in quinoa seeds. Genes identified include novel cytochrome P450 genes and known members of the betalain synthesis pathway, as well as genes annotated as being involved in seed development. Our work showcases the power of modern machine learning methods to extract biologically meaningful information from large sequencing data sets.
eSoil: A low-power bioelectronic growth scaffold that enhances crop seedling growth.
Oikonomou, V. K., Huerta, M., Sandéhn, A., Dreier, T., Daguerre, Y., Lim, H., Berggren, M., Pavlopoulou, E., Näsholm, T., Bech, M., & Stavrinidou, E.
Proceedings of the National Academy of Sciences, 121(2): e2304135120. January 2024.
Publisher: Proceedings of the National Academy of Sciences
Paper doi link bibtex abstract
Paper doi link bibtex abstract
@article{oikonomou_esoil_2024, title = {{eSoil}: {A} low-power bioelectronic growth scaffold that enhances crop seedling growth}, volume = {121}, shorttitle = {{eSoil}}, url = {https://www.pnas.org/doi/10.1073/pnas.2304135120}, doi = {10.1073/pnas.2304135120}, abstract = {Active hydroponic substrates that stimulate on demand the plant growth have not been demonstrated so far. Here, we developed the eSoil, a low-power bioelectronic growth scaffold that can provide electrical stimulation to the plants’ root system and growth environment in hydroponics settings. eSoil’s active material is an organic mixed ionic electronic conductor while its main structural component is cellulose, the most abundant biopolymer. We demonstrate that barley seedlings that are widely used for fodder grow within the eSoil with the root system integrated within its porous matrix. Simply by polarizing the eSoil, seedling growth is accelerated resulting in increase of dry weight on average by 50\% after 15 d of growth. The effect is evident both on root and shoot development and occurs during the growth period after the stimulation. The stimulated plants reduce and assimilate NO3− more efficiently than controls, a finding that may have implications on minimizing fertilizer use. However, more studies are required to provide a mechanistic understanding of the physical and biological processes involved. eSoil opens the pathway for the development of active hydroponic scaffolds that may increase crop yield in a sustainable manner.}, number = {2}, urldate = {2023-12-29}, journal = {Proceedings of the National Academy of Sciences}, author = {Oikonomou, Vasileios K. and Huerta, Miriam and Sandéhn, Alexandra and Dreier, Till and Daguerre, Yohann and Lim, Hyungwoo and Berggren, Magnus and Pavlopoulou, Eleni and Näsholm, Torgny and Bech, Martin and Stavrinidou, Eleni}, month = jan, year = {2024}, note = {Publisher: Proceedings of the National Academy of Sciences}, pages = {e2304135120}, }
Active hydroponic substrates that stimulate on demand the plant growth have not been demonstrated so far. Here, we developed the eSoil, a low-power bioelectronic growth scaffold that can provide electrical stimulation to the plants’ root system and growth environment in hydroponics settings. eSoil’s active material is an organic mixed ionic electronic conductor while its main structural component is cellulose, the most abundant biopolymer. We demonstrate that barley seedlings that are widely used for fodder grow within the eSoil with the root system integrated within its porous matrix. Simply by polarizing the eSoil, seedling growth is accelerated resulting in increase of dry weight on average by 50% after 15 d of growth. The effect is evident both on root and shoot development and occurs during the growth period after the stimulation. The stimulated plants reduce and assimilate NO3− more efficiently than controls, a finding that may have implications on minimizing fertilizer use. However, more studies are required to provide a mechanistic understanding of the physical and biological processes involved. eSoil opens the pathway for the development of active hydroponic scaffolds that may increase crop yield in a sustainable manner.
Quantitative and qualitative saccharide analysis of North Atlantic brown seaweed by gas chromatography/mass spectrometry and infrared spectroscopy.
Niemi, C., Takahashi, J., Gorzsás, A., & Gentili, F. G.
International Journal of Biological Macromolecules, 254: 127870. January 2024.
Paper doi link bibtex abstract
Paper doi link bibtex abstract
@article{niemi_quantitative_2024, title = {Quantitative and qualitative saccharide analysis of {North} {Atlantic} brown seaweed by gas chromatography/mass spectrometry and infrared spectroscopy}, volume = {254}, issn = {0141-8130}, url = {https://www.sciencedirect.com/science/article/pii/S0141813023047694}, doi = {10.1016/j.ijbiomac.2023.127870}, abstract = {Brown seaweeds contain a variety of saccharides which have potential industrial uses. The most abundant polysaccharide in brown seaweed is typically alginate, consisting of mannuronic (M) and guluronic acid (G). The ratio of these residues fundamentally determines the physicochemical properties of alginate. In the present study, gas chromatography/mass spectrometry (GC/MS) was used to give a detailed breakdown of the monosaccharide species in North Atlantic brown seaweeds. The anthrone method was used for determination of crystalline cellulose. The experimental data was used to calibrate multivariate prediction models for estimation of total carbohydrates, crystalline cellulose, total alginate and alginate M/G ratio directly in dried, brown seaweed using three types of infrared spectroscopy, using relative error (RE) as a measure of predictive accuracy. Diffuse reflectance infrared Fourier transform spectroscopy (DRIFTS) performed well for the estimation of total alginate (RE = 0.12, R2 = 0.82), and attenuated total reflectance (ATR) showed good prediction of M/G ratio (RE = 0.14, R2 = 0.86). Both DRIFTS, ATR and near infrared (NIR) were unable to predict crystalline cellulose and only DRIFTS performed better in determining total carbohydrates. Multivariate spectral analysis is a promising method for easy and rapid characterization of alginate and M/G ratio in seaweed.}, urldate = {2023-11-17}, journal = {International Journal of Biological Macromolecules}, author = {Niemi, Calle and Takahashi, Junko and Gorzsás, András and Gentili, Francesco G.}, month = jan, year = {2024}, keywords = {Alginate, FTIR, GC/MS, MG ratio, North Atlantic brown seaweed}, pages = {127870}, }
Brown seaweeds contain a variety of saccharides which have potential industrial uses. The most abundant polysaccharide in brown seaweed is typically alginate, consisting of mannuronic (M) and guluronic acid (G). The ratio of these residues fundamentally determines the physicochemical properties of alginate. In the present study, gas chromatography/mass spectrometry (GC/MS) was used to give a detailed breakdown of the monosaccharide species in North Atlantic brown seaweeds. The anthrone method was used for determination of crystalline cellulose. The experimental data was used to calibrate multivariate prediction models for estimation of total carbohydrates, crystalline cellulose, total alginate and alginate M/G ratio directly in dried, brown seaweed using three types of infrared spectroscopy, using relative error (RE) as a measure of predictive accuracy. Diffuse reflectance infrared Fourier transform spectroscopy (DRIFTS) performed well for the estimation of total alginate (RE = 0.12, R2 = 0.82), and attenuated total reflectance (ATR) showed good prediction of M/G ratio (RE = 0.14, R2 = 0.86). Both DRIFTS, ATR and near infrared (NIR) were unable to predict crystalline cellulose and only DRIFTS performed better in determining total carbohydrates. Multivariate spectral analysis is a promising method for easy and rapid characterization of alginate and M/G ratio in seaweed.
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