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Intermittent cell division dynamics in regenerating Arabidopsis roots reveals complex long-range interactions. 拟南芥根系再生过程中间歇性细胞分裂动力学揭示了复杂的远程相互作用。
Quantitative plant biology Pub Date : 2024-09-04 eCollection Date: 2024-01-01 DOI: 10.1017/qpb.2024.7
T Fallesen, S Amarteifio, G Pruessner, H J Jensen, G Sena
{"title":"Intermittent cell division dynamics in regenerating Arabidopsis roots reveals complex long-range interactions.","authors":"T Fallesen, S Amarteifio, G Pruessner, H J Jensen, G Sena","doi":"10.1017/qpb.2024.7","DOIUrl":"https://doi.org/10.1017/qpb.2024.7","url":null,"abstract":"<p><p>In this work, we present a quantitative comparison of the cell division dynamics between populations of intact and regenerating root tips in the plant model system <i>Arabidopsis thaliana.</i> To achieve the required temporal resolution and to sustain it for the duration of the regeneration process, we adopted a live imaging system based on light-sheet fluorescence microscopy, previously developed in the laboratory. We offer a straightforward quantitative analysis of the temporal and spatial patterns of cell division events showing a statistically significant difference in the frequency of mitotic events and spatial separation of mitotic event clusters between intact and regenerating roots.</p>","PeriodicalId":101358,"journal":{"name":"Quantitative plant biology","volume":"5 ","pages":"e7"},"PeriodicalIF":0.0,"publicationDate":"2024-09-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11706681/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142961002","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Homeostats: The hidden rulers of ion homeostasis in plants. 平衡器：植物体内离子平衡的隐藏统治者。
Quantitative plant biology Pub Date : 2024-09-03 eCollection Date: 2024-01-01 DOI: 10.1017/qpb.2024.8
Ingo Dreyer, Naomí Hernández-Rojas, Yasnaya Bolua-Hernández, Valentina de Los Angeles Tapia-Castillo, Sadith Z Astola-Mariscal, Erbio Díaz-Pico, Franko Mérida-Quesada, Fernando Vergara-Valladares, Oscar Arrey-Salas, María E Rubio-Meléndez, Janin Riedelsberger, Erwan Michard
{"title":"Homeostats: The hidden rulers of ion homeostasis in plants.","authors":"Ingo Dreyer, Naomí Hernández-Rojas, Yasnaya Bolua-Hernández, Valentina de Los Angeles Tapia-Castillo, Sadith Z Astola-Mariscal, Erbio Díaz-Pico, Franko Mérida-Quesada, Fernando Vergara-Valladares, Oscar Arrey-Salas, María E Rubio-Meléndez, Janin Riedelsberger, Erwan Michard","doi":"10.1017/qpb.2024.8","DOIUrl":"https://doi.org/10.1017/qpb.2024.8","url":null,"abstract":"<p><p>Ion homeostasis is a crucial process in plants that is closely linked to the efficiency of nutrient uptake, stress tolerance and overall plant growth and development. Nevertheless, our understanding of the fundamental processes of ion homeostasis is still incomplete and highly fragmented. Especially at the mechanistic level, we are still in the process of dissecting physiological systems to analyse the different parts in isolation. However, modelling approaches have shown that it is not individual transporters but rather transporter networks (homeostats) that control membrane transport and associated homeostatic processes in plant cells. To facilitate access to such theoretical approaches, the modelling of the potassium homeostat is explained here in detail to serve as a blueprint for other homeostats. The unbiased approach provided strong arguments for the abundant existence of electroneutral H<sup>+</sup>/K<sup>+</sup> antiporters in plants.</p>","PeriodicalId":101358,"journal":{"name":"Quantitative plant biology","volume":"5 ","pages":"e8"},"PeriodicalIF":0.0,"publicationDate":"2024-09-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11706688/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142960999","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Beyond stomatal development: SMF transcription factors as versatile toolkits for land plant evolution. 超越气孔发育：SMF 转录因子是陆生植物进化的多功能工具包。
Quantitative plant biology Pub Date : 2024-05-31 eCollection Date: 2024-01-01 DOI: 10.1017/qpb.2024.6
Yuki Doll, Hiroyuki Koga, Hirokazu Tsukaya
{"title":"Beyond stomatal development: SMF transcription factors as versatile toolkits for land plant evolution.","authors":"Yuki Doll, Hiroyuki Koga, Hirokazu Tsukaya","doi":"10.1017/qpb.2024.6","DOIUrl":"10.1017/qpb.2024.6","url":null,"abstract":"<p><p>As master transcription factors of stomatal development, SPEECHLESS, MUTE, and FAMA, collectively termed SMFs, are primary targets of molecular genetic analyses in the model plant <i>Arabidopsis thaliana</i>. Studies in other model systems identified SMF orthologs as key players in evolutionary developmental biology studies on stomata. However, recent studies on the astomatous liverwort <i>Marchantia polymorpha</i> revealed that the functions of these genes are not limited to the stomatal development, but extend to other types of tissues, namely sporophytic setal and gametophytic epidermal tissues. These studies provide insightful examples of gene-regulatory network co-opting, and highlight SMFs and related transcription factors as general toolkits for novel trait evolution in land plant lineages. Here, we critically review recent literature on the SMF-like gene in <i>M. polymorpha</i> and discuss their implications for plant evolutionary biology.</p>","PeriodicalId":101358,"journal":{"name":"Quantitative plant biology","volume":"5 ","pages":"e6"},"PeriodicalIF":0.0,"publicationDate":"2024-05-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11363000/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142116757","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Mechanically induced localisation of SECONDARY WALL INTERACTING bZIP is associated with thigmomorphogenic and secondary cell wall gene expression. 机械诱导的次生细胞壁互作蛋白 bZIP 的定位与植株形态和次生细胞壁基因的表达有关。
Quantitative plant biology Pub Date : 2024-05-03 eCollection Date: 2024-01-01 DOI: 10.1017/qpb.2024.5
Joshua H Coomey, Kirk J-M MacKinnon, Ian W McCahill, Bahman Khahani, Pubudu P Handakumbura, Gina M Trabucco, Jessica Mazzola, Nicole A Leblanc, Rithany Kheam, Miriam Hernandez-Romero, Kerrie Barry, Lifeng Liu, Ji E Lee, John P Vogel, Ronan C O'Malley, James J Chambers, Samuel P Hazen
{"title":"Mechanically induced localisation of SECONDARY WALL INTERACTING bZIP is associated with thigmomorphogenic and secondary cell wall gene expression.","authors":"Joshua H Coomey, Kirk J-M MacKinnon, Ian W McCahill, Bahman Khahani, Pubudu P Handakumbura, Gina M Trabucco, Jessica Mazzola, Nicole A Leblanc, Rithany Kheam, Miriam Hernandez-Romero, Kerrie Barry, Lifeng Liu, Ji E Lee, John P Vogel, Ronan C O'Malley, James J Chambers, Samuel P Hazen","doi":"10.1017/qpb.2024.5","DOIUrl":"10.1017/qpb.2024.5","url":null,"abstract":"<p><p>Plant growth requires the integration of internal and external cues, perceived and transduced into a developmental programme of cell division, elongation and wall thickening. Mechanical forces contribute to this regulation, and thigmomorphogenesis typically includes reducing stem height, increasing stem diameter, and a canonical transcriptomic response. We present data on a bZIP transcription factor involved in this process in grasses. <i>Brachypodium distachyon</i> SECONDARY WALL INTERACTING bZIP (SWIZ) protein translocated into the nucleus following mechanostimulation. Classical touch-responsive genes were upregulated in <i>B. distachyon</i> roots following touch, including significant induction of the glycoside hydrolase 17 family, which may be unique to grass thigmomorphogenesis. SWIZ protein binding to an E-box variant in exons and introns was associated with immediate activation followed by repression of gene expression. <i>SWIZ</i> overexpression resulted in plants with reduced stem and root elongation. These data further define plant touch-responsive transcriptomics and physiology, offering insights into grass mechanotranduction dynamics.</p>","PeriodicalId":101358,"journal":{"name":"Quantitative plant biology","volume":"5 ","pages":"e5"},"PeriodicalIF":0.0,"publicationDate":"2024-05-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11106548/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141077406","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
A coordinated switch in sucrose and callose metabolism enables enhanced symplastic unloading in potato tubers. 蔗糖和胼胝质新陈代谢的协调转换可增强马铃薯块茎的交错卸载能力。
Quantitative plant biology Pub Date : 2024-04-17 eCollection Date: 2024-01-01 DOI: 10.1017/qpb.2024.4
Bas van den Herik, Sara Bergonzi, Yingji Li, Christian W Bachem, Kirsten H Ten Tusscher
{"title":"A coordinated switch in sucrose and callose metabolism enables enhanced symplastic unloading in potato tubers.","authors":"Bas van den Herik, Sara Bergonzi, Yingji Li, Christian W Bachem, Kirsten H Ten Tusscher","doi":"10.1017/qpb.2024.4","DOIUrl":"https://doi.org/10.1017/qpb.2024.4","url":null,"abstract":"<p><p>One of the early changes upon tuber induction is the switch from apoplastic to symplastic unloading. Whether and how this change in unloading mode contributes to sink strength has remained unclear. In addition, developing tubers also change from energy to storage-based sucrose metabolism. Here, we investigated the coordination between changes in unloading mode and sucrose metabolism and their relative role in tuber sink strength by looking into callose and sucrose metabolism gene expression combined with a model of apoplastic and symplastic unloading. Gene expression analysis suggests that callose deposition in tubers is decreased by lower callose synthase expression. Furthermore, changes in callose and sucrose metabolism are strongly correlated, indicating a well-coordinated developmental switch. Modelling indicates that symplastic unloading is not the most efficient unloading mode per se. Instead, it is the concurrent metabolic switch that provides the physiological conditions necessary to potentiate symplastic transport and thereby enhance tuber sink strength .</p>","PeriodicalId":101358,"journal":{"name":"Quantitative plant biology","volume":"5 ","pages":"e4"},"PeriodicalIF":0.0,"publicationDate":"2024-04-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11058582/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140875119","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Debunking the idea of biological optimisation: quantitative biology to the rescue 驳斥生物优化理念：定量生物学的救星
Quantitative plant biology Pub Date : 2024-04-03 DOI: 10.1017/qpb.2024.3
Olivier Hamant
{"title":"Debunking the idea of biological optimisation: quantitative biology to the rescue","authors":"Olivier Hamant","doi":"10.1017/qpb.2024.3","DOIUrl":"https://doi.org/10.1017/qpb.2024.3","url":null,"abstract":"The idea that plants would be efficient, frugal or optimised echoes the recurrent semantics of ‘blueprint’ and ‘program’ in molecular genetics. However, when analysing plants with quantitative approaches and systems thinking, we instead find that plants are the results of stochastic processes with many inefficiencies, incoherence or delays fuelling their robustness. If one had to highlight the main value of quantitative biology, this could be it: plants are robust systems because they are not efficient. Such systemic insights extend to the way we conduct plant research and opens plant science publication to a much broader framework.","PeriodicalId":101358,"journal":{"name":"Quantitative plant biology","volume":"53 9","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-04-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140747962","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
The Arabidopsis leaf quantitative atlas: a cellular and subcellular mapping through unified data integration. 拟南芥叶片定量图谱：通过统一数据整合绘制细胞和亚细胞图谱。
Quantitative plant biology Pub Date : 2024-02-29 eCollection Date: 2024-01-01 DOI: 10.1017/qpb.2024.1
Dimitri Tolleter, Edward N Smith, Clémence Dupont-Thibert, Clarisse Uwizeye, Denis Vile, Pauline Gloaguen, Denis Falconet, Giovanni Finazzi, Yves Vandenbrouck, Gilles Curien
{"title":"The Arabidopsis leaf quantitative atlas: a cellular and subcellular mapping through unified data integration.","authors":"Dimitri Tolleter, Edward N Smith, Clémence Dupont-Thibert, Clarisse Uwizeye, Denis Vile, Pauline Gloaguen, Denis Falconet, Giovanni Finazzi, Yves Vandenbrouck, Gilles Curien","doi":"10.1017/qpb.2024.1","DOIUrl":"https://doi.org/10.1017/qpb.2024.1","url":null,"abstract":"<p><p>Quantitative analyses and models are required to connect a plant's cellular organisation with its metabolism. However, quantitative data are often scattered over multiple studies, and finding such data and converting them into useful information is time-consuming. Consequently, there is a need to centralise the available data and to highlight the remaining knowledge gaps. Here, we present a step-by-step approach to manually extract quantitative data from various information sources, and to unify the data format. First, data from Arabidopsis leaf were collated, checked for consistency and correctness and curated by cross-checking sources. Second, quantitative data were combined by applying calculation rules. They were then integrated into a unique comprehensive, referenced, modifiable and reusable data compendium representing an Arabidopsis reference leaf. This atlas contains the metrics of the 15 cell types found in leaves at the cellular and subcellular levels.</p>","PeriodicalId":101358,"journal":{"name":"Quantitative plant biology","volume":"5 ","pages":"e2"},"PeriodicalIF":0.0,"publicationDate":"2024-02-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10988163/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140874274","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Quantitative analysis of lateral root development with time-lapse imaging and deep neural network. 利用延时成像和深度神经网络对侧根发育进行定量分析。
Quantitative plant biology Pub Date : 2024-02-13 eCollection Date: 2024-01-01 DOI: 10.1017/qpb.2024.2
Yuta Uemura, Hironaka Tsukagoshi
{"title":"Quantitative analysis of lateral root development with time-lapse imaging and deep neural network.","authors":"Yuta Uemura, Hironaka Tsukagoshi","doi":"10.1017/qpb.2024.2","DOIUrl":"10.1017/qpb.2024.2","url":null,"abstract":"<p><p>During lateral root (LR) development, morphological alteration of the developing single LR primordium occurs continuously. Precise observation of this continuous alteration is important for understanding the mechanism involved in single LR development. Recently, we reported that very long-chain fatty acids are important signalling molecules that regulate LR development. In the study, we developed an efficient method to quantify the transition of single LR developmental stages using time-lapse imaging followed by a deep neural network (DNN) analysis. In this 'insight' paper, we discuss our DNN method and the importance of time-lapse imaging in studies on plant development. Integrating DNN analysis and imaging is a powerful technique for the quantification of the timing of the transition of organ morphology; it can become an important method to elucidate spatiotemporal molecular mechanisms in plant development.</p>","PeriodicalId":101358,"journal":{"name":"Quantitative plant biology","volume":"5 ","pages":"e1"},"PeriodicalIF":0.0,"publicationDate":"2024-02-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10877138/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139935030","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
A blast from the past: Understanding stem cell specification in plant roots using laser ablation. 来自过去的冲击:利用激光消融了解植物根部的干细胞规格。
Quantitative plant biology Pub Date : 2023-11-28 eCollection Date: 2023-01-01 DOI: 10.1017/qpb.2023.13
Wouter Smet, Ikram Blilou
{"title":"A blast from the past: Understanding stem cell specification in plant roots using laser ablation.","authors":"Wouter Smet, Ikram Blilou","doi":"10.1017/qpb.2023.13","DOIUrl":"10.1017/qpb.2023.13","url":null,"abstract":"<p><p>In the Arabidopsis root, growth is sustained by the meristem. Signalling from organiser cells, also termed the quiescent centre (QC), is essential for the maintenance and replenishment of the stem cells. Here, we highlight three publications from the founder of the concept of the stem cell niche in Arabidopsis and a pioneer in unravelling regulatory modules governing stem cell specification and maintenance, as well as tissue patterning in the root meristem: Ben Scheres. His research has tremendously impacted the plant field. We have selected three publications from the Scheres legacy, which can be considered a breakthrough in the field of plant developmental biology. van den Berg et al. (1995) and van den Berg et al. (1997) uncovered that positional information-directed patterning. Sabatini et al. (1999), discovered that auxin maxima determine tissue patterning and polarity. We describe how simple but elegant experimental designs have provided the foundation of our current understanding of the functioning of the root meristem.</p>","PeriodicalId":101358,"journal":{"name":"Quantitative plant biology","volume":"4 ","pages":"e14"},"PeriodicalIF":0.0,"publicationDate":"2023-11-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10685261/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"138465308","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
The 1991 review by Coen and Meyerowitz on the war of the whorls and the ABC model of floral organ identity. 1991年Coen和Meyerowitz对妓女之战和花器官身份的ABC模型的评论。
Quantitative plant biology Pub Date : 2023-10-23 eCollection Date: 2023-01-01 DOI: 10.1017/qpb.2023.12
Kay Schneitz
{"title":"The 1991 review by Coen and Meyerowitz on the war of the whorls and the ABC model of floral organ identity.","authors":"Kay Schneitz","doi":"10.1017/qpb.2023.12","DOIUrl":"https://doi.org/10.1017/qpb.2023.12","url":null,"abstract":"<p><p>The 1991 review paper by Coen and Meyerowitz on the control of floral organ development set out the evidence available at that time, which led to the now famous ABC model of floral organ identity control. The authors summarised the genetic and molecular analyses that had been carried out in a relatively short time by several laboratories, mainly in <i>Arabidopsis thaliana</i> and <i>Antirrhinum majus</i>. The work was a successful example of how systematic genetic and molecular analysis can decipher the mechanism that controls a developmental process in plants. The ABC model is a combinatorial model in which each floral whorl acquires its identity through a unique combination of floral homeotic gene activities. The review also highlights the similarities in the regulation of floral organ identity between evolutionarily distant plant species, emphasising the general relevance of the model and paving the way for comprehensive studies of the evolution of floral diversity.</p>","PeriodicalId":101358,"journal":{"name":"Quantitative plant biology","volume":"4 ","pages":"e13"},"PeriodicalIF":0.0,"publicationDate":"2023-10-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10600569/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"71416521","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
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