Journal of cell science最新文献_第8页

Machine learning in microscopy - insights, opportunities and challenges. 显微镜中的机器学习--见解、机遇与挑战。

IF 3.3 3区生物学

Journal of cell science Pub Date : 2024-10-15 Epub Date: 2024-10-28 DOI: 10.1242/jcs.262095

Inês Cunha, Emma Latron, Sebastian Bauer, Daniel Sage, Juliette Griffié

引用次数: 0

Back to the future - 20 years of progress and developments in photonic microscopy and biological imaging. 回到未来--光子显微镜和生物成像技术 20 年的进步与发展。

IF 3.3 3区生物学

Journal of cell science Pub Date : 2024-10-15 Epub Date: 2024-10-28 DOI: 10.1242/jcs.262344

Marie Erard, Cyril Favard, Luke D Lavis, Gaëlle Recher, Hervé Rigneault, Daniel Sage

{"title":"Back to the future - 20 years of progress and developments in photonic microscopy and biological imaging.","authors":"Marie Erard, Cyril Favard, Luke D Lavis, Gaëlle Recher, Hervé Rigneault, Daniel Sage","doi":"10.1242/jcs.262344","DOIUrl":"10.1242/jcs.262344","url":null,"abstract":"In 2023, the ImaBio consortium (imabio-cnrs.fr), an interdisciplinary life microscopy research group at the Centre National de la Recherche Scientifique, celebrated its 20th anniversary. ImaBio contributes to the biological imaging community through organization of MiFoBio conferences, which are interdisciplinary conferences featuring lectures and hands-on workshops that attract specialists from around the world. MiFoBio conferences provide the community with an opportunity to reflect on the evolution of the field, and the 2023 event offered retrospective talks discussing the past 20 years of topics in microscopy, including imaging of multicellular assemblies, image analysis, quantification of molecular motions and interactions within cells, advancements in fluorescent labels, and laser technology for multiphoton and label-free imaging of thick biological samples. In this Perspective, we compile summaries of these presentations overviewing 20 years of advancements in a specific area of microscopy, each of which concludes with a brief look towards the future. The full presentations are available on the ImaBio YouTube channel (youtube.com/@gdrimabio5724).","PeriodicalId":15227,"journal":{"name":"Journal of cell science","volume":"137 20","pages":""},"PeriodicalIF":3.3,"publicationDate":"2024-10-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142501124","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

The crucial role of bioimage analysts in scientific research and publication. 生物图像分析师在科学研究和出版中的关键作用。

IF 3.3 3区生物学

Journal of cell science Pub Date : 2024-10-15 Epub Date: 2024-10-30 DOI: 10.1242/jcs.262322

Beth A Cimini, Peter Bankhead, Rocco D'Antuono, Elnaz Fazeli, Julia Fernandez-Rodriguez, Caterina Fuster-Barceló, Robert Haase, Helena Klara Jambor, Martin L Jones, Florian Jug, Anna H Klemm, Anna Kreshuk, Stefania Marcotti, Gabriel G Martins, Sara McArdle, Kota Miura, Arrate Muñoz-Barrutia, Laura C Murphy, Michael S Nelson, Simon F Nørrelykke, Perrine Paul-Gilloteaux, Thomas Pengo, Joanna W Pylvänäinen, Lior Pytowski, Arianna Ravera, Annika Reinke, Yousr Rekik, Caterina Strambio-De-Castillia, Daniel Thédié, Virginie Uhlmann, Oliver Umney, Laura Wiggins, Kevin W Eliceiri

{"title":"The crucial role of bioimage analysts in scientific research and publication.","authors":"Beth A Cimini, Peter Bankhead, Rocco D'Antuono, Elnaz Fazeli, Julia Fernandez-Rodriguez, Caterina Fuster-Barceló, Robert Haase, Helena Klara Jambor, Martin L Jones, Florian Jug, Anna H Klemm, Anna Kreshuk, Stefania Marcotti, Gabriel G Martins, Sara McArdle, Kota Miura, Arrate Muñoz-Barrutia, Laura C Murphy, Michael S Nelson, Simon F Nørrelykke, Perrine Paul-Gilloteaux, Thomas Pengo, Joanna W Pylvänäinen, Lior Pytowski, Arianna Ravera, Annika Reinke, Yousr Rekik, Caterina Strambio-De-Castillia, Daniel Thédié, Virginie Uhlmann, Oliver Umney, Laura Wiggins, Kevin W Eliceiri","doi":"10.1242/jcs.262322","DOIUrl":"10.1242/jcs.262322","url":null,"abstract":"Bioimage analysis (BIA), a crucial discipline in biological research, overcomes the limitations of subjective analysis in microscopy through the creation and application of quantitative and reproducible methods. The establishment of dedicated BIA support within academic institutions is vital to improving research quality and efficiency and can significantly advance scientific discovery. However, a lack of training resources, limited career paths and insufficient recognition of the contributions made by bioimage analysts prevent the full realization of this potential. This Perspective - the result of the recent The Company of Biologists Workshop 'Effectively Communicating Bioimage Analysis', which aimed to summarize the global BIA landscape, categorize obstacles and offer possible solutions - proposes strategies to bring about a cultural shift towards recognizing the value of BIA by standardizing tools, improving training and encouraging formal credit for contributions. We also advocate for increased funding, standardized practices and enhanced collaboration, and we conclude with a call to action for all stakeholders to join efforts in advancing BIA.","PeriodicalId":15227,"journal":{"name":"Journal of cell science","volume":"137 20","pages":""},"PeriodicalIF":3.3,"publicationDate":"2024-10-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142545667","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

pHusion - a robust and versatile toolset for automated detection and analysis of exocytosis. pHusion：用于自动检测和分析外吞功能的强大而多用途的工具集。

IF 3.3 3区生物学

Journal of cell science Pub Date : 2024-10-15 Epub Date: 2024-06-07 DOI: 10.1242/jcs.261828

Ellen C O'Shaughnessy, Mable Lam, Samantha E Ryken, Theresa Wiesner, Kimberly Lukasik, J Bradley Zuchero, Christophe Leterrier, David Adalsteinsson, Stephanie L Gupton

{"title":"pHusion - a robust and versatile toolset for automated detection and analysis of exocytosis.","authors":"Ellen C O'Shaughnessy, Mable Lam, Samantha E Ryken, Theresa Wiesner, Kimberly Lukasik, J Bradley Zuchero, Christophe Leterrier, David Adalsteinsson, Stephanie L Gupton","doi":"10.1242/jcs.261828","DOIUrl":"10.1242/jcs.261828","url":null,"abstract":"Exocytosis is a fundamental process used by eukaryotes to regulate the composition of the plasma membrane and facilitate cell-cell communication. To investigate exocytosis in neuronal morphogenesis, previously we developed computational tools with a graphical user interface to enable the automatic detection and analysis of exocytic events from fluorescence timelapse images. Although these tools were useful, we found the code was brittle and not easily adapted to different experimental conditions. Here, we developed and validated a robust and versatile toolkit, named pHusion, for the analysis of exocytosis, written in ImageTank, a graphical programming language that combines image visualization and numerical methods. We tested pHusion using a variety of imaging modalities and pH-sensitive fluorophores, diverse cell types and various exocytic markers, to generate a flexible and intuitive package. Using this system, we show that VAMP3-mediated exocytosis occurs 30-times more frequently in melanoma cells compared with primary oligodendrocytes, that VAMP2-mediated fusion events in mature rat hippocampal neurons are longer lasting than those in immature murine cortical neurons, and that exocytic events are clustered in space yet random in time in developing cortical neurons.","PeriodicalId":15227,"journal":{"name":"Journal of cell science","volume":" ","pages":""},"PeriodicalIF":3.3,"publicationDate":"2024-10-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11190432/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140848842","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Lipid droplet dynamics are essential for the development of the malaria parasite Plasmodium falciparum. 脂滴动力学对恶性疟原虫的发育至关重要。

IF 3.3 3区生物学

Journal of cell science Pub Date : 2024-10-15 Epub Date: 2024-08-08 DOI: 10.1242/jcs.262162

Jiwon Lee, Kai Matuschewski, Giel van Dooren, Alexander G Maier, Melanie Rug

{"title":"Lipid droplet dynamics are essential for the development of the malaria parasite Plasmodium falciparum.","authors":"Jiwon Lee, Kai Matuschewski, Giel van Dooren, Alexander G Maier, Melanie Rug","doi":"10.1242/jcs.262162","DOIUrl":"10.1242/jcs.262162","url":null,"abstract":"Lipid droplets (LDs) are organelles that are central to lipid and energy homeostasis across all eukaryotes. In the malaria-causing parasite Plasmodium falciparum the roles of LDs in lipid acquisition from its host cells and their metabolism are poorly understood, despite the high demand for lipids in parasite membrane synthesis. We systematically characterised LD size, composition and dynamics across the disease-causing blood infection. Applying split fluorescence emission analysis and three-dimensional (3D) focused ion beam-scanning electron microscopy (FIB-SEM), we observed a decrease in LD size in late schizont stages. LD contraction likely signifies a switch from lipid accumulation to lipid utilisation in preparation for parasite egress from host red blood cells. We demonstrate connections between LDs and several parasite organelles, pointing to potential functional interactions. Chemical inhibition of triacylglyerol (TAG) synthesis or breakdown revealed essential LD functions for schizogony and in counteracting lipid toxicity. The dynamics of lipid synthesis, storage and utilisation in P. falciparum LDs might provide a target for new anti-malarial intervention strategies.","PeriodicalId":15227,"journal":{"name":"Journal of cell science","volume":" ","pages":""},"PeriodicalIF":3.3,"publicationDate":"2024-10-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141498149","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

ExoJ - a Fiji/ImageJ2 plugin for automated spatiotemporal detection and analysis of exocytosis. ExoJ：用于自动时空检测和分析外泌的 ImageJ2/Fiji 插件。

IF 3.3 3区生物学

Journal of cell science Pub Date : 2024-10-15 Epub Date: 2024-10-23 DOI: 10.1242/jcs.261938

Junjun Liu, Frederik Johannes Verweij, Guillaume van Niel, Thierry Galli, Lydia Danglot, Philippe Bun

{"title":"ExoJ - a Fiji/ImageJ2 plugin for automated spatiotemporal detection and analysis of exocytosis.","authors":"Junjun Liu, Frederik Johannes Verweij, Guillaume van Niel, Thierry Galli, Lydia Danglot, Philippe Bun","doi":"10.1242/jcs.261938","DOIUrl":"10.1242/jcs.261938","url":null,"abstract":"Exocytosis is a dynamic physiological process that enables the release of biomolecules to the surrounding environment via the fusion of membrane compartments to the plasma membrane. Understanding its mechanisms is crucial, as defects can compromise essential biological functions. The development of pH-sensitive optical reporters alongside fluorescence microscopy enables the assessment of individual vesicle exocytosis events at the cellular level. Manual annotation represents, however, a time-consuming task that is prone to selection biases and human operational errors. Here, we introduce ExoJ, an automated plugin based on Fiji/ImageJ2 software. ExoJ identifies user-defined genuine populations of exocytosis events, recording quantitative features including intensity, apparent size and duration. We designed ExoJ to be fully user-configurable, making it suitable for studying distinct forms of vesicle exocytosis regardless of the imaging quality. Our plugin demonstrates its capabilities by showcasing distinct exocytic dynamics among tetraspanins and vesicular SNARE protein reporters. Assessment of performance on synthetic data shows that ExoJ is a robust tool that is capable of correctly identifying exocytosis events independently of signal-to-noise ratio conditions. We propose ExoJ as a standard solution for future comparative and quantitative studies of exocytosis.","PeriodicalId":15227,"journal":{"name":"Journal of cell science","volume":" ","pages":""},"PeriodicalIF":3.3,"publicationDate":"2024-10-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142107731","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Super-resolution imaging reveals nucleolar encapsulation by single-stranded DNA. 超分辨率成像揭示了单链 DNA 对细胞核的包裹。

IF 3.3 3区生物学

Journal of cell science Pub Date : 2024-10-15 Epub Date: 2024-10-04 DOI: 10.1242/jcs.262039

Koichiro Maki, Jumpei Fukute, Taiji Adachi

{"title":"Super-resolution imaging reveals nucleolar encapsulation by single-stranded DNA.","authors":"Koichiro Maki, Jumpei Fukute, Taiji Adachi","doi":"10.1242/jcs.262039","DOIUrl":"10.1242/jcs.262039","url":null,"abstract":"In eukaryotic cell nuclei, specific sets of proteins gather in nuclear bodies and facilitate distinct genomic processes. The nucleolus, a nuclear body, functions as a factory for ribosome biogenesis by accumulating constitutive proteins, such as RNA polymerase I and nucleophosmin 1 (NPM1). Although in vitro assays have suggested the importance of liquid-liquid phase separation (LLPS) of constitutive proteins in nucleolar formation, how the nucleolus is structurally maintained with the intranuclear architecture remains unknown. This study revealed that the nucleolus is encapsulated by a single-stranded (ss)DNA-based molecular complex inside the cell nucleus. Super-resolution lattice-structured illumination microscopy (lattice-SIM) showed that there was a high abundance of ssDNA beyond the 'outer shell' of the nucleolus. Nucleolar disruption and the release of NPM1 were caused by in situ digestion of ssDNA, suggesting that ssDNA has a structural role in nucleolar encapsulation. Furthermore, we identified that ssDNA forms a molecular complex with histone H1 for nucleolar encapsulation. Thus, this study illustrates how an ssDNA-based molecular complex upholds the structural integrity of nuclear bodies to coordinate genomic processes such as gene transcription and replication.","PeriodicalId":15227,"journal":{"name":"Journal of cell science","volume":" ","pages":""},"PeriodicalIF":3.3,"publicationDate":"2024-10-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11463959/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142107733","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Precision in situ cryogenic correlative light and electron microscopy of optogenetically positioned organelles. 对光遗传定位细胞器进行精确的原位冷冻相关光镜和电子显微镜观察。

IF 3.3 3区生物学

Journal of cell science Pub Date : 2024-10-15 Epub Date: 2024-10-30 DOI: 10.1242/jcs.262163

Vikas A Tillu, Gregory M I Redpath, James Rae, Juanfang Ruan, Yin Yao, Maria L Cagigas, Renee Whan, Edna C Hardeman, Peter W Gunning, Vaishnavi Ananthanarayanan, Robert G Parton, Nicholas Ariotti

引用次数: 0

Synchrotron X-ray imaging of soft biological tissues - principles, applications and future prospects. 软生物组织的同步辐射 X 射线成像--原理、应用和前景。

IF 3.3 3区生物学

Journal of cell science Pub Date : 2024-10-15 Epub Date: 2024-10-23 DOI: 10.1242/jcs.261953

Jonas Albers, Angelika Svetlove, Elizabeth Duke

引用次数: 0

Erythroblast enucleation at a glance. 红细胞去核术一览。

IF 3.3 3区生物学

Journal of cell science Pub Date : 2024-10-01 Epub Date: 2024-10-14 DOI: 10.1242/jcs.261673

Lucas M Newton, Velia M Fowler, Patrick O Humbert

引用次数: 0