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Quantitative plant biology最新文献

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Synthetic gene circuits in plants: recent advances and challenges. 植物合成基因回路：最新进展与挑战。
Quantitative plant biology Pub Date : 2025-02-27 eCollection Date: 2025-01-01 DOI: 10.1017/qpb.2025.3
Adil Khan, Ryan Lister
{"title":"Synthetic gene circuits in plants: recent advances and challenges.","authors":"Adil Khan, Ryan Lister","doi":"10.1017/qpb.2025.3","DOIUrl":"10.1017/qpb.2025.3","url":null,"abstract":"<p><p>Plant synthetic biology is a rapidly advancing multidisciplinary research area that applies engineering principles to design, construct, and implement new plant capabilities at the molecular, cellular, and whole organism scales. Synthetic gene circuits are important tools for enabling increased customizability in the control of gene expression in plants, with widespread applications spanning new approaches for basic biology to introduction of new traits for advancing agriculture. In this review, we first aimed to provide a comprehensive understanding of synthetic circuits. Next, we discuss recent progress in the construction of advanced synthetic gene circuits in plants for programmable control of gene expression. Finally, we discuss the current challenges associated with developing and applying effective circuits while also highlighting future prospects and research directions, including quantitative measurement, high-throughput testing, and circuit modelling.</p>","PeriodicalId":101358,"journal":{"name":"Quantitative plant biology","volume":"6 ","pages":"e6"},"PeriodicalIF":0.0,"publicationDate":"2025-02-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11894408/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143607676","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
Cellular calcium homeostasis and regulation of its dynamic perturbation. 细胞钙稳态及其动态扰动的调控。
Quantitative plant biology Pub Date : 2025-02-14 eCollection Date: 2025-01-01 DOI: 10.1017/qpb.2025.2
Colin Brownlee, Glen L Wheeler
{"title":"Cellular calcium homeostasis and regulation of its dynamic perturbation.","authors":"Colin Brownlee, Glen L Wheeler","doi":"10.1017/qpb.2025.2","DOIUrl":"10.1017/qpb.2025.2","url":null,"abstract":"<p><p>Calcium ions (Ca<sup>2+</sup>) play pivotal roles in a host of cellular signalling processes. The requirement to maintain resting cytosolic Ca<sup>2+</sup> levels in the 100-200 nM range provides a baseline for dynamic excursions from resting levels that determine the nature of many physiological responses to external stimuli and developmental processes. This review provides an overview of the key components of the Ca<sup>2+</sup> homeostatic machinery, including known channel-mediated Ca<sup>2+</sup> entry pathways along with transporters that act to shape the cytosolic Ca<sup>2+</sup> signature. The relative roles of the vacuole and endoplasmic reticulum as sources or sinks for cytosolic Ca<sup>2+</sup> are considered, highlighting significant gaps in our understanding. The components contributing to mitochondrial, chloroplast and nuclear Ca<sup>2+</sup> homeostasis and organellar Ca<sup>2+</sup> signals are also considered. Taken together, a complex picture of the cellular Ca<sup>2+</sup> homeostatic machinery emerges with some clear differences from mechanisms operating in many animal cells.</p>","PeriodicalId":101358,"journal":{"name":"Quantitative plant biology","volume":"6 ","pages":"e5"},"PeriodicalIF":0.0,"publicationDate":"2025-02-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11894410/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143607675","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
Why participatory plant research now? 为什么现在是参与式植物研究？
Quantitative plant biology Pub Date : 2025-02-13 eCollection Date: 2025-01-01 DOI: 10.1017/qpb.2024.20
Sofía Correa, Marie-Thérèse Charreyre, Olivier Hamant, Mathieu Thomas
{"title":"Why participatory plant research now?","authors":"Sofía Correa, Marie-Thérèse Charreyre, Olivier Hamant, Mathieu Thomas","doi":"10.1017/qpb.2024.20","DOIUrl":"10.1017/qpb.2024.20","url":null,"abstract":"<p><p>In the current polycrisis era, plant science, particularly when applied to agronomy, becomes instrumental: because our main substantial and renewable resource is plant biomass, many future solutions will depend on our ability to grow and transform plant material in a sustainable way. This also questions the way we conduct plant research and thus quantitative plant biology. In response to the increasing polarization between science and society, participatory plant research offers a pertinent framework. Far from moving away from quantitative approaches, participatory plant research builds on complexity associated with biology and situated knowledge. When researchers and citizens work together on societal issues, such friction becomes more fertile, quantitative questions become more complex, societal issues are addressed at their roots and outcomes often exceed that of top-down strategies. This article serves as an introduction to this ongoing bifurcation in plant science, using plant breeding as a key example.</p>","PeriodicalId":101358,"journal":{"name":"Quantitative plant biology","volume":"6 ","pages":"e4"},"PeriodicalIF":0.0,"publicationDate":"2025-02-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11894404/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143607677","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
Mobilization and recycling of intracellular phosphorus in response to availability. 细胞内磷的动员和再循环对有效性的响应。
Quantitative plant biology Pub Date : 2025-01-30 eCollection Date: 2025-01-01 DOI: 10.1017/qpb.2025.1
Chih-Pin Chiang, Joseph Yayen, Tzyy-Jen Chiou
{"title":"Mobilization and recycling of intracellular phosphorus in response to availability.","authors":"Chih-Pin Chiang, Joseph Yayen, Tzyy-Jen Chiou","doi":"10.1017/qpb.2025.1","DOIUrl":"10.1017/qpb.2025.1","url":null,"abstract":"<p><p>Phosphorus (P) is a non-renewable resource that limits plant productivity due to its low bioavailability in the soil. Large amounts of P fertilizer are required to sustain high yields, which is both inefficient and hazardous to the environment. Plants have evolved various adaptive responses to cope with low external P availability, including mobilizing cellular P through phosphate (P<sub>i</sub>) transporters and recycling P<sub>i</sub> from P-containing biomolecules to maintain cellular P homeostasis. This mini-review summarizes the current research on intracellular P recycling and mobilization in response to P availability. We introduce the roles of P<sub>i</sub> transporters and the P metabolic enzymes and expand on their gene regulation and mechanisms. The relevance of these processes in the search for targets to improve phosphorus use efficiency and some of the current challenges and gaps in our understanding of P starvation responses are discussed.</p>","PeriodicalId":101358,"journal":{"name":"Quantitative plant biology","volume":"6 ","pages":"e3"},"PeriodicalIF":0.0,"publicationDate":"2025-01-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11811851/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143412158","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
Microtubule flexibility, microtubule-based nucleation and ROP pattern co-alignment enhance protoxylem microtubule patterning. 微管的灵活性、基于微管的成核和 ROP 模式的共同对齐增强了原胚乳微管的模式化。
Quantitative plant biology Pub Date : 2025-01-27 eCollection Date: 2025-01-01 DOI: 10.1017/qpb.2024.17
Bas Jacobs, Marco Saltini, Jaap Molenaar, Laura Filion, Eva E Deinum
{"title":"Microtubule flexibility, microtubule-based nucleation and ROP pattern co-alignment enhance protoxylem microtubule patterning.","authors":"Bas Jacobs, Marco Saltini, Jaap Molenaar, Laura Filion, Eva E Deinum","doi":"10.1017/qpb.2024.17","DOIUrl":"10.1017/qpb.2024.17","url":null,"abstract":"<p><p>The development of the water transporting xylem tissue in plants involves an intricate interplay of Rho-of-Plants (ROP) proteins and cortical microtubules to generate highly functional secondary cell wall patterns, such as the ringed or spiral patterns in early-developing protoxylem. We study the requirements of protoxylem microtubule band formation with simulations in CorticalSim, extended to include finite microtubule persistence length and a novel algorithm for microtubule-based nucleation. We find that microtubule flexibility facilitates pattern formation for all realistic degrees of mismatch between array and pattern orientation. At the same time, flexibility leads to more density loss, both from collisions and the microtubule-hostile gap regions, making it harder to maintain microtubule bands. Microtubule-dependent nucleation helps to counteract this effect by gradually shifting nucleation from the gap regions to the bands as microtubules disappear from the gaps. Our results reveal mechanisms that can result in robust protoxylem band formation.</p>","PeriodicalId":101358,"journal":{"name":"Quantitative plant biology","volume":"6 ","pages":"e2"},"PeriodicalIF":0.0,"publicationDate":"2025-01-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11811878/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143412156","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 Turing heritage for plant biology: all spots and stripes? 图灵留给植物生物学的遗产：所有的斑点和条纹？
Quantitative plant biology Pub Date : 2025-01-13 eCollection Date: 2025-01-01 DOI: 10.1017/qpb.2024.16
Eric Siero, Eva E Deinum
{"title":"The Turing heritage for plant biology: all spots and stripes?","authors":"Eric Siero, Eva E Deinum","doi":"10.1017/qpb.2024.16","DOIUrl":"10.1017/qpb.2024.16","url":null,"abstract":"<p><p>In 'The chemical basis of morphogenesis' (1952), Alan Turing introduced an idea that revolutionised our thinking about pattern formation. He proposed that diffusion could lead to the spontaneous formation of regular patterns. Here, we discuss the impact of Turing's idea on plant science using three well-established examples at different scales: ROP patterning inside single cells, epidermal patterning across several cells and whole vegetation patterns. Also at intermediate levels, e.g., organ spacing, plants look surprisingly regular. But not all regular patterns are Turing patterns, careful observation and prediction of the patterning process-not just the final pattern-is critical to distinguish between mechanisms.</p>","PeriodicalId":101358,"journal":{"name":"Quantitative plant biology","volume":"6 ","pages":"e1"},"PeriodicalIF":0.0,"publicationDate":"2025-01-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11811860/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143412166","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
Silicon transport and its "homeostasis" in rice. 水稻中硅的迁移及其“稳态”。
Quantitative plant biology Pub Date : 2025-01-09 eCollection Date: 2024-01-01 DOI: 10.1017/qpb.2024.19
Sheng Huang, Jian Feng Ma
{"title":"Silicon transport and its \"homeostasis\" in rice.","authors":"Sheng Huang, Jian Feng Ma","doi":"10.1017/qpb.2024.19","DOIUrl":"10.1017/qpb.2024.19","url":null,"abstract":"<p><p>Silicon (Si), the most abundant mineral element in soil, functions as a beneficial element for plant growth. Higher Si accumulation in the shoots is required for high and stable production of rice, a typical Si-accumulating plant species. During the last two decades, great progresses has been made in the identification of Si transporters involved in uptake, xylem loading and unloading as well as preferential distribution and deposition of Si in rice. In addition to these transporters, simulation by mathematical models revealed several other key factors required for efficient uptake and distribution of Si. The expression of <i>Lsi1</i>, <i>Lsi2</i> and <i>Lsi3</i> genes is down-regulated by Si deposition in the shoots rather than in the roots, but the exact mechanisms underlying this down-regulation are still unknown. In this short review, we focus on Si transporters identified in rice and discuss how rice optimizes Si accumulation (\"homeostasis\") through regulating Si transporters in response to the fluctuations of this element in the soil solution.</p>","PeriodicalId":101358,"journal":{"name":"Quantitative plant biology","volume":"5 ","pages":"e15"},"PeriodicalIF":0.0,"publicationDate":"2025-01-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11729502/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142985403","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
Nf-Root: A Best-Practice Pipeline for Deep-Learning-Based Analysis of Apoplastic pH in Microscopy Images of Developmental Zones in Plant Root Tissue. Nf-Root：基于深度学习分析植物根组织发育区域显微图像中外胞体pH值的最佳实践管道。
Quantitative plant biology Pub Date : 2024-12-23 eCollection Date: 2024-01-01 DOI: 10.1017/qpb.2024.11
Julian Wanner, Luis Kuhn Cuellar, Luiselotte Rausch, Kenneth W Berendzen, Friederike Wanke, Gisela Gabernet, Klaus Harter, Sven Nahnsen
{"title":"Nf-Root: A Best-Practice Pipeline for Deep-Learning-Based Analysis of Apoplastic pH in Microscopy Images of Developmental Zones in Plant Root Tissue.","authors":"Julian Wanner, Luis Kuhn Cuellar, Luiselotte Rausch, Kenneth W Berendzen, Friederike Wanke, Gisela Gabernet, Klaus Harter, Sven Nahnsen","doi":"10.1017/qpb.2024.11","DOIUrl":"https://doi.org/10.1017/qpb.2024.11","url":null,"abstract":"<p><p>Hormonal mechanisms associated with cell elongation play a vital role in the development and growth of plants. Here, we report Nextflow-root (nf-root), a novel best-practice pipeline for deep-learning-based analysis of fluorescence microscopy images of plant root tissue from A. thaliana. This bioinformatics pipeline performs automatic identification of developmental zones in root tissue images. This also includes apoplastic pH measurements, which is useful for modeling hormone signaling and cell physiological responses. We show that this nf-core standard-based pipeline successfully automates tissue zone segmentation and is both high-throughput and highly reproducible. In short, a deep-learning module deploys deterministically trained convolutional neural network models and augments the segmentation predictions with measures of prediction uncertainty and model interpretability, while aiming to facilitate result interpretation and verification by experienced plant biologists. We observed a high statistical similarity between the manually generated results and the output of the nf-root.</p>","PeriodicalId":101358,"journal":{"name":"Quantitative plant biology","volume":"5 ","pages":"e12"},"PeriodicalIF":0.0,"publicationDate":"2024-12-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11706687/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142961009","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 viscoelastic-plastic deformation model of hemisphere-like tip growth in Arabidopsis zygotes. 拟南芥受精卵半球形尖端生长的粘弹塑性变形模型。
Quantitative plant biology Pub Date : 2024-12-12 eCollection Date: 2024-01-01 DOI: 10.1017/qpb.2024.13
Zichen Kang, Tomonobu Nonoyama, Yukitaka Ishimoto, Hikari Matsumoto, Sakumi Nakagawa, Minako Ueda, Satoru Tsugawa
{"title":"A viscoelastic-plastic deformation model of hemisphere-like tip growth in Arabidopsis zygotes.","authors":"Zichen Kang, Tomonobu Nonoyama, Yukitaka Ishimoto, Hikari Matsumoto, Sakumi Nakagawa, Minako Ueda, Satoru Tsugawa","doi":"10.1017/qpb.2024.13","DOIUrl":"https://doi.org/10.1017/qpb.2024.13","url":null,"abstract":"<p><p>Plant zygote cells exhibit tip growth, producing a hemisphere-like tip. To understand how this hemisphere-like tip shape is formed, we revisited a viscoelastic-plastic deformation model that enabled us to simultaneously evaluate the shape, stress and strain of Arabidopsis (<i>Arabidopsis thaliana</i>) zygote cells undergoing tip growth. Altering the spatial distribution of cell wall extensibility revealed that cosine-type distribution and growth in a normal direction to the surface create a stable hemisphere-like tip shape. Assuming these as constraints for cell elongation, we determined the best-fitting parameters for turgor pressure and wall extensibility to computationally reconstruct an elongating zygote that retained its hemisphere-like shape using only cell contour data, leading to the formulation of non-dimensional growth parameters. Our computational results demonstrate the different morphologies in elongating zygotes through effective non-dimensional parameters.</p>","PeriodicalId":101358,"journal":{"name":"Quantitative plant biology","volume":"5 ","pages":"e13"},"PeriodicalIF":0.0,"publicationDate":"2024-12-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11706690/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142960952","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
Molecular markers in cell cycle visualisation during development and stress conditions in Arabidopsis thaliana. 拟南芥发育和胁迫条件下细胞周期可视化的分子标记。
Quantitative plant biology Pub Date : 2024-12-12 eCollection Date: 2024-01-01 DOI: 10.1017/qpb.2024.18
Olivia S Hazelwood, M Arif Ashraf
{"title":"Molecular markers in cell cycle visualisation during development and stress conditions in <i>Arabidopsis thaliana</i>.","authors":"Olivia S Hazelwood, M Arif Ashraf","doi":"10.1017/qpb.2024.18","DOIUrl":"https://doi.org/10.1017/qpb.2024.18","url":null,"abstract":"<p><p>Plant growth and development are tightly regulated by cell division, elongation, and differentiation. A visible plant phenotype at the tissue or organ level is coordinated at the cellular level. Among these cellular regulations (cell division, elongation and differentiation), cell division in plants follows the same universal mechanisms across kingdoms of life, and involves conserved cell cycle regulatory proteins (cyclins, cyclin-dependent kinase and cell cycle inhibitors). Cell division is regulated through distinct cell cycle steps (G1, S, G2 and M), and these individual steps are visualised using transgenic marker lines. As a result, a quantitative cell cycle approach in plants during development and stress conditions relies on the accuracy of cell cycle markers. In this perspective article, we highlight the available cell cycle marker lines in plants, common practices within plant biology communities based on existing literature and provide a road map to a thorough quantitative approach of cell cycle regulation in plants.</p>","PeriodicalId":101358,"journal":{"name":"Quantitative plant biology","volume":"5 ","pages":"e14"},"PeriodicalIF":0.0,"publicationDate":"2024-12-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11706682/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142961005","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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