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Smith MB, Sparks H, Almagro J, Chaigne A, Behrens A, Dunsby C, Salbreux G. Active mesh and neural network pipeline for cell aggregate segmentation. Biophys J 2023; 122:1586-1599. [PMID: 37002604 PMCID: PMC10183373 DOI: 10.1016/j.bpj.2023.03.038] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2022] [Revised: 02/16/2023] [Accepted: 03/24/2023] [Indexed: 04/03/2023] Open
Abstract
Segmenting cells within cellular aggregates in 3D is a growing challenge in cell biology due to improvements in capacity and accuracy of microscopy techniques. Here, we describe a pipeline to segment images of cell aggregates in 3D. The pipeline combines neural network segmentations with active meshes. We apply our segmentation method to cultured mouse mammary gland organoids imaged over 24 h with oblique plane microscopy, a high-throughput light-sheet fluorescence microscopy technique. We show that our method can also be applied to images of mouse embryonic stem cells imaged with a spinning disc microscope. We segment individual cells based on nuclei and cell membrane fluorescent markers, and track cells over time. We describe metrics to quantify the quality of the automated segmentation. Our segmentation pipeline involves a Fiji plugin that implements active mesh deformation and allows a user to create training data, automatically obtain segmentation meshes from original image data or neural network prediction, and manually curate segmentation data to identify and correct mistakes. Our active meshes-based approach facilitates segmentation postprocessing, correction, and integration with neural network prediction.
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Affiliation(s)
| | - Hugh Sparks
- Photonics Group, Department of Physics, Imperial College London, London, United Kingdom
| | | | - Agathe Chaigne
- Cell Biology, Neurobiology and Biophysics, Department of Biology, Faculty of Science, Utrecht University, Utrecht, the Netherlands
| | - Axel Behrens
- Cancer Stem Cell Team, The Institute of Cancer Research, London, United Kingdom
| | - Chris Dunsby
- Photonics Group, Department of Physics, Imperial College London, London, United Kingdom
| | - Guillaume Salbreux
- The Francis Crick Institute, London, United Kingdom; Department of Genetics and Evolution, Geneva, Switzerland.
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2
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Li Y, Liang W, Li C. Exogenous adenosine and/or guanosine enhances tetracycline sensitivity of persister cells. Microbiol Res 2023; 270:127321. [PMID: 36773473 DOI: 10.1016/j.micres.2023.127321] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2022] [Revised: 01/25/2023] [Accepted: 02/04/2023] [Indexed: 02/11/2023]
Abstract
Vibrio splendidus is an opportunistic pathogen, its pathogenicity continues to be a major aquaculture disease infection problem in many parts of the world. Bacteria can form dormant and persister cells, which may be responsible for the difficulty in treating latent infections. Bacterial persister cells are a small subpopulation with high phenotypic heterogeneity that have the ability to persist in response to high concentrations of antibiotics. In our previous work, we have confirmed tetracycline could induce V. splendidus AJ01 persister cells formation. Here, we show that exogenous adenosine and/or guanosine supply restores susceptibility of AJ01 persister cells to tetracycline, leading to effective killing of this persist subpopulation upon wake-up. Mechanistically, exogenous adenosine and/or guanosine promotes the intracellular ATP level, reduces percentage of cells with protein aggresomes, and destroys membrane stability. In addition, when cells were exposed to tetracycline, we found that cells with small nucleocytoplasmic ratio is easy to survive. Overall, our results support that exogenous adenosine or guanosine could be an effective strategy for treating infections with antibiotic-persist bacteria via regulating persisters cells formation.
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Affiliation(s)
- Yanan Li
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Ningbo University, Ningbo 315211, PR China; Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266071, PR China
| | - Weikang Liang
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Ningbo University, Ningbo 315211, PR China
| | - Chenghua Li
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Ningbo University, Ningbo 315211, PR China; Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266071, PR China.
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3
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Kirkland NJ, Skalak SH, Whitehead AJ, Hocker JD, Beri P, Vogler G, Hum B, Wang M, Lakatta EG, Ren B, Bodmer R, Engler AJ. Age-dependent Lamin changes induce cardiac dysfunction via dysregulation of cardiac transcriptional programs. NATURE AGING 2023; 3:17-33. [PMID: 36845078 PMCID: PMC9956937 DOI: 10.1038/s43587-022-00323-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/26/2021] [Accepted: 10/31/2022] [Indexed: 12/24/2022]
Abstract
As we age, structural changes contribute to progressive decline in organ function, which in the heart act through poorly characterized mechanisms. Taking advantage of the short lifespan and conserved cardiac proteome of the fruit fly, we found that cardiomyocytes exhibit progressive loss of Lamin C (mammalian Lamin A/C homologue) with age, coincident with decreasing nuclear size and increasing nuclear stiffness. Premature genetic reduction of Lamin C phenocopies aging's effects on the nucleus, and subsequently decreases heart contractility and sarcomere organization. Surprisingly, Lamin C reduction downregulates myogenic transcription factors and cytoskeletal regulators, possibly via reduced chromatin accessibility. Subsequently, we find a role for cardiac transcription factors in regulating adult heart contractility and show that maintenance of Lamin C, and cardiac transcription factor expression, prevents age-dependent cardiac decline. Our findings are conserved in aged non-human primates and mice, demonstrating that age-dependent nuclear remodeling is a major mechanism contributing to cardiac dysfunction.
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Affiliation(s)
- Natalie J. Kirkland
- Department of Bioengineering, University California San Diego; La Jolla, CA, USA 92093
- Sanford Consortium for Regenerative Medicine; La Jolla, CA, USA 92037
| | - Scott H. Skalak
- Department of Bioengineering, University California San Diego; La Jolla, CA, USA 92093
- Sanford Consortium for Regenerative Medicine; La Jolla, CA, USA 92037
| | - Alexander J. Whitehead
- Department of Bioengineering, University California San Diego; La Jolla, CA, USA 92093
- Sanford Consortium for Regenerative Medicine; La Jolla, CA, USA 92037
| | - James D. Hocker
- Cell and Molecular Medicine, University California San Diego; La Jolla, CA, USA 92093
- Biomedical Sciences Program, University California San Diego; La Jolla, CA, USA 92093
| | - Pranjali Beri
- Department of Bioengineering, University California San Diego; La Jolla, CA, USA 92093
- Sanford Consortium for Regenerative Medicine; La Jolla, CA, USA 92037
| | - Geo Vogler
- Development, Aging and Regeneration Program, Sanford-Burnham-Prebys Medical Discovery Institute; La Jolla, CA, USA 92037
| | - Bill Hum
- Development, Aging and Regeneration Program, Sanford-Burnham-Prebys Medical Discovery Institute; La Jolla, CA, USA 92037
| | - Mingyi Wang
- Laboratory of Cardiovascular Science, Intramural Research Program, National Institute on Aging, National Institutes of Health, Baltimore, MD, USA 21224
| | - Edward G. Lakatta
- Laboratory of Cardiovascular Science, Intramural Research Program, National Institute on Aging, National Institutes of Health, Baltimore, MD, USA 21224
| | - Bing Ren
- Cell and Molecular Medicine, University California San Diego; La Jolla, CA, USA 92093
- Biomedical Sciences Program, University California San Diego; La Jolla, CA, USA 92093
- Ludwig Institute for Cancer Research; La Jolla, CA, USA 92037
| | - Rolf Bodmer
- Development, Aging and Regeneration Program, Sanford-Burnham-Prebys Medical Discovery Institute; La Jolla, CA, USA 92037
| | - Adam J. Engler
- Department of Bioengineering, University California San Diego; La Jolla, CA, USA 92093
- Biomedical Sciences Program, University California San Diego; La Jolla, CA, USA 92093
- Sanford Consortium for Regenerative Medicine; La Jolla, CA, USA 92037
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Zamora-Bello I, Hernandez-Baltazar D, Rodríguez-Landa JF, Rivadeneyra-Domínguez E. Optimizing rat and human blood cells sampling for in silico morphometric analysis. Acta Histochem 2022; 124:151917. [PMID: 35716583 DOI: 10.1016/j.acthis.2022.151917] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2022] [Revised: 05/31/2022] [Accepted: 06/07/2022] [Indexed: 11/01/2022]
Abstract
Measurements of Morphometric Parameters of the Blood Cells (MPBC) are key for the diagnosis of both mental and metabolic diseases. Several manual approaches or computational methodologies are useful to provide reliable clinical diagnosis. The sample processing and data analysis is relevant, however the sample handling on the pre-analytical phase remains scarcely evaluated. The main goal of this study was to favor the preservation of blood smear using a histological resin. This strategy lead us two practical approaches, give a detailed morphometric description of white blood cells and establish reference intervals in male Wistar rats, which are scarcely reported. Blood smears from male Wistar rats (n = 120) and adult men were collected at room temperature. The integrity of Wright-stained cells was evaluated by an in silico image analysis from rat and human blood smear preserved with a toluene-based synthetic resin mounting medium. A single sample of human blood was used as a control of procedure. The reference intervals was established by cell counting. Based on the results of segmentation algorithm followed by an automatic thresholding analysis, the incorporation of resin favor the conservation of cell blood populations, and lead to identify morphologic features such as nucleus/cytoplasmic shape, granules presence and DNA appearance in nucleus of white blood cells. The use of a histological resin could favor a fast and efficient sample handling in silico MPBC measurements both in the species studied as in wild animals.
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Affiliation(s)
- Isaac Zamora-Bello
- Facultad de Química Farmacéutica Biológica, Universidad Veracruzana, Xalapa, Veracruz, Mexico.
| | - Daniel Hernandez-Baltazar
- Investigadoras e investigadores por México. Consejo Nacional de Ciencia y Tecnología (CONACyT), CDMX, Mexico; Instituto de Neuroetología, Universidad Veracruzana, Xalapa, Veracruz, Mexico.
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Chaigne A, Smith MB, Lopez Cavestany R, Hannezo E, Chalut KJ, Paluch EK. Three-dimensional geometry controls division symmetry in stem cell colonies. J Cell Sci 2021; 134:jcs255018. [PMID: 34323278 PMCID: PMC8349555 DOI: 10.1242/jcs.255018] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2020] [Accepted: 06/16/2021] [Indexed: 11/24/2022] Open
Abstract
Proper control of division orientation and symmetry, largely determined by spindle positioning, is essential to development and homeostasis. Spindle positioning has been extensively studied in cells dividing in two-dimensional (2D) environments and in epithelial tissues, where proteins such as NuMA (also known as NUMA1) orient division along the interphase long axis of the cell. However, little is known about how cells control spindle positioning in three-dimensional (3D) environments, such as early mammalian embryos and a variety of adult tissues. Here, we use mouse embryonic stem cells (ESCs), which grow in 3D colonies, as a model to investigate division in 3D. We observe that, at the periphery of 3D colonies, ESCs display high spindle mobility and divide asymmetrically. Our data suggest that enhanced spindle movements are due to unequal distribution of the cell-cell junction protein E-cadherin between future daughter cells. Interestingly, when cells progress towards differentiation, division becomes more symmetric, with more elongated shapes in metaphase and enhanced cortical NuMA recruitment in anaphase. Altogether, this study suggests that in 3D contexts, the geometry of the cell and its contacts with neighbors control division orientation and symmetry. This article has an associated First Person interview with the first author of the paper.
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Affiliation(s)
- Agathe Chaigne
- MRC Laboratory for Molecular Cell Biology, University College London, London WC1E 6BT, UK
| | - Matthew B. Smith
- MRC Laboratory for Molecular Cell Biology, University College London, London WC1E 6BT, UK
| | - Rocio Lopez Cavestany
- MRC Laboratory for Molecular Cell Biology, University College London, London WC1E 6BT, UK
| | | | - Kevin J. Chalut
- Wellcome/MRC Stem Cell Institute, University of Cambridge, Cambridge CB2 0AW, UK
- Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge CB2 3DY, UK
| | - Ewa K. Paluch
- MRC Laboratory for Molecular Cell Biology, University College London, London WC1E 6BT, UK
- Wellcome/MRC Stem Cell Institute, University of Cambridge, Cambridge CB2 0AW, UK
- Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge CB2 3DY, UK
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Chaigne A, Labouesse C, White IJ, Agnew M, Hannezo E, Chalut KJ, Paluch EK. Abscission Couples Cell Division to Embryonic Stem Cell Fate. Dev Cell 2020; 55:195-208.e5. [PMID: 32979313 PMCID: PMC7594744 DOI: 10.1016/j.devcel.2020.09.001] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2020] [Revised: 06/22/2020] [Accepted: 08/30/2020] [Indexed: 12/30/2022]
Abstract
Cell fate transitions are key to development and homeostasis. It is thus essential to understand the cellular mechanisms controlling fate transitions. Cell division has been implicated in fate decisions in many stem cell types, including neuronal and epithelial progenitors. In other stem cells, such as embryonic stem (ES) cells, the role of division remains unclear. Here, we show that exit from naive pluripotency in mouse ES cells generally occurs after a division. We further show that exit timing is strongly correlated between sister cells, which remain connected by cytoplasmic bridges long after division, and that bridge abscission progressively accelerates as cells exit naive pluripotency. Finally, interfering with abscission impairs naive pluripotency exit, and artificially inducing abscission accelerates it. Altogether, our data indicate that a switch in the division machinery leading to faster abscission regulates pluripotency exit. Our study identifies abscission as a key cellular process coupling cell division to fate transitions. Mouse embryonic stem cells exit naive pluripotency after mitosis Naive embryonic stem cells display slow abscission and remain connected by bridges Cells exiting naive pluripotency display faster abscission Accelerating abscission facilitates exit from naive pluripotency
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Affiliation(s)
- Agathe Chaigne
- MRC Laboratory for Molecular Cell Biology, University College London, London WC1E 6BT, UK.
| | - Céline Labouesse
- Wellcome/MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge CB2 0AW, UK
| | - Ian J White
- MRC Laboratory for Molecular Cell Biology, University College London, London WC1E 6BT, UK
| | - Meghan Agnew
- MRC Laboratory for Molecular Cell Biology, University College London, London WC1E 6BT, UK
| | - Edouard Hannezo
- Institute of Science and Technology Austria, Klosterneuburg 3400, Austria
| | - Kevin J Chalut
- Wellcome/MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge CB2 0AW, UK
| | - Ewa K Paluch
- MRC Laboratory for Molecular Cell Biology, University College London, London WC1E 6BT, UK; Wellcome/MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge CB2 0AW, UK; Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge CB2 3DY, UK.
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