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TipQuant: a robust algorithm for quantitative analysis of spatiotemporally dynamic activities in tip-growing cells.

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Τίτλος: TipQuant: a robust algorithm for quantitative analysis of spatiotemporally dynamic activities in tip-growing cells.
Συγγραφείς: Guo J; Institute for Integrative Genome Biology and Department of Botany and Plant Sciences, University of California, Riverside, CA, 92521, USA., Le Gouic J; Capgemini Invent, 92130, Issy-les-Moulineaux, France., Rosenthal R; Quantmetry, 52, rue d'Anjou, 75008, Paris, France., Zou A; Metabolomics Research Center, Haixia Institute of Science and Technology, Fujian Agriculture and Forestry University, Fuzhou, 350002, China., Zhou X; State Key Laboratory of Quantitative Synthetic Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, China., Brunel N; Capgemini Invent, 92130, Issy-les-Moulineaux, France.; ENSIIE & Laboratoire de Mathématiques et Modélisation d'Evry, Université Paris Saclay, 91025, Evry, France., Yang Z; Institute for Integrative Genome Biology and Department of Botany and Plant Sciences, University of California, Riverside, CA, 92521, USA.; Institute of Emerging Agricultural Technology, Shenzhen University of Advanced Technology, Shenzhen, 518107, Guangdong, China.; Faculty of Synthetic Biology, Shenzhen University of Advanced Technology, Shenzhen, 518107, Guangdong, China., Cui X; Institute for Integrative Genome Biology and Department of Statistics, University of California, Riverside, CA, 92521, USA.
Πηγή: The New phytologist [New Phytol] 2026 Oct; Vol. 252 (2), pp. 926-935. Date of Electronic Publication: 2026 Aug 20.
Τύπος έκδοσης: Journal Article
Γλώσσα: English
Στοιχεία περιοδικού: Publisher: Wiley on behalf of New Phytologist Trust Country of Publication: England NLM ID: 9882884 Publication Model: Print-Electronic Cited Medium: Internet ISSN: 1469-8137 (Electronic) Linking ISSN: 0028646X NLM ISO Abbreviation: New Phytol Subsets: MEDLINE
Imprint Name(s): Publication: Oxford : Wiley on behalf of New Phytologist Trust
Original Publication: London, New York [etc.] Academic Press.
Ιατρικοί όροι (MeSH): Arabidopsis*/cytology , Arabidopsis*/metabolism , Arabidopsis*/growth & development , Pollen Tube*/cytology , Pollen Tube*/growth & development , Pollen Tube*/metabolism , Algorithms*, Fusarium/cytology ; Fusarium/growth & development ; Hyphae/growth & development ; Calcium/metabolism ; Arabidopsis Proteins/metabolism ; Cell Polarity ; Spatio-Temporal Analysis ; Image Processing, Computer-Assisted
Περίληψη: Cell polarity and tip growth rely on the dynamic spatial organization of signaling and structural components. Quantitative characterization of these spatiotemporal dynamics is critical for understanding polarized cell growth, yet manual quantification is labor-intensive and existing computational tools often lack the flexibility and robustness needed to analyze molecular and structural dynamics in tip-growing cells. Tip Quantification (TipQuant) identifies the cell apex by detecting the site of maximum expansion and automatically quantifies fluorescence distribution along the plasma membrane and within the apical cytoplasm from live-cell imaging data, enabling analysis of the spatiotemporal dynamics of molecular and structural components in tip-growing cells. TipQuant accurately identified cell apices and quantified the spatiotemporal behavior of fluorescently labeled proteins and cellular structures in Arabidopsis thaliana pollen tubes and Fusarium graminearum hyphae, reproducing manual measurements while reducing user bias and improving efficiency, consistency, and analytical flexibility. The tool also revealed a strong positive correlation between rho-like GTPase from plants activity and apical Ca2+ influx in Arabidopsis pollen tubes, demonstrating its utility for analyzing dynamic cellular processes. TipQuant is a robust analytical tool for quantifying spatiotemporal dynamics in tip-growing cells, providing a flexible alternative to manual image analysis and enabling studies of the molecular mechanisms underlying polarized growth.
(© 2026 The Author(s). New Phytologist © 2026 New Phytologist Foundation.)
References: Annu Rev Plant Biol. 2008;59:547-72. (PMID: 18444907)
J Exp Bot. 2017 Jun 01;68(12):3267-3281. (PMID: 28369603)
Elife. 2021 Apr 26;10:. (PMID: 33899733)
Semin Cell Dev Biol. 2011 Oct;22(8):816-24. (PMID: 21729760)
Front Plant Sci. 2022 May 25;13:847671. (PMID: 35693156)
Science. 2018 May 4;360(6388):533-536. (PMID: 29724955)
Nature. 2009 Mar 19;458(7236):357-61. (PMID: 19295610)
J Cell Sci. 2010 Feb 1;123(Pt 3):340-50. (PMID: 20053639)
Plant Cell. 1999 Sep;11(9):1731-42. (PMID: 10488239)
Mol Plant. 2013 Jul;6(4):998-1017. (PMID: 23770837)
Dev Cell. 2021 Apr 5;56(7):1030-1042.e6. (PMID: 33756107)
Plant J. 2026 Jan;125(2):e70691. (PMID: 41558033)
Nat Commun. 2017 Nov 22;8(1):1687. (PMID: 29162819)
J Exp Bot. 2010 Apr;61(7):1939-57. (PMID: 20378665)
Plant Cell. 2009 Feb;21(2):526-44. (PMID: 19208902)
Dev Biol. 1996 Feb 25;174(1):160-73. (PMID: 8626016)
J Cell Biol. 2008 Jun 30;181(7):1155-68. (PMID: 18591430)
Methods Mol Biol. 2020;2160:293-306. (PMID: 32529445)
Plant Physiol. 2022 Mar 28;188(4):2253-2271. (PMID: 35218352)
J Vis Exp. 2023 Jun 23;(196):. (PMID: 37427934)
Plant Cell Physiol. 2023 Dec 6;64(11):1279-1288. (PMID: 36943754)
Proc Natl Acad Sci U S A. 2009 Dec 22;106(51):22002-7. (PMID: 19955439)
J Math Biol. 2019 Sep;79(4):1319-1355. (PMID: 31280334)
Cell. 1996 Feb 9;84(3):335-44. (PMID: 8608587)
J Cell Biol. 2005 Apr 11;169(1):127-38. (PMID: 15824136)
J Cell Biol. 2001 Mar 5;152(5):1019-32. (PMID: 11238457)
Plant Cell. 2002 Apr;14(4):763-76. (PMID: 11971133)
New Phytol. 2021 Feb;229(3):1665-1683. (PMID: 32978966)
Annu Rev Cell Dev Biol. 2008;24:551-75. (PMID: 18837672)
J Exp Bot. 2020 Apr 23;71(8):2428-2438. (PMID: 32173729)
Plant Reprod. 2019 Mar;32(1):45-54. (PMID: 30543045)
Nat Methods. 2012 Jul;9(7):671-5. (PMID: 22930834)
Science. 2001 Aug 24;293(5534):1480-3. (PMID: 11520985)
Mol Biol Cell. 2005 Nov;16(11):5385-99. (PMID: 16148045)
Methods Mol Biol. 2020;2160:275-292. (PMID: 32529444)
Mol Plant. 2013 Jul;6(4):1053-64. (PMID: 23873928)
Grant Information: CA-R-STA-7132-H National Institute of Food and Agriculture; 1853698 National Science Foundation, Division of Mathematical Science
Contributed Indexing: Keywords: cell polarity; quantitative analysis; robust algorithm; spatiotemporal dynamics; tip growth
Substance Nomenclature: SY7Q814VUP (Calcium)
0 (Arabidopsis Proteins)
Entry Date(s): Date Created: 20260820 Date Completed: 20260917 Latest Revision: 20260919
Update Code: 20260919
PubMed Central ID: PMC13583362
DOI: 10.1111/nph.71474
PMID: 42619582
Βάση Δεδομένων: MEDLINE
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  Data: <searchLink fieldCode="MM" term="%22Arabidopsis%22">Arabidopsis*</searchLink>/<searchLink fieldCode="MM" term="%22Arabidopsis+cytology%22">cytology</searchLink> <br /><searchLink fieldCode="MM" term="%22Arabidopsis%22">Arabidopsis*</searchLink>/<searchLink fieldCode="MM" term="%22Arabidopsis+metabolism%22">metabolism</searchLink> <br /><searchLink fieldCode="MM" term="%22Arabidopsis%22">Arabidopsis*</searchLink>/<searchLink fieldCode="MM" term="%22Arabidopsis+growth+%26+development%22">growth & development</searchLink> <br /><searchLink fieldCode="MM" term="%22Pollen+Tube%22">Pollen Tube*</searchLink>/<searchLink fieldCode="MM" term="%22Pollen+Tube+cytology%22">cytology</searchLink> <br /><searchLink fieldCode="MM" term="%22Pollen+Tube%22">Pollen Tube*</searchLink>/<searchLink fieldCode="MM" term="%22Pollen+Tube+growth+%26+development%22">growth & development</searchLink> <br /><searchLink fieldCode="MM" term="%22Pollen+Tube%22">Pollen Tube*</searchLink>/<searchLink fieldCode="MM" term="%22Pollen+Tube+metabolism%22">metabolism</searchLink> <br /><searchLink fieldCode="MM" term="%22Algorithms%22">Algorithms*</searchLink><br /><searchLink fieldCode="MH" term="%22Fusarium%22">Fusarium</searchLink>/<searchLink fieldCode="MH" term="%22Fusarium+cytology%22">cytology</searchLink> ; <searchLink fieldCode="MH" term="%22Fusarium%22">Fusarium</searchLink>/<searchLink fieldCode="MH" term="%22Fusarium+growth+%26+development%22">growth & development</searchLink> ; <searchLink fieldCode="MH" term="%22Hyphae%22">Hyphae</searchLink>/<searchLink fieldCode="MH" term="%22Hyphae+growth+%26+development%22">growth & development</searchLink> ; <searchLink fieldCode="MH" term="%22Calcium%22">Calcium</searchLink>/<searchLink fieldCode="MH" term="%22Calcium+metabolism%22">metabolism</searchLink> ; <searchLink fieldCode="MH" term="%22Arabidopsis+Proteins%22">Arabidopsis Proteins</searchLink>/<searchLink fieldCode="MH" term="%22Arabidopsis+Proteins+metabolism%22">metabolism</searchLink> ; <searchLink fieldCode="MH" term="%22Cell+Polarity%22">Cell Polarity</searchLink> ; <searchLink fieldCode="MH" term="%22Spatio-Temporal+Analysis%22">Spatio-Temporal Analysis</searchLink> ; <searchLink fieldCode="MH" term="%22Image+Processing%2C+Computer-Assisted%22">Image Processing, Computer-Assisted</searchLink>
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  Data: Cell polarity and tip growth rely on the dynamic spatial organization of signaling and structural components. Quantitative characterization of these spatiotemporal dynamics is critical for understanding polarized cell growth, yet manual quantification is labor-intensive and existing computational tools often lack the flexibility and robustness needed to analyze molecular and structural dynamics in tip-growing cells. Tip Quantification (TipQuant) identifies the cell apex by detecting the site of maximum expansion and automatically quantifies fluorescence distribution along the plasma membrane and within the apical cytoplasm from live-cell imaging data, enabling analysis of the spatiotemporal dynamics of molecular and structural components in tip-growing cells. TipQuant accurately identified cell apices and quantified the spatiotemporal behavior of fluorescently labeled proteins and cellular structures in Arabidopsis thaliana pollen tubes and Fusarium graminearum hyphae, reproducing manual measurements while reducing user bias and improving efficiency, consistency, and analytical flexibility. The tool also revealed a strong positive correlation between rho-like GTPase from plants activity and apical Ca<superscript>2+</superscript> influx in Arabidopsis pollen tubes, demonstrating its utility for analyzing dynamic cellular processes. TipQuant is a robust analytical tool for quantifying spatiotemporal dynamics in tip-growing cells, providing a flexible alternative to manual image analysis and enabling studies of the molecular mechanisms underlying polarized growth.<br /> (© 2026 The Author(s). New Phytologist © 2026 New Phytologist Foundation.)
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  Label: References
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  Data: Annu Rev Plant Biol. 2008;59:547-72. (PMID: <searchLink fieldCode="PM" term="%2218444907%22">18444907)</searchLink><br />J Exp Bot. 2017 Jun 01;68(12):3267-3281. (PMID: <searchLink fieldCode="PM" term="%2228369603%22">28369603)</searchLink><br />Elife. 2021 Apr 26;10:. (PMID: <searchLink fieldCode="PM" term="%2233899733%22">33899733)</searchLink><br />Semin Cell Dev Biol. 2011 Oct;22(8):816-24. (PMID: <searchLink fieldCode="PM" term="%2221729760%22">21729760)</searchLink><br />Front Plant Sci. 2022 May 25;13:847671. (PMID: <searchLink fieldCode="PM" term="%2235693156%22">35693156)</searchLink><br />Science. 2018 May 4;360(6388):533-536. (PMID: <searchLink fieldCode="PM" term="%2229724955%22">29724955)</searchLink><br />Nature. 2009 Mar 19;458(7236):357-61. (PMID: <searchLink fieldCode="PM" term="%2219295610%22">19295610)</searchLink><br />J Cell Sci. 2010 Feb 1;123(Pt 3):340-50. (PMID: <searchLink fieldCode="PM" term="%2220053639%22">20053639)</searchLink><br />Plant Cell. 1999 Sep;11(9):1731-42. (PMID: <searchLink fieldCode="PM" term="%2210488239%22">10488239)</searchLink><br />Mol Plant. 2013 Jul;6(4):998-1017. (PMID: <searchLink fieldCode="PM" term="%2223770837%22">23770837)</searchLink><br />Dev Cell. 2021 Apr 5;56(7):1030-1042.e6. (PMID: <searchLink fieldCode="PM" term="%2233756107%22">33756107)</searchLink><br />Plant J. 2026 Jan;125(2):e70691. (PMID: <searchLink fieldCode="PM" term="%2241558033%22">41558033)</searchLink><br />Nat Commun. 2017 Nov 22;8(1):1687. (PMID: <searchLink fieldCode="PM" term="%2229162819%22">29162819)</searchLink><br />J Exp Bot. 2010 Apr;61(7):1939-57. (PMID: <searchLink fieldCode="PM" term="%2220378665%22">20378665)</searchLink><br />Plant Cell. 2009 Feb;21(2):526-44. (PMID: <searchLink fieldCode="PM" term="%2219208902%22">19208902)</searchLink><br />Dev Biol. 1996 Feb 25;174(1):160-73. (PMID: <searchLink fieldCode="PM" term="%228626016%22">8626016)</searchLink><br />J Cell Biol. 2008 Jun 30;181(7):1155-68. (PMID: <searchLink fieldCode="PM" term="%2218591430%22">18591430)</searchLink><br />Methods Mol Biol. 2020;2160:293-306. (PMID: <searchLink fieldCode="PM" term="%2232529445%22">32529445)</searchLink><br />Plant Physiol. 2022 Mar 28;188(4):2253-2271. (PMID: <searchLink fieldCode="PM" term="%2235218352%22">35218352)</searchLink><br />J Vis Exp. 2023 Jun 23;(196):. (PMID: <searchLink fieldCode="PM" term="%2237427934%22">37427934)</searchLink><br />Plant Cell Physiol. 2023 Dec 6;64(11):1279-1288. (PMID: <searchLink fieldCode="PM" term="%2236943754%22">36943754)</searchLink><br />Proc Natl Acad Sci U S A. 2009 Dec 22;106(51):22002-7. (PMID: <searchLink fieldCode="PM" term="%2219955439%22">19955439)</searchLink><br />J Math Biol. 2019 Sep;79(4):1319-1355. (PMID: <searchLink fieldCode="PM" term="%2231280334%22">31280334)</searchLink><br />Cell. 1996 Feb 9;84(3):335-44. (PMID: <searchLink fieldCode="PM" term="%228608587%22">8608587)</searchLink><br />J Cell Biol. 2005 Apr 11;169(1):127-38. (PMID: <searchLink fieldCode="PM" term="%2215824136%22">15824136)</searchLink><br />J Cell Biol. 2001 Mar 5;152(5):1019-32. (PMID: <searchLink fieldCode="PM" term="%2211238457%22">11238457)</searchLink><br />Plant Cell. 2002 Apr;14(4):763-76. (PMID: <searchLink fieldCode="PM" term="%2211971133%22">11971133)</searchLink><br />New Phytol. 2021 Feb;229(3):1665-1683. (PMID: <searchLink fieldCode="PM" term="%2232978966%22">32978966)</searchLink><br />Annu Rev Cell Dev Biol. 2008;24:551-75. (PMID: <searchLink fieldCode="PM" term="%2218837672%22">18837672)</searchLink><br />J Exp Bot. 2020 Apr 23;71(8):2428-2438. (PMID: <searchLink fieldCode="PM" term="%2232173729%22">32173729)</searchLink><br />Plant Reprod. 2019 Mar;32(1):45-54. (PMID: <searchLink fieldCode="PM" term="%2230543045%22">30543045)</searchLink><br />Nat Methods. 2012 Jul;9(7):671-5. (PMID: <searchLink fieldCode="PM" term="%2222930834%22">22930834)</searchLink><br />Science. 2001 Aug 24;293(5534):1480-3. (PMID: <searchLink fieldCode="PM" term="%2211520985%22">11520985)</searchLink><br />Mol Biol Cell. 2005 Nov;16(11):5385-99. (PMID: <searchLink fieldCode="PM" term="%2216148045%22">16148045)</searchLink><br />Methods Mol Biol. 2020;2160:275-292. (PMID: <searchLink fieldCode="PM" term="%2232529444%22">32529444)</searchLink><br />Mol Plant. 2013 Jul;6(4):1053-64. (PMID: <searchLink fieldCode="PM" term="%2223873928%22">23873928)</searchLink>
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