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Li T, Gachet Y, Tournier S. MAARS Software for Automatic and Quantitative Analysis of Mitotic Progression. Methods Mol Biol 2024; 2740:275-293. [PMID: 38393482 DOI: 10.1007/978-1-0716-3557-5_17] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/25/2024]
Abstract
In this chapter, we describe a software called MAARS (Mitotic Analysis And Recording System) that enables automatic and quantitative analysis of mitotic progression on an open-source platform. This computer-assisted analysis of cell division allows the unbiased acquisition of multiple parameters such as cell shape or size, metaphase or anaphase delays, as well as various mitotic abnormalities. This chapter describes the power of such an expert system to highlight the complexity of the mechanisms required to prevent mitotic chromosome segregation errors, leading to aneuploidy.
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Affiliation(s)
- Tong Li
- MCD, Centre de Biologie Intégrative, Université de Toulouse, CNRS, UPS, Toulouse Cedex, France
- Wellcome Sanger Institute, Cambridge, UK
| | - Yannick Gachet
- MCD, Centre de Biologie Intégrative, Université de Toulouse, CNRS, UPS, Toulouse Cedex, France.
| | - Sylvie Tournier
- MCD, Centre de Biologie Intégrative, Université de Toulouse, CNRS, UPS, Toulouse Cedex, France.
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2
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Ohira M, Rhind N. pomBseen: An automated pipeline for analysis of fission yeast images. PLoS One 2023; 18:e0291391. [PMID: 37699057 PMCID: PMC10497161 DOI: 10.1371/journal.pone.0291391] [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: 01/06/2023] [Accepted: 08/25/2023] [Indexed: 09/14/2023] Open
Abstract
Fission yeast is a model organism widely used for studies of eukaryotic cell biology. As such, it is subject to bright-field and fluorescent microscopy. Manual analysis of such data can be laborious and subjective. Therefore, we have developed pomBseen, an image analysis pipeline for the quantitation of fission yeast micrographs containing a bright-field channel and up to two fluorescent channels. It accepts a wide range of image formats and produces a table with the size and total and nuclear fluorescent intensities of the cells in the image. Benchmarking of the pipeline against manually annotated datasets demonstrates that it reliably segments cells and acquires their image parameters. Written in MATLAB, pomBseen is also available as a standalone application.
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Affiliation(s)
- Makoto Ohira
- Department of Biochemistry and Molecular Biotechnology, University of Massachusetts Medical School, Worcester, Massachusetts, United States of America
| | - Nicholas Rhind
- Department of Biochemistry and Molecular Biotechnology, University of Massachusetts Medical School, Worcester, Massachusetts, United States of America
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3
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Chen K, Watanabe M, Takeda Y, Maruyama T, Uesugi M, Takeuchi A, Suzuki M, Uesugi K, Yasutake M, Kawai M, Mitsumata T. In Situ Observation of the Movement of Magnetic Particles in Polyurethane Elastomer Densely Packed Magnetic Particles Using Synchrotron Radiation X-ray Computed Tomography. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2022; 38:13497-13505. [PMID: 36288501 DOI: 10.1021/acs.langmuir.2c02004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
In situ observation of the migration and structure formation of magnetic particles in polyurethane elastomers was carried out by X-ray computed tomography using synchrotron radiation. The mean diameter of the magnetic particles was 7.0 μm, and the volume fraction was ϕ= 0.24 at its maximum. The exposure time was 100 ms/frame, and the pixel size was 0.458 μm/pixel. The orientation angle and the volume fraction of the maximum aggregate were analyzed using commercial software for image analysis. The orientation angle for magnetic elastomers with ϕ = 0.24 was approximately 55° at 0 mT and decreased remarkably with the magnetic field. At magnetic fields above 150 mT, the orientation angle gradually decreased with the field and showed a constant value of 38° at 300 mT, suggesting that magnetic particles move and form a chain-like structure although the chains do not align perfectly in the direction of the magnetic field. On the other hand, the volume fraction of the maximum aggregate was constant at magnetic fields below 100 mT, and it significantly increased with the field, indicating that magnetic particles were connected to each other and developed into a macroscopic structure with anisotropy. Dynamic viscoelastic measurements revealed that the storage modulus of the magnetic elastomers cannot be simply scaled by the orientation angle. It was also found that the volume fraction of the maximum aggregate is a good parameter for explaining the huge increase in the storage modulus. The dynamic movement of magnetic particles when a magnetic field of 300 mT was switched on and off was also successfully observed. When the field was switched on, magnetic particles connected instantly and their aggregates were rapidly elongated in the direction of the magnetic field. When the field was switched off, some of the connections between aggregates were broken; however, most of the aggregates did not return to the original position even 5 min after being switched off.
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Affiliation(s)
- Kejun Chen
- Graduate School of Science and Technology, Niigata University, Niigata950-2181, Japan
| | - Mayuko Watanabe
- Graduate School of Science and Technology, Niigata University, Niigata950-2181, Japan
| | | | | | - Masayuki Uesugi
- Japan Synchrotron Radiation Research Institute (JASRI), Sayo, Hyogo679-5198, Japan
| | - Akihisa Takeuchi
- Japan Synchrotron Radiation Research Institute (JASRI), Sayo, Hyogo679-5198, Japan
| | - Motohiro Suzuki
- Japan Synchrotron Radiation Research Institute (JASRI), Sayo, Hyogo679-5198, Japan
| | - Kentaro Uesugi
- Japan Synchrotron Radiation Research Institute (JASRI), Sayo, Hyogo679-5198, Japan
| | - Masahiro Yasutake
- Japan Synchrotron Radiation Research Institute (JASRI), Sayo, Hyogo679-5198, Japan
| | - Mika Kawai
- Graduate School of Science and Technology, Niigata University, Niigata950-2181, Japan
| | - Tetsu Mitsumata
- Graduate School of Science and Technology, Niigata University, Niigata950-2181, Japan
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Esposito E, Weidemann DE, Rogers JM, Morton CM, Baybay EK, Chen J, Hauf S. Mitotic checkpoint gene expression is tuned by codon usage bias. EMBO J 2022; 41:e107896. [PMID: 35811551 PMCID: PMC9340482 DOI: 10.15252/embj.2021107896] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2021] [Revised: 05/30/2022] [Accepted: 06/06/2022] [Indexed: 11/09/2022] Open
Abstract
The mitotic checkpoint (also called spindle assembly checkpoint, SAC) is a signaling pathway that safeguards proper chromosome segregation. Correct functioning of the SAC depends on adequate protein concentrations and appropriate stoichiometries between SAC proteins. Yet very little is known about the regulation of SAC gene expression. Here, we show in the fission yeast Schizosaccharomyces pombe that a combination of short mRNA half-lives and long protein half-lives supports stable SAC protein levels. For the SAC genes mad2+ and mad3+ , their short mRNA half-lives are caused, in part, by a high frequency of nonoptimal codons. In contrast, mad1+ mRNA has a short half-life despite a higher frequency of optimal codons, and despite the lack of known RNA-destabilizing motifs. Hence, different SAC genes employ different strategies of expression. We further show that Mad1 homodimers form co-translationally, which may necessitate a certain codon usage pattern. Taken together, we propose that the codon usage of SAC genes is fine-tuned to ensure proper SAC function. Our work shines light on gene expression features that promote spindle assembly checkpoint function and suggests that synonymous mutations may weaken the checkpoint.
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Affiliation(s)
- Eric Esposito
- Department of Biological Sciences, Virginia Tech, Blacksburg, VA, USA.,Fralin Life Sciences Institute, Virginia Tech, Blacksburg, VA, USA
| | - Douglas E Weidemann
- Department of Biological Sciences, Virginia Tech, Blacksburg, VA, USA.,Fralin Life Sciences Institute, Virginia Tech, Blacksburg, VA, USA
| | - Jessie M Rogers
- Department of Biological Sciences, Virginia Tech, Blacksburg, VA, USA.,Fralin Life Sciences Institute, Virginia Tech, Blacksburg, VA, USA
| | - Claire M Morton
- Department of Biological Sciences, Virginia Tech, Blacksburg, VA, USA.,Fralin Life Sciences Institute, Virginia Tech, Blacksburg, VA, USA
| | - Erod Keaton Baybay
- Department of Biological Sciences, Virginia Tech, Blacksburg, VA, USA.,Fralin Life Sciences Institute, Virginia Tech, Blacksburg, VA, USA
| | - Jing Chen
- Department of Biological Sciences, Virginia Tech, Blacksburg, VA, USA.,Fralin Life Sciences Institute, Virginia Tech, Blacksburg, VA, USA
| | - Silke Hauf
- Department of Biological Sciences, Virginia Tech, Blacksburg, VA, USA.,Fralin Life Sciences Institute, Virginia Tech, Blacksburg, VA, USA
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García-Ruano D, Venkova L, Jain A, Ryan JC, Balasubramaniam VR, Piel M, Coudreuse D. Fluorescence exclusion: a rapid, accurate and powerful method for measuring yeast cell volume. J Cell Sci 2022; 135:275598. [PMID: 35662333 DOI: 10.1242/jcs.259392] [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: 10/11/2021] [Accepted: 05/26/2022] [Indexed: 11/20/2022] Open
Abstract
Cells exist in an astonishing range of volumes across and within species. However, our understanding of cell size control remains limited, due in large part to the challenges associated with accurate determination of cell volume. Much of our comprehension of size regulation derives from yeast models, but even for these morphologically stereotypical cells, assessment of cell volume has mostly relied on proxies and extrapolations from two-dimensional measurements. Recently, the fluorescence exclusion method (FXm) was developed to evaluate the size of mammalian cells, but whether it could be applied to smaller cells remained unknown. Using specifically designed microfluidic chips and an improved data analysis pipeline, we show here that FXm reliably detects subtle differences in the volume of fission yeast cells, even for those with altered shapes. Moreover, it allows for the monitoring of dynamic volume changes at the single-cell level with high time resolution. Collectively, our work highlights how the coupling of FXm with yeast genetics will bring new insights into the complex biology of cell growth.
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Affiliation(s)
- Daniel García-Ruano
- Institute of Genetics and Development of Rennes, UMR 6290, CNRS - University of Rennes 1, France
| | - Larisa Venkova
- Institut Curie and Institut Pierre Gilles de Gennes, PSL Research University, CNRS UMR 144, Paris, France.,Institute of Biochemistry and Cellular Genetics, CNRS UMR 5095, Bordeaux, France
| | - Akanksha Jain
- Institute of Genetics and Development of Rennes, UMR 6290, CNRS - University of Rennes 1, France
| | - Joseph C Ryan
- Institute of Genetics and Development of Rennes, UMR 6290, CNRS - University of Rennes 1, France
| | | | - Matthieu Piel
- Institut Curie and Institut Pierre Gilles de Gennes, PSL Research University, CNRS UMR 144, Paris, France
| | - Damien Coudreuse
- Institute of Genetics and Development of Rennes, UMR 6290, CNRS - University of Rennes 1, France.,Institute of Biochemistry and Cellular Genetics, CNRS UMR 5095, Bordeaux, France
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Cuny AP, Schlottmann FP, Ewald JC, Pelet S, Schmoller KM. Live cell microscopy: From image to insight. BIOPHYSICS REVIEWS 2022; 3:021302. [PMID: 38505412 PMCID: PMC10903399 DOI: 10.1063/5.0082799] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/18/2021] [Accepted: 03/18/2022] [Indexed: 03/21/2024]
Abstract
Live-cell microscopy is a powerful tool that can reveal cellular behavior as well as the underlying molecular processes. A key advantage of microscopy is that by visualizing biological processes, it can provide direct insights. Nevertheless, live-cell imaging can be technically challenging and prone to artifacts. For a successful experiment, many careful decisions are required at all steps from hardware selection to downstream image analysis. Facing these questions can be particularly intimidating due to the requirement for expertise in multiple disciplines, ranging from optics, biophysics, and programming to cell biology. In this review, we aim to summarize the key points that need to be considered when setting up and analyzing a live-cell imaging experiment. While we put a particular focus on yeast, many of the concepts discussed are applicable also to other organisms. In addition, we discuss reporting and data sharing strategies that we think are critical to improve reproducibility in the field.
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Affiliation(s)
| | - Fabian P. Schlottmann
- Interfaculty Institute of Cell Biology, University of Tuebingen, 72076 Tuebingen, Germany
| | - Jennifer C. Ewald
- Interfaculty Institute of Cell Biology, University of Tuebingen, 72076 Tuebingen, Germany
| | - Serge Pelet
- Department of Fundamental Microbiology, University of Lausanne, 1015 Lausanne, Switzerland
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