Quantitative Plant Biology最新文献_第5页

Spatio-temporal imaging of cell fate dynamics in single plant cells using luminescence microscope. 利用发光显微镜对单个植物细胞命运动态的时空成像。

Quantitative Plant Biology Pub Date : 2022-01-01 DOI: 10.1017/qpb.2022.12

Shunji Shimadzu, Tomoyuki Furuya, Yasuko Ozawa, Hiroo Fukuda, Yuki Kondo

{"title":"Spatio-temporal imaging of cell fate dynamics in single plant cells using luminescence microscope.","authors":"Shunji Shimadzu, Tomoyuki Furuya, Yasuko Ozawa, Hiroo Fukuda, Yuki Kondo","doi":"10.1017/qpb.2022.12","DOIUrl":"https://doi.org/10.1017/qpb.2022.12","url":null,"abstract":"Stem cell fates are spatio-temporally regulated during plant development. Time-lapse imaging of fluorescence reporters is the most widely used method for spatio-temporal analysis of biological processes. However, excitation light for imaging fluorescence reporters causes autofluorescence and photobleaching. Unlike fluorescence reporters, luminescence proteins do not require excitation light, and therefore offer an alternative reporter for long-term and quantitative spatio-temporal analysis. We established an imaging system for luciferase, which enabled monitoring cell fate marker dynamics during vascular development in a vascular cell induction system called VISUAL. Single cells expressing the cambium marker, proAtHB8:ELUC, had sharp luminescence peaks at different time points. Furthermore, dual-color luminescence imaging revealed spatio-temporal relationships between cells that differentiated into xylem or phloem, and cells that transitioned from procambium to cambium. This imaging system enables not only the detection of temporal gene expression, but also facilitates monitoring of spatio-temporal dynamics of cell identity transitions at the single cell level.","PeriodicalId":20825,"journal":{"name":"Quantitative Plant Biology","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2022-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://ftp.ncbi.nlm.nih.gov/pub/pmc/oa_pdf/aa/fe/S2632882822000121a.PMC10095866.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9389984","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: 1

Boolean modelling in plant biology. 植物生物学中的布尔模型。

Quantitative Plant Biology Pub Date : 2022-01-01 DOI: 10.1017/qpb.2022.26

Aravind Karanam, Wouter-Jan Rappel

引用次数: 0

ACORBA: Automated workflow to measure Arabidopsis thaliana root tip angle dynamics. ACORBA:测量拟南芥根尖角动态的自动化工作流程。

Quantitative Plant Biology Pub Date : 2022-01-01 DOI: 10.1017/qpb.2022.4

Nelson B C Serre, Matyáš Fendrych

{"title":"ACORBA: Automated workflow to measure Arabidopsis thaliana root tip angle dynamics.","authors":"Nelson B C Serre, Matyáš Fendrych","doi":"10.1017/qpb.2022.4","DOIUrl":"https://doi.org/10.1017/qpb.2022.4","url":null,"abstract":"Plants respond to the surrounding environment in countless ways. One of these responses is their ability to sense and orient their root growth toward the gravity vector. Root gravitropism is studied in many laboratories as a hallmark of auxin-related phenotypes. However, manual analysis of images and microscopy data is known to be subjected to human bias. This is particularly the case for manual measurements of root bending as the selection lines to calculate the angle are set subjectively. Therefore, it is essential to develop and use automated or semi-automated image analysis to produce reproducible and unbiased data. Moreover, the increasing usage of vertical-stage microscopy in plant root biology yields gravitropic experiments with an unprecedented spatiotemporal resolution. To this day, there is no available solution to measure root bending angle over time for vertical-stage microscopy. To address these problems, we developed ACORBA (Automatic Calculation Of Root Bending Angles), a fully automated software to measure root bending angle over time from vertical-stage microscope and flatbed scanner images. Moreover, the software can be used semi-automated for camera, mobile phone or stereomicroscope images. ACORBA represents a flexible approach based on both traditional image processing and deep machine learning segmentation to measure root angle progression over time. By its automated nature, the workflow is limiting human interactions and has high reproducibility. ACORBA will support the plant biologist community by reducing time and labor and by producing quality results from various kinds of inputs. Significance statement ACORBA is implementing an automated and semi-automated workflow to quantify root bending and waving angles from images acquired with a microscope, a scanner, a stereomicroscope or a camera. It will support the plant biology community by reducing time and labor and by producing trustworthy and reproducible quantitative data.","PeriodicalId":20825,"journal":{"name":"Quantitative Plant Biology","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2022-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://ftp.ncbi.nlm.nih.gov/pub/pmc/oa_pdf/5e/48/S2632882822000042a.PMC10095971.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9385672","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: 4

Focus on biosensors: Looking through the lens of quantitative biology. 聚焦生物传感器：从定量生物学的角度看问题。

Quantitative Plant Biology Pub Date : 2021-10-12 eCollection Date: 2021-01-01 DOI: 10.1017/qpb.2021.10

James H Rowe, Alexander M Jones

{"title":"Focus on biosensors: Looking through the lens of quantitative biology.","authors":"James H Rowe, Alexander M Jones","doi":"10.1017/qpb.2021.10","DOIUrl":"10.1017/qpb.2021.10","url":null,"abstract":"In recent years, plant biologists interested in quantifying molecules and molecular events in vivo have started to complement reporter systems with genetically encoded fluorescent biosensors (GEFBs) that directly sense an analyte. Such biosensors can allow measurements at the level of individual cells and over time. This information is proving valuable to mathematical modellers interested in representing biological phenomena in silico, because improved measurements can guide improved model construction and model parametrisation. Advances in synthetic biology have accelerated the pace of biosensor development, and the simultaneous expression of spectrally compatible biosensors now allows quantification of multiple nodes in signalling networks. For biosensors that directly respond to stimuli, targeting to specific cellular compartments allows the observation of differential accumulation of analytes in distinct organelles, bringing insights to reactive oxygen species/calcium signalling and photosynthesis research. In conjunction with improved image analysis methods, advances in biosensor imaging can help close the loop between experimentation and mathematical modelling.","PeriodicalId":20825,"journal":{"name":"Quantitative Plant Biology","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2021-10-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10095858/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9737933","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

What is quantitative plant biology? 什么是定量植物生物学？

Quantitative Plant Biology Pub Date : 2021-05-20 eCollection Date: 2021-01-01 DOI: 10.1017/qpb.2021.8

Daphné Autran, George W Bassel, Eunyoung Chae, Daphne Ezer, Ali Ferjani, Christian Fleck, Olivier Hamant, Félix P Hartmann, Yuling Jiao, Iain G Johnston, Dorota Kwiatkowska, Boon L Lim, Ari Pekka Mahönen, Richard J Morris, Bela M Mulder, Naomi Nakayama, Ross Sozzani, Lucia C Strader, Kirsten Ten Tusscher, Minako Ueda, Sebastian Wolf

{"title":"What is quantitative plant biology?","authors":"Daphné Autran, George W Bassel, Eunyoung Chae, Daphne Ezer, Ali Ferjani, Christian Fleck, Olivier Hamant, Félix P Hartmann, Yuling Jiao, Iain G Johnston, Dorota Kwiatkowska, Boon L Lim, Ari Pekka Mahönen, Richard J Morris, Bela M Mulder, Naomi Nakayama, Ross Sozzani, Lucia C Strader, Kirsten Ten Tusscher, Minako Ueda, Sebastian Wolf","doi":"10.1017/qpb.2021.8","DOIUrl":"10.1017/qpb.2021.8","url":null,"abstract":"Quantitative plant biology is an interdisciplinary field that builds on a long history of biomathematics and biophysics. Today, thanks to high spatiotemporal resolution tools and computational modelling, it sets a new standard in plant science. Acquired data, whether molecular, geometric or mechanical, are quantified, statistically assessed and integrated at multiple scales and across fields. They feed testable predictions that, in turn, guide further experimental tests. Quantitative features such as variability, noise, robustness, delays or feedback loops are included to account for the inner dynamics of plants and their interactions with the environment. Here, we present the main features of this ongoing revolution, through new questions around signalling networks, tissue topology, shape plasticity, biomechanics, bioenergetics, ecology and engineering. In the end, quantitative plant biology allows us to question and better understand our interactions with plants. In turn, this field opens the door to transdisciplinary projects with the society, notably through citizen science.","PeriodicalId":20825,"journal":{"name":"Quantitative Plant Biology","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2021-05-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://ftp.ncbi.nlm.nih.gov/pub/pmc/oa_pdf/71/2f/S2632882821000084a.PMC10095877.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9752852","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 plant biology-Old and new. 定量植物生物学--新与旧

Quantitative Plant Biology Pub Date : 2021-05-18 eCollection Date: 2021-01-01 DOI: 10.1017/qpb.2021.4

Richard J Morris, Kirsten H Ten Tusscher

引用次数: 0

Comparative transcriptomics reveals desynchronisation of gene expression during the floral transition between Arabidopsis and Brassica rapa cultivars. 比较转录组学揭示了拟南芥和油菜品种花过渡过程中基因表达的不同步。

Quantitative Plant Biology Pub Date : 2021-04-26 eCollection Date: 2021-01-01 DOI: 10.1017/qpb.2021.6

Alexander Calderwood, Jo Hepworth, Shannon Woodhouse, Lorelei Bilham, D Marc Jones, Eleri Tudor, Mubarak Ali, Caroline Dean, Rachel Wells, Judith A Irwin, Richard J Morris

{"title":"Comparative transcriptomics reveals desynchronisation of gene expression during the floral transition between Arabidopsis and Brassica rapa cultivars.","authors":"Alexander Calderwood, Jo Hepworth, Shannon Woodhouse, Lorelei Bilham, D Marc Jones, Eleri Tudor, Mubarak Ali, Caroline Dean, Rachel Wells, Judith A Irwin, Richard J Morris","doi":"10.1017/qpb.2021.6","DOIUrl":"10.1017/qpb.2021.6","url":null,"abstract":"Comparative transcriptomics can be used to translate an understanding of gene regulatory networks from model systems to less studied species. Here, we use RNA-Seq to determine and compare gene expression dynamics through the floral transition in the model species Arabidopsis thaliana and the closely related crop Brassica rapa. We find that different curve registration functions are required for different genes, indicating that there is no single common 'developmental time' between Arabidopsis and B. rapa. A detailed comparison between Arabidopsis and B. rapa and between two B. rapa accessions reveals different modes of regulation of the key floral integrator SOC1, and that the floral transition in the B. rapa accessions is triggered by different pathways. Our study adds to the mechanistic understanding of the regulatory network of flowering time in rapid cycling B. rapa and highlights the importance of registration methods for the comparison of developmental gene expression data.","PeriodicalId":20825,"journal":{"name":"Quantitative Plant Biology","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2021-04-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1017/qpb.2021.6","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9582017","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: 2

The Arabidopsis embryo as a quantifiable model for studying pattern formation. 拟南芥胚胎是研究模式形成的可量化模型。

Quantitative Plant Biology Pub Date : 2021-04-12 eCollection Date: 2021-01-01 DOI: 10.1017/qpb.2021.3

Yosapol Harnvanichvech, Vera Gorelova, Joris Sprakel, Dolf Weijers

引用次数: 0

A hybrid model connecting regulatory interactions with stem cell divisions in the root. 一个连接调控相互作用与根中干细胞分裂的混合模型。

Quantitative Plant Biology Pub Date : 2021-01-01 DOI: 10.1017/qpb.2021.1

Lisa Van den Broeck, Ryan J Spurney, Adam P Fisher, Michael Schwartz, Natalie M Clark, Thomas T Nguyen, Imani Madison, Mariah Gobble, Terri Long, Rosangela Sozzani

{"title":"A hybrid model connecting regulatory interactions with stem cell divisions in the root.","authors":"Lisa Van den Broeck, Ryan J Spurney, Adam P Fisher, Michael Schwartz, Natalie M Clark, Thomas T Nguyen, Imani Madison, Mariah Gobble, Terri Long, Rosangela Sozzani","doi":"10.1017/qpb.2021.1","DOIUrl":"https://doi.org/10.1017/qpb.2021.1","url":null,"abstract":"Stem cells give rise to the entirety of cells within an organ. Maintaining stem cell identity and coordinately regulating stem cell divisions is crucial for proper development. In plants, mobile proteins, such as WUSCHEL-RELATED HOMEOBOX 5 (WOX5) and SHORTROOT (SHR), regulate divisions in the root stem cell niche. However, how these proteins coordinately function to establish systemic behaviour is not well understood. We propose a non-cell autonomous role for WOX5 in the cortex endodermis initial (CEI) and identify a regulator, ANGUSTIFOLIA (AN3)/GRF-INTERACTING FACTOR 1, that coordinates CEI divisions. Here, we show with a multi-scale hybrid model integrating ordinary differential equations (ODEs) and agent-based modeling that quiescent center (QC) and CEI divisions have different dynamics. Specifically, by combining continuous models to describe regulatory networks and agent-based rules, we model systemic behaviour, which led us to predict cell-type-specific expression dynamics of SHR, SCARECROW, WOX5, AN3 and CYCLIND6;1, and experimentally validate CEI cell divisions. Conclusively, our results show an interdependency between CEI and QC divisions.","PeriodicalId":20825,"journal":{"name":"Quantitative Plant Biology","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2021-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1017/qpb.2021.1","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10593272","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: 5

A plausible mechanism for longitudinal lock-in of the plant cortical microtubule array after light-induced reorientation. 植物皮质微管阵列在光诱导定向后纵向锁定的可能机制。

Quantitative Plant Biology Pub Date : 2021-01-01 DOI: 10.1017/qpb.2021.9

Marco Saltini, Bela M Mulder

{"title":"A plausible mechanism for longitudinal lock-in of the plant cortical microtubule array after light-induced reorientation.","authors":"Marco Saltini, Bela M Mulder","doi":"10.1017/qpb.2021.9","DOIUrl":"https://doi.org/10.1017/qpb.2021.9","url":null,"abstract":"The light-induced reorientation of the cortical microtubule array in dark-grown Arabidopsis thaliana hypocotyl cells is a striking example of the dynamical plasticity of the microtubule cytoskeleton. A consensus model, based on katanin-mediated severing at microtubule crossovers, has been developed that successfully describes the onset of the observed switch between a transverse and longitudinal array orientation. However, we currently lack an understanding of why the newly populated longitudinal array direction remains stable for longer times and re-equilibration effects would tend to drive the system back to a mixed orientation state. Using both simulations and analytical calculations, we show that the assumption of a small orientation-dependent shift in microtubule dynamics is sufficient to explain the long-term lock-in of the longitudinal array orientation. Furthermore, we show that the natural alternative hypothesis that there is a selective advantage in severing longitudinal microtubules, is neither necessary nor sufficient to achieve cortical array reorientation, but is able to accelerate this process significantly.","PeriodicalId":20825,"journal":{"name":"Quantitative Plant Biology","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2021-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1017/qpb.2021.9","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9752846","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: 2