1
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La Cavera S, Chauhan VM, Hardiman W, Yao M, Fuentes-Domínguez R, Setchfield K, Abayzeed SA, Pérez-Cota F, Smith RJ, Clark M. Label-free Brillouin endo-microscopy for the quantitative 3D imaging of sub-micrometre biology. Commun Biol 2024; 7:451. [PMID: 38622287 PMCID: PMC11018753 DOI: 10.1038/s42003-024-06126-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2023] [Accepted: 03/29/2024] [Indexed: 04/17/2024] Open
Abstract
This report presents an optical fibre-based endo-microscopic imaging tool that simultaneously measures the topographic profile and 3D viscoelastic properties of biological specimens through the phenomenon of time-resolved Brillouin scattering. This uses the intrinsic viscoelasticity of the specimen as a contrast mechanism without fluorescent tags or photoacoustic contrast mechanisms. We demonstrate 2 μm lateral resolution and 320 nm axial resolution for the 3D imaging of biological cells and Caenorhabditis elegans larvae. This has enabled the first ever 3D stiffness imaging and characterisation of the C. elegans larva cuticle in-situ. A label-free, subcellular resolution, and endoscopic compatible technique that reveals structural biologically-relevant material properties of tissue could pave the way toward in-vivo elasticity-based diagnostics down to the single cell level.
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Affiliation(s)
- Salvatore La Cavera
- Optics and Photonics Group, Faculty of Engineering, University of Nottingham, University Park, Nottingham, NG7 2RD, UK.
| | - Veeren M Chauhan
- Advanced Materials & Healthcare Technologies, School of Pharmacy, University of Nottingham, University Park, Nottingham, NG7 2RD, UK.
| | - William Hardiman
- Optics and Photonics Group, Faculty of Engineering, University of Nottingham, University Park, Nottingham, NG7 2RD, UK
| | - Mengting Yao
- Optics and Photonics Group, Faculty of Engineering, University of Nottingham, University Park, Nottingham, NG7 2RD, UK
| | - Rafael Fuentes-Domínguez
- Optics and Photonics Group, Faculty of Engineering, University of Nottingham, University Park, Nottingham, NG7 2RD, UK
| | - Kerry Setchfield
- Optics and Photonics Group, Faculty of Engineering, University of Nottingham, University Park, Nottingham, NG7 2RD, UK
| | - Sidahmed A Abayzeed
- Optics and Photonics Group, Faculty of Engineering, University of Nottingham, University Park, Nottingham, NG7 2RD, UK
| | - Fernando Pérez-Cota
- Optics and Photonics Group, Faculty of Engineering, University of Nottingham, University Park, Nottingham, NG7 2RD, UK
| | - Richard J Smith
- Optics and Photonics Group, Faculty of Engineering, University of Nottingham, University Park, Nottingham, NG7 2RD, UK
| | - Matt Clark
- Optics and Photonics Group, Faculty of Engineering, University of Nottingham, University Park, Nottingham, NG7 2RD, UK
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2
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Friedrichsen K, Hsiang JC, Lin CI, McCoy L, Valkova K, Kerschensteiner D, Morgan JL. Subcellular pathways through VGluT3-expressing mouse amacrine cells provide locally tuned object-motion-selective signals in the retina. Nat Commun 2024; 15:2965. [PMID: 38580652 PMCID: PMC10997783 DOI: 10.1038/s41467-024-46996-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2023] [Accepted: 03/15/2024] [Indexed: 04/07/2024] Open
Abstract
VGluT3-expressing mouse retinal amacrine cells (VG3s) respond to small-object motion and connect to multiple types of bipolar cells (inputs) and retinal ganglion cells (RGCs, outputs). Because these input and output connections are intermixed on the same dendrites, making sense of VG3 circuitry requires comparing the distribution of synapses across their arbors to the subcellular flow of signals. Here, we combine subcellular calcium imaging and electron microscopic connectomic reconstruction to analyze how VG3s integrate and transmit visual information. VG3s receive inputs from all nearby bipolar cell types but exhibit a strong preference for the fast type 3a bipolar cells. By comparing input distributions to VG3 dendrite responses, we show that VG3 dendrites have a short functional length constant that likely depends on inhibitory shunting. This model predicts that RGCs that extend dendrites into the middle layers of the inner plexiform encounter VG3 dendrites whose responses vary according to the local bipolar cell response type.
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Affiliation(s)
- Karl Friedrichsen
- Department of Ophthalmology and Visual Sciences, Washington University in St. Louis, St. Louis, MO, USA
- Department of Neuroscience, Washington University in St. Louis, St. Louis, MO, USA
- Department of Biomedical Engineering, Washington University in St. Louis, St. Louis, MO, USA
- Graduate Program in Neuroscience, Washington University in St. Louis, St. Louis, USA
| | - Jen-Chun Hsiang
- Department of Ophthalmology and Visual Sciences, Washington University in St. Louis, St. Louis, MO, USA
- Department of Neuroscience, Washington University in St. Louis, St. Louis, MO, USA
- Department of Biomedical Engineering, Washington University in St. Louis, St. Louis, MO, USA
- Graduate Program in Neuroscience, Washington University in St. Louis, St. Louis, USA
| | - Chin-I Lin
- Department of Ophthalmology and Visual Sciences, Washington University in St. Louis, St. Louis, MO, USA
- Department of Neuroscience, Washington University in St. Louis, St. Louis, MO, USA
- Department of Biomedical Engineering, Washington University in St. Louis, St. Louis, MO, USA
- Graduate Program in Neuroscience, Washington University in St. Louis, St. Louis, USA
| | - Liam McCoy
- Department of Ophthalmology and Visual Sciences, Washington University in St. Louis, St. Louis, MO, USA
- Department of Neuroscience, Washington University in St. Louis, St. Louis, MO, USA
- Department of Biomedical Engineering, Washington University in St. Louis, St. Louis, MO, USA
| | - Katia Valkova
- Department of Ophthalmology and Visual Sciences, Washington University in St. Louis, St. Louis, MO, USA
- Department of Neuroscience, Washington University in St. Louis, St. Louis, MO, USA
- Department of Biomedical Engineering, Washington University in St. Louis, St. Louis, MO, USA
| | - Daniel Kerschensteiner
- Department of Ophthalmology and Visual Sciences, Washington University in St. Louis, St. Louis, MO, USA
- Department of Neuroscience, Washington University in St. Louis, St. Louis, MO, USA
- Department of Biomedical Engineering, Washington University in St. Louis, St. Louis, MO, USA
| | - Josh L Morgan
- Department of Ophthalmology and Visual Sciences, Washington University in St. Louis, St. Louis, MO, USA.
- Department of Neuroscience, Washington University in St. Louis, St. Louis, MO, USA.
- Department of Biomedical Engineering, Washington University in St. Louis, St. Louis, MO, USA.
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3
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Lozano D, López JM, Chinarro A, Morona R, Moreno N. A detailed 3D MRI brain atlas of the African lungfish Protopterus annectens. Sci Rep 2024; 14:7999. [PMID: 38580713 PMCID: PMC10997765 DOI: 10.1038/s41598-024-58671-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2024] [Accepted: 04/02/2024] [Indexed: 04/07/2024] Open
Abstract
The study of the brain by magnetic resonance imaging (MRI) in evolutionary analyses is still in its incipient stage, however, it is particularly useful as it allows us to analyze detailed anatomical images and compare brains of rare or otherwise inaccessible species, evolutionarily contextualizing possible differences, while at the same time being non-invasive. A good example is the lungfishes, sarcopterygians that are the closest living relatives of tetrapods and thus have an interesting phylogenetic position in the evolutionary conquest of the terrestrial environment. In the present study, we have developed a three-dimensional representation of the brain of the lungfish Protopterus annectens together with a rostrocaudal anatomical atlas. This methodological approach provides a clear delineation of the major brain subdivisions of this model and allows to measure both brain and ventricular volumes. Our results confirm that lungfish show neuroanatomical patterns reminiscent of those of extant basal sarcopterygians, with an evaginated telencephalon, and distinctive characters like a small optic tectum. These and additional characters uncover lungfish as a remarkable model to understand the origins of tetrapod diversity, indicating that their brain may contain significant clues to the characters of the brain of ancestral tetrapods.
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Affiliation(s)
- Daniel Lozano
- Department of Cell Biology, Faculty of Biological Sciences, Complutense University, 28040, Madrid, Spain.
| | - Jesús M López
- Department of Cell Biology, Faculty of Biological Sciences, Complutense University, 28040, Madrid, Spain
| | - Adrián Chinarro
- Department of Cell Biology, Faculty of Biological Sciences, Complutense University, 28040, Madrid, Spain
| | - Ruth Morona
- Department of Cell Biology, Faculty of Biological Sciences, Complutense University, 28040, Madrid, Spain
| | - Nerea Moreno
- Department of Cell Biology, Faculty of Biological Sciences, Complutense University, 28040, Madrid, Spain
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4
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Kvåle Løvmo M, Deng S, Moser S, Leitgeb R, Drexler W, Ritsch-Marte M. Ultrasound-induced reorientation for multi-angle optical coherence tomography. Nat Commun 2024; 15:2391. [PMID: 38493195 PMCID: PMC10944478 DOI: 10.1038/s41467-024-46506-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2023] [Accepted: 02/29/2024] [Indexed: 03/18/2024] Open
Abstract
Organoid and spheroid technology provide valuable insights into developmental biology and oncology. Optical coherence tomography (OCT) is a label-free technique that has emerged as an excellent tool for monitoring the structure and function of these samples. However, mature organoids are often too opaque for OCT. Access to multi-angle views is highly desirable to overcome this limitation, preferably with non-contact sample handling. To fulfil these requirements, we present an ultrasound-induced reorientation method for multi-angle-OCT, which employs a 3D-printed acoustic trap inserted into an OCT imaging system, to levitate and reorient zebrafish larvae and tumor spheroids in a controlled and reproducible manner. A model-based algorithm was developed for the physically consistent fusion of multi-angle data from a priori unknown angles. We demonstrate enhanced penetration depth in the joint 3D-recovery of reflectivity, attenuation, refractive index, and position registration for zebrafish larvae, creating an enabling tool for future applications in volumetric imaging.
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Affiliation(s)
- Mia Kvåle Løvmo
- Institute of Biomedical Physics, Medical University of Innsbruck, Innsbruck, Austria
| | - Shiyu Deng
- Center for Medical Physics and Biomedical Engineering, Medical University of Vienna, Vienna, Austria
| | - Simon Moser
- Institute of Biomedical Physics, Medical University of Innsbruck, Innsbruck, Austria
| | - Rainer Leitgeb
- Center for Medical Physics and Biomedical Engineering, Medical University of Vienna, Vienna, Austria
| | - Wolfgang Drexler
- Center for Medical Physics and Biomedical Engineering, Medical University of Vienna, Vienna, Austria
| | - Monika Ritsch-Marte
- Institute of Biomedical Physics, Medical University of Innsbruck, Innsbruck, Austria.
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5
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Hua X, Han K, Mandracchia B, Radmand A, Liu W, Kim H, Yuan Z, Ehrlich SM, Li K, Zheng C, Son J, Silva Trenkle AD, Kwong GA, Zhu C, Dahlman JE, Jia S. Light-field flow cytometry for high-resolution, volumetric and multiparametric 3D single-cell analysis. Nat Commun 2024; 15:1975. [PMID: 38438356 PMCID: PMC10912605 DOI: 10.1038/s41467-024-46250-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2023] [Accepted: 02/15/2024] [Indexed: 03/06/2024] Open
Abstract
Imaging flow cytometry (IFC) combines flow cytometry and fluorescence microscopy to enable high-throughput, multiparametric single-cell analysis with rich spatial details. However, current IFC techniques remain limited in their ability to reveal subcellular information with a high 3D resolution, throughput, sensitivity, and instrumental simplicity. In this study, we introduce a light-field flow cytometer (LFC), an IFC system capable of high-content, single-shot, and multi-color acquisition of up to 5,750 cells per second with a near-diffraction-limited resolution of 400-600 nm in all three dimensions. The LFC system integrates optical, microfluidic, and computational strategies to facilitate the volumetric visualization of various 3D subcellular characteristics through convenient access to commonly used epi-fluorescence platforms. We demonstrate the effectiveness of LFC in assaying, analyzing, and enumerating intricate subcellular morphology, function, and heterogeneity using various phantoms and biological specimens. The advancement offered by the LFC system presents a promising methodological pathway for broad cell biological and translational discoveries, with the potential for widespread adoption in biomedical research.
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Affiliation(s)
- Xuanwen Hua
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, GA, USA
| | - Keyi Han
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, GA, USA
| | - Biagio Mandracchia
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, GA, USA
| | - Afsane Radmand
- Parker H. Petit Institute for Bioengineering and Biosciences, Georgia Institute of Technology, Atlanta, GA, USA
- Department of Chemical Engineering, Georgia Institute of Technology, Atlanta, GA, USA
| | - Wenhao Liu
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, GA, USA
| | - Hyejin Kim
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, GA, USA
| | - Zhou Yuan
- Parker H. Petit Institute for Bioengineering and Biosciences, Georgia Institute of Technology, Atlanta, GA, USA
- Georgia W. Woodruff School of Mechanical Engineering, Georgia Institute of Technology, Atlanta, GA, USA
| | - Samuel M Ehrlich
- Parker H. Petit Institute for Bioengineering and Biosciences, Georgia Institute of Technology, Atlanta, GA, USA
- Georgia W. Woodruff School of Mechanical Engineering, Georgia Institute of Technology, Atlanta, GA, USA
| | - Kaitao Li
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, GA, USA
| | - Corey Zheng
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, GA, USA
| | - Jeonghwan Son
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, GA, USA
| | - Aaron D Silva Trenkle
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, GA, USA
| | - Gabriel A Kwong
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, GA, USA
- Parker H. Petit Institute for Bioengineering and Biosciences, Georgia Institute of Technology, Atlanta, GA, USA
| | - Cheng Zhu
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, GA, USA
- Parker H. Petit Institute for Bioengineering and Biosciences, Georgia Institute of Technology, Atlanta, GA, USA
| | - James E Dahlman
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, GA, USA
- Parker H. Petit Institute for Bioengineering and Biosciences, Georgia Institute of Technology, Atlanta, GA, USA
| | - Shu Jia
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, GA, USA.
- Parker H. Petit Institute for Bioengineering and Biosciences, Georgia Institute of Technology, Atlanta, GA, USA.
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6
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Manafzadeh AR, Gatesy SM, Bhullar BAS. Articular surface interactions distinguish dinosaurian locomotor joint poses. Nat Commun 2024; 15:854. [PMID: 38365765 PMCID: PMC10873393 DOI: 10.1038/s41467-024-44832-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2023] [Accepted: 01/08/2024] [Indexed: 02/18/2024] Open
Abstract
Our knowledge of vertebrate functional evolution depends on inferences about joint function in extinct taxa. Without rigorous criteria for evaluating joint articulation, however, such analyses risk misleading reconstructions of vertebrate animal motion. Here we propose an approach for synthesizing raycast-based measurements of 3-D articular overlap, symmetry, and congruence into a quantitative "articulation score" for any non-interpenetrating six-degree-of-freedom joint configuration. We apply our methodology to bicondylar hindlimb joints of two extant dinosaurs (guineafowl, emu) and, through comparison with in vivo kinematics, find that locomotor joint poses consistently have high articulation scores. We then exploit this relationship to constrain reconstruction of a pedal walking stride cycle for the extinct dinosaur Deinonychus antirrhopus, demonstrating the utility of our approach. As joint articulation is investigated in more living animals, the framework we establish here can be expanded to accommodate additional joints and clades, facilitating improved understanding of vertebrate animal motion and its evolution.
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Affiliation(s)
- Armita R Manafzadeh
- Yale Institute for Biospheric Studies, Yale University, New Haven, CT, 06520, USA.
- Department of Earth & Planetary Sciences, Yale University, New Haven, CT, 06520, USA.
- Yale Peabody Museum of Natural History, New Haven, CT, 06520, USA.
| | - Stephen M Gatesy
- Department of Ecology, Evolution, and Organismal Biology, Brown University, Providence, RI, 02912, USA
| | - Bhart-Anjan S Bhullar
- Department of Earth & Planetary Sciences, Yale University, New Haven, CT, 06520, USA
- Yale Peabody Museum of Natural History, New Haven, CT, 06520, USA
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7
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Abd El-Sadek I, Morishita R, Mori T, Makita S, Mukherjee P, Matsusaka S, Yasuno Y. Label-free visualization and quantification of the drug-type-dependent response of tumor spheroids by dynamic optical coherence tomography. Sci Rep 2024; 14:3366. [PMID: 38336794 PMCID: PMC10858208 DOI: 10.1038/s41598-024-53171-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2023] [Accepted: 01/29/2024] [Indexed: 02/12/2024] Open
Abstract
We demonstrate label-free dynamic optical coherence tomography (D-OCT)-based visualization and quantitative assessment of patterns of tumor spheroid response to three anti-cancer drugs. The study involved treating human breast adenocarcinoma (MCF-7 cell-line) with paclitaxel (PTX), tamoxifen citrate (TAM), and doxorubicin (DOX) at concentrations of 0 (control), 0.1, 1, and 10 µM for 1, 3, and 6 days. In addition, fluorescence microscopy imaging was performed for reference. The D-OCT imaging was performed using a custom-built OCT device. Two algorithms, namely logarithmic intensity variance (LIV) and late OCT correlation decay speed (OCDS[Formula: see text]) were used to visualize the tissue dynamics. The spheroids treated with 0.1 and 1 µM TAM appeared similar to the control spheroid, whereas those treated with 10 µM TAM had significant structural corruption and decreasing LIV and OCDS[Formula: see text] over treatment time. The spheroids treated with PTX had decreasing volumes and decrease of LIV and OCDS[Formula: see text] signals over time at most PTX concentrations. The spheroids treated with DOX had decreasing and increasing volumes over time at DOX concentrations of 1 and 10 µM, respectively. Meanwhile, the LIV and OCDS[Formula: see text] signals decreased over treatment time at all DOX concentrations. The D-OCT, particularly OCDS[Formula: see text], patterns were consistent with the fluorescence microscopic patterns. The diversity in the structural and D-OCT results among the drug types and among the concentrations are explained by the mechanisms of the drugs. The presented results suggest that D-OCT is useful for evaluating the difference in the tumor spheroid response to different drugs and it can be a useful tool for anti-cancer drug testing.
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Affiliation(s)
- Ibrahim Abd El-Sadek
- Computational Optics Group, University of Tsukuba, Tsukuba, Ibaraki, 305-8573, Japan
- Department of Physics, Faculty of Science, Damietta University, New Damietta City, Damietta, 34517, Egypt
| | - Rion Morishita
- Computational Optics Group, University of Tsukuba, Tsukuba, Ibaraki, 305-8573, Japan
| | - Tomoko Mori
- Clinical Research and Regional Innovation, Faculty of Medicine, University of Tsukuba, Ibaraki, 305-8575, Japan
| | - Shuichi Makita
- Computational Optics Group, University of Tsukuba, Tsukuba, Ibaraki, 305-8573, Japan
| | - Pradipta Mukherjee
- Computational Optics Group, University of Tsukuba, Tsukuba, Ibaraki, 305-8573, Japan
| | - Satoshi Matsusaka
- Clinical Research and Regional Innovation, Faculty of Medicine, University of Tsukuba, Ibaraki, 305-8575, Japan
| | - Yoshiaki Yasuno
- Computational Optics Group, University of Tsukuba, Tsukuba, Ibaraki, 305-8573, Japan.
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8
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Martínez-Torres D, Maldonado V, Pérez-Gallardo C, Yañez R, Candia V, Kalaidzidis Y, Zerial M, Morales-Navarrete H, Segovia-Miranda F. Phenotypic characterization of liver tissue heterogeneity through a next-generation 3D single-cell atlas. Sci Rep 2024; 14:2823. [PMID: 38307948 PMCID: PMC10837128 DOI: 10.1038/s41598-024-53309-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2023] [Accepted: 01/30/2024] [Indexed: 02/04/2024] Open
Abstract
Three-dimensional (3D) geometrical models are potent tools for quantifying complex tissue features and exploring structure-function relationships. However, these models are generally incomplete due to experimental limitations in acquiring multiple (> 4) fluorescent channels in thick tissue sections simultaneously. Indeed, predictive geometrical and functional models of the liver have been restricted to few tissue and cellular components, excluding important cellular populations such as hepatic stellate cells (HSCs) and Kupffer cells (KCs). Here, we combined deep-tissue immunostaining, multiphoton microscopy, deep-learning techniques, and 3D image processing to computationally expand the number of simultaneously reconstructed tissue structures. We then generated a spatial single-cell atlas of hepatic architecture (Hep3D), including all main tissue and cellular components at different stages of post-natal development in mice. We used Hep3D to quantitatively study 1) hepatic morphodynamics from early post-natal development to adulthood, and 2) the effect on the liver's overall structure when changing the hepatic environment after removing KCs. In addition to a complete description of bile canaliculi and sinusoidal network remodeling, our analysis uncovered unexpected spatiotemporal patterns of non-parenchymal cells and hepatocytes differing in size, number of nuclei, and DNA content. Surprisingly, we found that the specific depletion of KCs results in morphological changes in hepatocytes and HSCs. These findings reveal novel characteristics of liver heterogeneity and have important implications for both the structural organization of liver tissue and its function. Our next-gen 3D single-cell atlas is a powerful tool to understand liver tissue architecture, opening up avenues for in-depth investigations into tissue structure across both normal and pathological conditions.
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Affiliation(s)
- Dilan Martínez-Torres
- Department of Cell Biology, Faculty of Biological Sciences, Universidad de Concepción, Concepción, Chile
- Grupo de Procesos en Biología del Desarrollo (GDeP), Faculty of Biological Sciences, Universidad de Concepción, Concepción, Chile
| | - Valentina Maldonado
- Department of Cell Biology, Faculty of Biological Sciences, Universidad de Concepción, Concepción, Chile
- Grupo de Procesos en Biología del Desarrollo (GDeP), Faculty of Biological Sciences, Universidad de Concepción, Concepción, Chile
| | - Cristian Pérez-Gallardo
- Department of Cell Biology, Faculty of Biological Sciences, Universidad de Concepción, Concepción, Chile
- Grupo de Procesos en Biología del Desarrollo (GDeP), Faculty of Biological Sciences, Universidad de Concepción, Concepción, Chile
| | - Rodrigo Yañez
- Department of Cell Biology, Faculty of Biological Sciences, Universidad de Concepción, Concepción, Chile
- Grupo de Procesos en Biología del Desarrollo (GDeP), Faculty of Biological Sciences, Universidad de Concepción, Concepción, Chile
| | - Valeria Candia
- Department of Cell Biology, Faculty of Biological Sciences, Universidad de Concepción, Concepción, Chile
- Grupo de Procesos en Biología del Desarrollo (GDeP), Faculty of Biological Sciences, Universidad de Concepción, Concepción, Chile
| | - Yannis Kalaidzidis
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
| | - Marino Zerial
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
| | - Hernán Morales-Navarrete
- Department of Systems Biology of Development, University of Konstanz, Konstanz, Germany.
- Facultad de Ciencias Técnicas, Universidad Internacional Del Ecuador UIDE, Quito, Ecuador.
| | - Fabián Segovia-Miranda
- Department of Cell Biology, Faculty of Biological Sciences, Universidad de Concepción, Concepción, Chile.
- Grupo de Procesos en Biología del Desarrollo (GDeP), Faculty of Biological Sciences, Universidad de Concepción, Concepción, Chile.
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9
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Yatsuzuka K, Kawakami R, Niko Y, Tsuda T, Kameda K, Kohri N, Yoshida S, Shiraishi K, Muto J, Mori H, Fujisawa Y, Imamura T, Murakami M. A fluorescence imaging technique suggests that sweat leakage in the epidermis contributes to the pathomechanism of palmoplantar pustulosis. Sci Rep 2024; 14:378. [PMID: 38172327 PMCID: PMC10764317 DOI: 10.1038/s41598-023-50875-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2023] [Accepted: 12/27/2023] [Indexed: 01/05/2024] Open
Abstract
Sweat is an essential protection system for the body, but its failure can result in pathologic conditions, including several skin diseases, such as palmoplantar pustulosis (PPP). As reduced intraepidermal E-cadherin expression in skin lesions was confirmed in PPP skin lesions, a role for interleukin (IL)-1-rich sweat in PPP has been proposed, and IL-1 has been implicated in the altered E-cadherin expression observed in both cultured keratinocytes and mice epidermis. For further investigation, live imaging of sweat perspiration on a mouse toe-pad under two-photon excitation microscopy was performed using a novel fluorescent dye cocktail (which we named JSAC). Finally, intraepidermal vesicle formation which is the main cause of PPP pathogenesis was successfully induced using our "LASER-snipe" technique with JSAC. "LASER-snipe" is a type of laser ablation technique that uses two-photon absorption of fluorescent material to destroy a few acrosyringium cells at a pinpoint location in three-dimensional space of living tissue to cause eccrine sweat leakage. These observatory techniques and this mouse model may be useful not only in live imaging for physiological phenomena in vivo such as PPP pathomechanism investigation, but also for the field of functional physiological morphology.
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Affiliation(s)
- Kazuki Yatsuzuka
- Department of Dermatology, Ehime University Graduate School of Medicine, Ehime, Japan
| | - Ryosuke Kawakami
- Department of Molecular Medicine for Pathogenesis, Ehime University Graduate School of Medicine, Ehime, Japan
| | - Yosuke Niko
- Research and Education Faculty, Multidisciplinary Science Cluster, Interdisciplinary Science Unit, Kochi University, Kochi, Japan
| | - Teruko Tsuda
- Department of Dermatology, Ehime University Graduate School of Medicine, Ehime, Japan
| | - Kenji Kameda
- Department of Dermatology, Ehime University Graduate School of Medicine, Ehime, Japan
| | - Nobushige Kohri
- Department of Dermatology, Ehime University Graduate School of Medicine, Ehime, Japan
| | - Satoshi Yoshida
- Department of Dermatology, Ehime University Graduate School of Medicine, Ehime, Japan
| | - Ken Shiraishi
- Department of Dermatology, Ehime University Graduate School of Medicine, Ehime, Japan
| | - Jun Muto
- Department of Dermatology, Ehime University Graduate School of Medicine, Ehime, Japan
| | - Hideki Mori
- Department of Dermatology, Ehime University Graduate School of Medicine, Ehime, Japan
| | - Yasuhiro Fujisawa
- Department of Dermatology, Ehime University Graduate School of Medicine, Ehime, Japan
| | - Takeshi Imamura
- Department of Molecular Medicine for Pathogenesis, Ehime University Graduate School of Medicine, Ehime, Japan
| | - Masamoto Murakami
- Department of Dermatology, Ehime University Graduate School of Medicine, Ehime, Japan.
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10
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Abbasian V, Darafsheh A. A dataset of digital holograms of normal and thalassemic cells. Sci Data 2024; 11:3. [PMID: 38168104 PMCID: PMC10762191 DOI: 10.1038/s41597-023-02818-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2023] [Accepted: 12/04/2023] [Indexed: 01/05/2024] Open
Abstract
Digital holographic microscopy (DHM) is an intriguing medical diagnostic tool due to its label-free and quantitative nature, providing high-contrast images of phase samples. By capturing both intensity and phase information, DHM enables the numerical reconstruction of quantitative phase images. However, the lateral resolution is limited by the diffraction limit, which prompted the recent suggestion of microsphere-assisted DHM to enhance the DHM resolution straightforwardly. The use of such a technique as a medical diagnostic tool requires testing and validation of the proposed assays to prove their feasibility and viability. This paper publishes 760 and 609 microsphere-assisted DHM images of normal and thalassemic red blood cells obtained from a normal and thalassemic male individual, respectively.
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Affiliation(s)
- Vahid Abbasian
- Department of Radiation Oncology, Washington University School of Medicine in St. Louis, St. Louis, MO, 63110, USA.
- Imaging Science Program, McKelvey School of Engineering, Washington University in St. Louis, St. Louis, MO, 63130, USA.
- Department of Physics, Institute for Advanced Studies in Basic Sciences (IASBS), Zanjan, 45137-66731, Iran.
| | - Arash Darafsheh
- Department of Radiation Oncology, Washington University School of Medicine in St. Louis, St. Louis, MO, 63110, USA
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11
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Yi C, Zhu L, Sun J, Wang Z, Zhang M, Zhong F, Yan L, Tang J, Huang L, Zhang YH, Li D, Fei P. Video-rate 3D imaging of living cells using Fourier view-channel-depth light field microscopy. Commun Biol 2023; 6:1259. [PMID: 38086994 PMCID: PMC10716377 DOI: 10.1038/s42003-023-05636-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2023] [Accepted: 11/27/2023] [Indexed: 12/18/2023] Open
Abstract
Interrogation of subcellular biological dynamics occurring in a living cell often requires noninvasive imaging of the fragile cell with high spatiotemporal resolution across all three dimensions. It thereby poses big challenges to modern fluorescence microscopy implementations because the limited photon budget in a live-cell imaging task makes the achievable performance of conventional microscopy approaches compromise between their spatial resolution, volumetric imaging speed, and phototoxicity. Here, we incorporate a two-stage view-channel-depth (VCD) deep-learning reconstruction strategy with a Fourier light-field microscope based on diffractive optical element to realize fast 3D super-resolution reconstructions of intracellular dynamics from single diffraction-limited 2D light-filed measurements. This VCD-enabled Fourier light-filed imaging approach (F-VCD), achieves video-rate (50 volumes per second) 3D imaging of intracellular dynamics at a high spatiotemporal resolution of ~180 nm × 180 nm × 400 nm and strong noise-resistant capability, with which light field images with a signal-to-noise ratio (SNR) down to -1.62 dB could be well reconstructed. With this approach, we successfully demonstrate the 4D imaging of intracellular organelle dynamics, e.g., mitochondria fission and fusion, with ~5000 times of observation.
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Affiliation(s)
- Chengqiang Yi
- School of Optical and Electronic Information-Wuhan National Laboratory for Optoelectronics-Advanced Biomedical Imaging Facility, Huazhong University of Science and Technology, Wuhan, 430074, China
| | - Lanxin Zhu
- School of Optical and Electronic Information-Wuhan National Laboratory for Optoelectronics-Advanced Biomedical Imaging Facility, Huazhong University of Science and Technology, Wuhan, 430074, China
| | - Jiahao Sun
- School of Optical and Electronic Information-Wuhan National Laboratory for Optoelectronics-Advanced Biomedical Imaging Facility, Huazhong University of Science and Technology, Wuhan, 430074, China
| | - Zhaofei Wang
- School of Optical and Electronic Information-Wuhan National Laboratory for Optoelectronics-Advanced Biomedical Imaging Facility, Huazhong University of Science and Technology, Wuhan, 430074, China
| | - Meng Zhang
- School of Optical and Electronic Information-Wuhan National Laboratory for Optoelectronics-Advanced Biomedical Imaging Facility, Huazhong University of Science and Technology, Wuhan, 430074, China
- Britton Chance Center for Biomedical Photonics-MoE Key Laboratory for Biomedical Photonics, Advanced Biomedical Imaging Facility-Wuhan National Laboratory for Optoelectronics, Huazhong University of Science and Technology, Wuhan, Hubei, 430074, China
| | - Fenghe Zhong
- School of Optical and Electronic Information-Wuhan National Laboratory for Optoelectronics-Advanced Biomedical Imaging Facility, Huazhong University of Science and Technology, Wuhan, 430074, China
| | - Luxin Yan
- State Education Commission Key Laboratory for Image Processing and Intelligent Control, Huazhong University of Science and Technology, Wuhan, Hubei, 430074, China
| | - Jiang Tang
- School of Optical and Electronic Information-Wuhan National Laboratory for Optoelectronics-Advanced Biomedical Imaging Facility, Huazhong University of Science and Technology, Wuhan, 430074, China
| | - Liang Huang
- Department of Hematology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, 430030, China
| | - Yu-Hui Zhang
- Britton Chance Center for Biomedical Photonics-MoE Key Laboratory for Biomedical Photonics, Advanced Biomedical Imaging Facility-Wuhan National Laboratory for Optoelectronics, Huazhong University of Science and Technology, Wuhan, Hubei, 430074, China
| | - Dongyu Li
- School of Optical and Electronic Information-Wuhan National Laboratory for Optoelectronics-Advanced Biomedical Imaging Facility, Huazhong University of Science and Technology, Wuhan, 430074, China.
| | - Peng Fei
- School of Optical and Electronic Information-Wuhan National Laboratory for Optoelectronics-Advanced Biomedical Imaging Facility, Huazhong University of Science and Technology, Wuhan, 430074, China
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12
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Obando M, Bassi A, Ducros N, Mato G, Correia TM. Model-based deep learning framework for accelerated optical projection tomography. Sci Rep 2023; 13:21735. [PMID: 38066010 PMCID: PMC10709405 DOI: 10.1038/s41598-023-47650-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2023] [Accepted: 11/16/2023] [Indexed: 12/18/2023] Open
Abstract
In this work, we propose a model-based deep learning reconstruction algorithm for optical projection tomography (ToMoDL), to greatly reduce acquisition and reconstruction times. The proposed method iterates over a data consistency step and an image domain artefact removal step achieved by a convolutional neural network. A preprocessing stage is also included to avoid potential misalignments between the sample center of rotation and the detector. The algorithm is trained using a database of wild-type zebrafish (Danio rerio) at different stages of development to minimise the mean square error for a fixed number of iterations. Using a cross-validation scheme, we compare the results to other reconstruction methods, such as filtered backprojection, compressed sensing and a direct deep learning method where the pseudo-inverse solution is corrected by a U-Net. The proposed method performs equally well or better than the alternatives. For a highly reduced number of projections, only the U-Net method provides images comparable to those obtained with ToMoDL. However, ToMoDL has a much better performance if the amount of data available for training is limited, given that the number of network trainable parameters is smaller.
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Affiliation(s)
- Marcos Obando
- Medical Physics Department, Centro Atómico Bariloche and Instituto Balseiro, 8400, Bariloche, Argentina
| | - Andrea Bassi
- Dipartimento di Fisica, Politecnico di Milano, Piazza Leonardo da Vinci 32, I-20133, Milano, Italy
| | - Nicolas Ducros
- University of Lyon INSA-Lyon, Université Claude Bernard Lyon 1, UJM Saint-Etienne, CREATIS CNRS UMR 5220, Inserm, U1294, Lyon, France
- IUF, Institut Universitaire de France, Paris, France
| | - Germán Mato
- Medical Physics Department, Centro Atómico Bariloche and Instituto Balseiro, 8400, Bariloche, Argentina
| | - Teresa M Correia
- Centre of Marine Sciences (CCMAR), Universidade do Algarve, Campus de Gambelas, 8005-139, Faro, Portugal.
- School of Biomedical Engineering and Imaging Sciences, King's College London, SE1 7EH, London, United Kingdom.
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13
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Ide T, Koyama A. The formation of a rolling larval chamber as the unique structural gall of a new species of cynipid gall wasps. Sci Rep 2023; 13:18149. [PMID: 37903850 PMCID: PMC10616116 DOI: 10.1038/s41598-023-43641-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2023] [Accepted: 09/26/2023] [Indexed: 11/01/2023] Open
Abstract
Insect galls, which often have complex external and internal structures, are believed to have adaptive significance for the survival of insects inside galls. A unique internal structure was discovered in the gall of a new cynipid species, Belizinella volutum Ide & Koyama, sp. nov., where the larval chamber could roll freely in the internal air space of the gall. Observations of the live galls using micro-computed tomography (micro-CT) revealed its formation process. The larval chamber becomes isolated from the internal parenchyma soon after the gall reaches the maximum diameter and is able to roll as the internal air space is expanding from the surrounding parenchyma to the outer gall wall. The enemy hypothesis could partly explain the adaptive significance of the unique structure of the gall of B. volutum.
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Affiliation(s)
- Tatsuya Ide
- Department of Zoology, National Museum of Nature and Science, 4-1-1 Amakubo, Tsukuba, Ibaraki, Japan.
| | - Asuka Koyama
- Center for Biodiversity and Climate Change, Forestry and Forest Products Research Institute, 1 Matsunosato, Tsukuba, Ibaraki, Japan
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14
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Bui TQ, Henn MA, Tew WL, Catterton MA, Woods SI. Harmonic dependence of thermal magnetic particle imaging. Sci Rep 2023; 13:15762. [PMID: 37737290 PMCID: PMC10516919 DOI: 10.1038/s41598-023-42620-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2023] [Accepted: 09/12/2023] [Indexed: 09/23/2023] Open
Abstract
Advances in instrumentation and tracer materials are still required to enable sensitive, accurate, and localized in situ 3D temperature monitoring by magnetic particle imaging (MPI). We have developed a high-resolution magnetic particle imaging instrument and implemented a low-noise multi-harmonic lock-in detection method to observe and quantify temperature variations in iron oxide nanoparticle tracers using the harmonic ratio method for determining temperature. Using isolated harmonics for MPI and temperature imaging revealed an apparent dependence of imaging resolution on harmonic number. Thus, we present experimental and simulation studies to quantify the imaging resolution dependence on temperature and harmonic number, and directly validate the fundamental origin of MPI imaging resolution on harmonic number based on the concept of a harmonic point-spread-function.
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Affiliation(s)
- Thinh Q Bui
- National Institute of Standards and Technology, Gaithersburg, MD, 20895, USA.
| | - Mark-Alexander Henn
- National Institute of Standards and Technology, Gaithersburg, MD, 20895, USA
- Department of Chemistry and Biochemistry, University of Maryland, College Park, MD, 20742, USA
| | - Weston L Tew
- National Institute of Standards and Technology, Gaithersburg, MD, 20895, USA
| | - Megan A Catterton
- National Institute of Standards and Technology, Gaithersburg, MD, 20895, USA
- Department of Mechanical Engineering, Johns Hopkins University, Baltimore, MD, 21287, USA
| | - Solomon I Woods
- National Institute of Standards and Technology, Gaithersburg, MD, 20895, USA
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15
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Huh J, Liu J, Yu JH, Choi YJ, Ahn HK, Chung CJ, Cha JY, Kim KH. Three-dimensional evaluation of a virtual setup considering the roots and alveolar bone in molar distalization cases. Sci Rep 2023; 13:14955. [PMID: 37696835 PMCID: PMC10495328 DOI: 10.1038/s41598-023-41480-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2023] [Accepted: 08/27/2023] [Indexed: 09/13/2023] Open
Abstract
We aimed to evaluate root parallelism and the dehiscence or fenestrations of virtual teeth setup using roots isolated from cone beam computed tomography (CBCT) images. Sixteen patients undergoing non-extraction orthodontic treatment with molar distalization were selected. Composite teeth were created by merging CBCT-isolated roots with intraoral scan-derived crowns. Three setups were performed sequentially: crown setup considering only the crowns, root setup-1 considering root alignment, and root setup-2 considering the roots and surrounding alveolar bone. We evaluated the parallelism and exposure of the roots and compared the American Board of Orthodontics Objective Grading System (ABO-OGS) scores using three-dimensionally printed models among the setups. The mean angulation differences between adjacent teeth in root setups-1 and -2 were significantly smaller than in the crown setup, except for some posterior teeth (p < 0.05). The amount of root exposure was significantly smaller in root setup-2 compared to crown setup and root setup-1 except when the mean exposure was less than 0.6 mm (p < 0.05). There was no significant difference in ABO-OGS scores among the setups. Thus, virtual setup considering the roots and alveolar bone can improve root parallelism and reduce the risk of root exposure without compromising occlusion quality.
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Affiliation(s)
- Jaewook Huh
- Department of Orthodontics, Yonsei University College of Dentistry, Seoul, Korea
| | - Jing Liu
- Department of Orthodontics, Institute of Craniofacial Deformity, Yonsei University College of Dentistry, Seoul, Korea
| | - Jae-Hun Yu
- Department of Orthodontics, Institute of Craniofacial Deformity, Yonsei University College of Dentistry, Seoul, Korea
| | - Yoon Jeong Choi
- Department of Orthodontics, Institute of Craniofacial Deformity, Yonsei University College of Dentistry, Seoul, Korea
| | - Hee-Kap Ahn
- Graduate School of Artificial Intelligence, Department of Computer Science and Engineering, Pohang University of Science and Technology, Pohang, Korea
- Institute for Convergence Research and Education in Advanced Technology, Yonsei University, Seoul, Korea
| | - Chooryung J Chung
- Department of Orthodontics, Institute of Craniofacial Deformity, Gangnam Severance Dental Hospital, College of Dentistry, Yonsei University, Seoul, Korea
| | - Jung-Yul Cha
- Department of Orthodontics, Institute of Craniofacial Deformity, College of Dentistry, Institute for Innovation in Digital Healthcare, Yonsei University, 50-1 Yonsei-ro, Seodaemun-gu, Seoul, 03722, Korea.
| | - Kyung-Ho Kim
- Department of Orthodontics, Institute of Craniofacial Deformity, Gangnam Severance Dental Hospital, College of Dentistry, Yonsei University, Seoul, Korea.
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16
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Bonnier F, Pedrazzani M, Fischman S, Viel T, Lavoix A, Pegoud D, Nili M, Jimenez Y, Ralambondrainy S, Cauchard JH, Korichi R. Line-field confocal optical coherence tomography coupled with artificial intelligence algorithms to identify quantitative biomarkers of facial skin ageing. Sci Rep 2023; 13:13881. [PMID: 37620374 PMCID: PMC10449778 DOI: 10.1038/s41598-023-40340-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2023] [Accepted: 08/09/2023] [Indexed: 08/26/2023] Open
Abstract
Quantitative biomarkers of facial skin ageing were studied from one hundred healthy Caucasian female volunteers, aged 20-70 years, using in vivo 3D Line-field Confocal Optical Coherence Tomography (LC-OCT) imaging coupled with Artificial Intelligence (AI)-based quantification algorithms. Layer metrics, i.e. stratum corneum thickness (SC), viable epidermal thickness and Dermal-Epidermal Junction (DEJ) undulation, as well as cellular metrics were measured for the temple, cheekbone and mandible. For all three investigated facial areas, minimal age-related variations were observed in the thickness of the SC and viable epidermis layers. A flatter and more homogeneous epidermis (decrease in the standard deviation of the number of layers means), a less dense cellular network with fewer cells per layer (decrease in cell surface density), and larger and more heterogeneous nuclei within each layer (increase in nuclei volume and their standard deviation) were found with significant variations with age. The higher atypia scores further reflected the heterogeneity of nuclei throughout the viable epidermis. The 3D visualisation of fine structures in the skin at the micrometric resolution and the 1200 µm × 500 µm field of view achieved with LC-OCT imaging enabled to compute relevant quantitative biomarkers for a better understanding of skin biology and the ageing process in vivo.
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Affiliation(s)
- Franck Bonnier
- LVMH Recherche, 185 Avenue de Verdun, 45804, Saint Jean de Braye, France.
| | | | | | - Théo Viel
- DAMAE Medical, 14 Rue Sthrau, 75013, Paris, France
| | - Agnes Lavoix
- DERMATECH, 8 Rue Jacqueline Auriol, 69008, Lyon, France
| | - Didier Pegoud
- DERMATECH, 8 Rue Jacqueline Auriol, 69008, Lyon, France
| | - Meryem Nili
- DERMATECH, 8 Rue Jacqueline Auriol, 69008, Lyon, France
| | | | | | | | - Rodolphe Korichi
- LVMH Recherche, 185 Avenue de Verdun, 45804, Saint Jean de Braye, France
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17
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Chorghay Z, Li VJ, Schohl A, Ghosh A, Ruthazer ES. The effects of the NMDAR co-agonist D-serine on the structure and function of optic tectal neurons in the developing visual system. Sci Rep 2023; 13:13383. [PMID: 37591903 PMCID: PMC10435543 DOI: 10.1038/s41598-023-39951-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2023] [Accepted: 08/02/2023] [Indexed: 08/19/2023] Open
Abstract
The N-methyl-D-aspartate type glutamate receptor (NMDAR) is a molecular coincidence detector which converts correlated patterns of neuronal activity into cues for the structural and functional refinement of developing circuits in the brain. D-serine is an endogenous co-agonist of the NMDAR. We investigated the effects of potent enhancement of NMDAR-mediated currents by chronic administration of saturating levels of D-serine on the developing Xenopus retinotectal circuit. Chronic exposure to the NMDAR co-agonist D-serine resulted in structural and functional changes in the optic tectum. In immature tectal neurons, D-serine administration led to more compact and less dynamic tectal dendritic arbors, and increased synapse density. Calcium imaging to examine retinotopy of tectal neurons revealed that animals raised in D-serine had more compact visual receptive fields. These findings provide insight into how the availability of endogenous NMDAR co-agonists like D-serine at glutamatergic synapses can regulate the refinement of circuits in the developing brain.
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Affiliation(s)
- Zahraa Chorghay
- Montreal Neurological Institute-Hospital and Department of Neurology and Neurosurgery, McGill University, 3801 Rue University, Montréal, QC, H3A 2B4, Canada
| | - Vanessa J Li
- Montreal Neurological Institute-Hospital and Department of Neurology and Neurosurgery, McGill University, 3801 Rue University, Montréal, QC, H3A 2B4, Canada
| | - Anne Schohl
- Montreal Neurological Institute-Hospital and Department of Neurology and Neurosurgery, McGill University, 3801 Rue University, Montréal, QC, H3A 2B4, Canada
| | - Arna Ghosh
- MILA, 6666 Rue St Urbain, Montréal, QC, H2S 3H1, Canada
| | - Edward S Ruthazer
- Montreal Neurological Institute-Hospital and Department of Neurology and Neurosurgery, McGill University, 3801 Rue University, Montréal, QC, H3A 2B4, Canada.
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18
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Pchitskaya E, Vasiliev P, Smirnova D, Chukanov V, Bezprozvanny I. SpineTool is an open-source software for analysis of morphology of dendritic spines. Sci Rep 2023; 13:10561. [PMID: 37386071 PMCID: PMC10310755 DOI: 10.1038/s41598-023-37406-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2023] [Accepted: 06/21/2023] [Indexed: 07/01/2023] Open
Abstract
Dendritic spines form most excitatory synaptic inputs in neurons and these spines are altered in many neurodevelopmental and neurodegenerative disorders. Reliable methods to assess and quantify dendritic spines morphology are needed, but most existing methods are subjective and labor intensive. To solve this problem, we developed an open-source software that allows segmentation of dendritic spines from 3D images, extraction of their key morphological features, and their classification and clustering. Instead of commonly used spine descriptors based on numerical metrics we used chord length distribution histogram (CLDH) approach. CLDH method depends on distribution of lengths of chords randomly generated within dendritic spines volume. To achieve less biased analysis, we developed a classification procedure that uses machine-learning algorithm based on experts' consensus and machine-guided clustering tool. These approaches to unbiased and automated measurements, classification and clustering of synaptic spines that we developed should provide a useful resource for a variety of neuroscience and neurodegenerative research applications.
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Affiliation(s)
- Ekaterina Pchitskaya
- Laboratory of Molecular Neurodegeneration, Peter the Great St. Petersburg Polytechnic University, Khlopina St. 11, St. Petersburg, Russia, 194021.
| | - Peter Vasiliev
- Laboratory of Molecular Neurodegeneration, Peter the Great St. Petersburg Polytechnic University, Khlopina St. 11, St. Petersburg, Russia, 194021
- Department of Applied Mathematics, Peter the Great St. Petersburg Polytechnic University, Polytechnicheskaya St. 29, St. Petersburg, Russia, 195251
| | - Daria Smirnova
- Department of Applied Mathematics, Peter the Great St. Petersburg Polytechnic University, Polytechnicheskaya St. 29, St. Petersburg, Russia, 195251
| | - Vyacheslav Chukanov
- Laboratory of Molecular Neurodegeneration, Peter the Great St. Petersburg Polytechnic University, Khlopina St. 11, St. Petersburg, Russia, 194021
- Department of Applied Mathematics, Peter the Great St. Petersburg Polytechnic University, Polytechnicheskaya St. 29, St. Petersburg, Russia, 195251
| | - Ilya Bezprozvanny
- Laboratory of Molecular Neurodegeneration, Peter the Great St. Petersburg Polytechnic University, Khlopina St. 11, St. Petersburg, Russia, 194021.
- Department of Physiology, UT Southwestern Medical Center at Dallas, Dallas, TX, 75390, USA.
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19
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Fujiwara RJ, Ishiyama G, Lopez IA, Ishiyama A. Morphometric Analysis and Linear Measurements of the Scala Tympani and Implications in Cochlear Implant Electrodes. Otol Neurotol 2023; 44:e343-e349. [PMID: 36893208 PMCID: PMC10175138 DOI: 10.1097/mao.0000000000003848] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/10/2023]
Abstract
HYPOTHESIS The objective of this study was to perform detailed height and cross-sectional area measurements of the scala tympani in histologic sections of nondiseased human temporal bones and correlate them with cochlear implant electrode dimensions. BACKGROUND Previous investigations in scala tympani dimensions have used microcomputed tomography or casting modalities, which cannot be correlated directly with microanatomy visible on histologic specimens. METHODS Three-dimensional reconstructions of 10 archival human temporal bone specimens with no history of middle or inner ear disease were generated using hematoxylin and eosin histopathologic slides. At 90-degree intervals, the heights of the scala tympani at lateral wall, midscala, and perimodiolar locations were measured, along with cross-sectional area. RESULTS The vertical height of the scala tympani at its lateral wall significantly decreased from 1.28 to 0.88 mm from 0 to 180 degrees, and the perimodiolar height decreased from 1.20 to 0.85 mm. The cross-sectional area decreased from 2.29 (standard deviation, 0.60) mm 2 to 1.38 (standard deviation, 0.13) mm 2 from 0 to 180 degrees ( p = 0.001). After 360 degrees, the scala tympani shape transitioned from an ovoid to triangular shape, corresponding with a significantly decreased lateral height relative to perimodiolar height. Wide variability was observed among the cochlear implant electrode sizes relative to scala tympani measurements. CONCLUSION The present study is the first to conduct detailed measurements of heights and cross-sectional area of the scala tympani and the first to statistically characterize the change in its shape after the basal turn. These measurements have important implications in understanding locations of intracochlear trauma during insertion and electrode design.
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Affiliation(s)
- Rance J.T. Fujiwara
- David Geffen School of Medicine at UCLA, Department of Head and Neck Surgery, Los Angeles 90095
| | - Gail Ishiyama
- David Geffen School of Medicine at UCLA, Department of Neurology, Los Angeles 90095
| | - Ivan A. Lopez
- David Geffen School of Medicine at UCLA, Department of Head and Neck Surgery, Los Angeles 90095
| | - Akira Ishiyama
- David Geffen School of Medicine at UCLA, Department of Head and Neck Surgery, Los Angeles 90095
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20
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Jaiswal A, Nenonen J, Parkkonen L. On electromagnetic head digitization in MEG and EEG. Sci Rep 2023; 13:3801. [PMID: 36882438 PMCID: PMC9992397 DOI: 10.1038/s41598-023-30223-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2022] [Accepted: 02/17/2023] [Indexed: 03/09/2023] Open
Abstract
In MEG and EEG studies, the accuracy of the head digitization impacts the co-registration between functional and structural data. The co-registration is one of the major factors that affect the spatial accuracy in MEG/EEG source imaging. Precisely digitized head-surface (scalp) points do not only improve the co-registration but can also deform a template MRI. Such an individualized-template MRI can be used for conductivity modeling in MEG/EEG source imaging if the individual's structural MRI is unavailable. Electromagnetic tracking (EMT) systems (particularly Fastrak, Polhemus Inc., Colchester, VT, USA) have been the most common solution for digitization in MEG and EEG. However, they may occasionally suffer from ambient electromagnetic interference which makes it challenging to achieve (sub-)millimeter digitization accuracy. The current study-(i) evaluated the performance of the Fastrak EMT system under different conditions in MEG/EEG digitization, and (ii) explores the usability of two alternative EMT systems (Aurora, NDI, Waterloo, ON, Canada; Fastrak with a short-range transmitter) for digitization. Tracking fluctuation, digitization accuracy, and robustness of the systems were evaluated in several test cases using test frames and human head models. The performance of the two alternative systems was compared against the Fastrak system. The results showed that the Fastrak system is accurate and robust for MEG/EEG digitization if the recommended operating conditions are met. The Fastrak with the short-range transmitter shows comparatively higher digitization error if digitization is not carried out very close to the transmitter. The study also evinces that the Aurora system can be used for MEG/EEG digitization within a constrained range; however, some modifications would be required to make the system a practical and easy-to-use digitizer. Its real-time error estimation feature can potentially improve digitization accuracy.
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Affiliation(s)
- Amit Jaiswal
- MEGIN Oy, Espoo, Finland. .,Department of Neuroscience and Biomedical Engineering, School of Science, Aalto University, Espoo, Finland.
| | | | - Lauri Parkkonen
- MEGIN Oy, Espoo, Finland.,Department of Neuroscience and Biomedical Engineering, School of Science, Aalto University, Espoo, Finland
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21
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Renauld E, Théberge A, Petit L, Houde JC, Descoteaux M. Validate your white matter tractography algorithms with a reappraised ISMRM 2015 Tractography Challenge scoring system. Sci Rep 2023; 13:2347. [PMID: 36759653 PMCID: PMC9911766 DOI: 10.1038/s41598-023-28560-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2022] [Accepted: 01/20/2023] [Indexed: 02/11/2023] Open
Abstract
Since 2015, research groups have sought to produce the ne plus ultra of tractography algorithms using the ISMRM 2015 Tractography Challenge as evaluation. In particular, since 2017, machine learning has made its entrance into the tractography world. The ISMRM 2015 Tractography Challenge is the most used phantom during tractography validation, although it contains limitations. Here, we offer a new scoring system for this phantom, where segmentation of the bundles is now based on manually defined regions of interest rather than on bundle recognition. Bundles are now more reliably segmented, offering more representative metrics for future users. New code is available online. Scores of the initial 96 submissions to the challenge are updated. Overall, conclusions from the 2015 challenge are confirmed with the new scoring, but individual tractogram scores have changed, and the data is much improved at the bundle- and streamline-level. This work also led to the production of a ground truth tractogram with less broken or looping streamlines and of an example of processed data, all available on the Tractometer website. This enhanced scoring system and new data should continue helping researchers develop and evaluate the next generation of tractography techniques.
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Affiliation(s)
- Emmanuelle Renauld
- Sherbrooke Connectivity Imaging Laboratory (SCIL), Computer Sciences Department, Université de Sherbrooke, Sherbrooke, Canada.
| | - Antoine Théberge
- Sherbrooke Connectivity Imaging Laboratory (SCIL), Computer Sciences Department, Université de Sherbrooke, Sherbrooke, Canada
| | - Laurent Petit
- Université de Bordeaux, CNRS, CEA, IMN, GIN, UMR 5293, 33000, Bordeaux, France
| | | | - Maxime Descoteaux
- Sherbrooke Connectivity Imaging Laboratory (SCIL), Computer Sciences Department, Université de Sherbrooke, Sherbrooke, Canada.,Imeka Solutions Inc, Sherbrooke, QC, Canada
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22
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Fernando D, Kowalczyk M, Guindos P, Auer M, Daniel G. Electron tomography unravels new insights into fiber cell wall nanostructure; exploring 3D macromolecular biopolymeric nano-architecture of spruce fiber secondary walls. Sci Rep 2023; 13:2350. [PMID: 36759530 DOI: 10.1038/s41598-023-29113-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2022] [Accepted: 01/31/2023] [Indexed: 02/11/2023] Open
Abstract
Lignocellulose biomass has a tremendous potential as renewable biomaterials for fostering the "bio-based society" and circular bioeconomy paradigm. It requires efficient use and breakdown of fiber cell walls containing mainly cellulose, hemicellulose and lignin biopolymers. Despite their great importance, there is an extensive debate on the true structure of fiber walls and knowledge on the macromolecular nano-organization is limited and remains elusive in 3D. We employed dual-axis electron tomography that allows visualization of previously unseen 3D macromolecular organization/biopolymeric nano-architecture of the secondary S2 layer of Norway spruce fiber wall. Unprecedented 3D nano-structural details with novel insights into cellulose microfibrils (~ 2 nm diameter), macrofibrils, nano-pore network and cell wall chemistry (volume %) across the S2 were explored and quantified including simulation of structure related permeability. Matrix polymer association with cellulose varied between microfibrils and macrofibrils with lignin directly associated with MFs. Simulated bio-nano-mechanical properties revealed stress distribution within the S2 and showed similar properties between the idealized 3D model and the native S2 (actual tomogram). Present work has great potential for significant advancements in lignocellulose research on nano-scale understanding of cell wall assembly/disassembly processes leading to more efficient industrial processes of functionalization, valorization and target modification technologies.
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23
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Shin S, Kim MW, Jin KH, Yi KM, Kohmura Y, Ishikawa T, Je JH, Park J. Deep 3D reconstruction of synchrotron X-ray computed tomography for intact lungs. Sci Rep 2023; 13:1738. [PMID: 36720962 DOI: 10.1038/s41598-023-27627-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2022] [Accepted: 01/04/2023] [Indexed: 02/02/2023] Open
Abstract
Synchrotron X-rays can be used to obtain highly detailed images of parts of the lung. However, micro-motion artifacts induced by such as cardiac motion impede quantitative visualization of the alveoli in the lungs. This paper proposes a method that applies a neural network for synchrotron X-ray Computed Tomography (CT) data to reconstruct the high-quality 3D structure of alveoli in intact mouse lungs at expiration, without needing ground-truth data. Our approach reconstructs the spatial sequence of CT images by using a deep-image prior with interpolated input latent variables, and in this way significantly enhances the images of alveolar structure compared with the prior art. The approach successfully visualizes 3D alveolar units of intact mouse lungs at expiration and enables us to measure the diameter of the alveoli. We believe that our approach helps to accurately visualize other living organs hampered by micro-motion.
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24
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Warr R, Handschuh S, Glösmann M, Cernik RJ, Withers PJ. Quantifying multiple stain distributions in bioimaging by hyperspectral X-ray tomography. Sci Rep 2022; 12:21945. [PMID: 36535963 PMCID: PMC9763266 DOI: 10.1038/s41598-022-23592-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2022] [Accepted: 11/02/2022] [Indexed: 12/23/2022] Open
Abstract
Chemical staining of biological specimens is commonly utilised to boost contrast in soft tissue structures, but unambiguous identification of staining location and distribution is difficult without confirmation of the elemental signature, especially for chemicals of similar density contrast. Hyperspectral X-ray computed tomography (XCT) enables the non-destructive identification, segmentation and mapping of elemental composition within a sample. With the availability of hundreds of narrow, high resolution (~ 1 keV) energy channels, the technique allows the simultaneous detection of multiple contrast agents across different tissue structures. Here we describe a hyperspectral imaging routine for distinguishing multiple chemical agents, regardless of contrast similarity. Using a set of elemental calibration phantoms, we perform a first instance of direct stain concentration measurement using spectral absorption edge markers. Applied to a set of double- and triple-stained biological specimens, the study analyses the extent of stain overlap and uptake regions for commonly used contrast markers. An improved understanding of stain concentration as a function of position, and the interaction between multiple stains, would help inform future studies on multi-staining procedures, as well as enable future exploration of heavy metal uptake across medical, agricultural and ecological fields.
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Affiliation(s)
- Ryan Warr
- grid.5379.80000000121662407Henry Royce Institute, Department of Materials, The University of Manchester, Manchester, M13 9PL UK
| | - Stephan Handschuh
- grid.6583.80000 0000 9686 6466VetCore Facility for Research, University of Veterinary Medicine Vienna, Vienna, Austria
| | - Martin Glösmann
- grid.6583.80000 0000 9686 6466VetCore Facility for Research, University of Veterinary Medicine Vienna, Vienna, Austria
| | - Robert J. Cernik
- grid.5379.80000000121662407Henry Royce Institute, Department of Materials, The University of Manchester, Manchester, M13 9PL UK
| | - Philip J. Withers
- grid.5379.80000000121662407Henry Royce Institute, Department of Materials, The University of Manchester, Manchester, M13 9PL UK
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25
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Torres-García E, Pinto-Cámara R, Linares A, Martínez D, Abonza V, Brito-Alarcón E, Calcines-Cruz C, Valdés-Galindo G, Torres D, Jabloñski M, Torres-Martínez HH, Martínez JL, Hernández HO, Ocelotl-Oviedo JP, Garcés Y, Barchi M, D’Antuono R, Bošković A, Dubrovsky JG, Darszon A, Buffone MG, Morales RR, Rendon-Mancha JM, Wood CD, Hernández-García A, Krapf D, Crevenna ÁH, Guerrero A. Extending resolution within a single imaging frame. Nat Commun 2022; 13:7452. [PMID: 36460648 PMCID: PMC9718789 DOI: 10.1038/s41467-022-34693-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2021] [Accepted: 10/27/2022] [Indexed: 12/05/2022] Open
Abstract
The resolution of fluorescence microscopy images is limited by the physical properties of light. In the last decade, numerous super-resolution microscopy (SRM) approaches have been proposed to deal with such hindrance. Here we present Mean-Shift Super Resolution (MSSR), a new SRM algorithm based on the Mean Shift theory, which extends spatial resolution of single fluorescence images beyond the diffraction limit of light. MSSR works on low and high fluorophore densities, is not limited by the architecture of the optical setup and is applicable to single images as well as temporal series. The theoretical limit of spatial resolution, based on optimized real-world imaging conditions and analysis of temporal image stacks, has been measured to be 40 nm. Furthermore, MSSR has denoising capabilities that outperform other SRM approaches. Along with its wide accessibility, MSSR is a powerful, flexible, and generic tool for multidimensional and live cell imaging applications.
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Affiliation(s)
- Esley Torres-García
- grid.412873.b0000 0004 0484 1712Centro de Investigación en Ciencias, Instituto de Investigación en Ciencias Básicas y Aplicadas, Universidad Autónoma del Estado de Morelos, Cuernavaca, Morelos Mexico ,grid.9486.30000 0001 2159 0001Laboratorio Nacional de Microscopía Avanzada, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Morelos Mexico
| | - Raúl Pinto-Cámara
- grid.412873.b0000 0004 0484 1712Centro de Investigación en Ciencias, Instituto de Investigación en Ciencias Básicas y Aplicadas, Universidad Autónoma del Estado de Morelos, Cuernavaca, Morelos Mexico ,grid.9486.30000 0001 2159 0001Laboratorio Nacional de Microscopía Avanzada, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Morelos Mexico
| | - Alejandro Linares
- grid.9486.30000 0001 2159 0001Laboratorio Nacional de Microscopía Avanzada, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Morelos Mexico ,grid.144532.5000000012169920XAnalytical and Quantitative Light Microscopy, Marine Biological Laboratory, Woods Hole, MA USA
| | - Damián Martínez
- grid.9486.30000 0001 2159 0001Laboratorio Nacional de Microscopía Avanzada, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Morelos Mexico
| | - Víctor Abonza
- grid.9486.30000 0001 2159 0001Laboratorio Nacional de Microscopía Avanzada, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Morelos Mexico
| | - Eduardo Brito-Alarcón
- grid.9486.30000 0001 2159 0001Laboratorio Nacional de Microscopía Avanzada, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Morelos Mexico
| | - Carlos Calcines-Cruz
- grid.9486.30000 0001 2159 0001Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Ciudad de México, Mexico
| | - Gustavo Valdés-Galindo
- grid.9486.30000 0001 2159 0001Departamento de Química de Biomacromoléculas, Instituto de Química. Universidad Nacional Autónoma de México, Ciudad de México, Mexico
| | - David Torres
- grid.9486.30000 0001 2159 0001Laboratorio Nacional de Microscopía Avanzada, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Morelos Mexico
| | - Martina Jabloñski
- grid.464644.00000 0004 0637 7271Instituto de Biología y Medicina Experimental (IBYME‐CONICET), Buenos Aires, Argentina
| | - Héctor H. Torres-Martínez
- grid.9486.30000 0001 2159 0001Departamento de Biología Molecular de Plantas, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Morelos Mexico
| | - José L. Martínez
- grid.9486.30000 0001 2159 0001Departamento de Genética del Desarrollo y Fisiología Molecular, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Morelos Mexico
| | - Haydee O. Hernández
- grid.9486.30000 0001 2159 0001Instituto de Investigaciones en Matemáticas Aplicadas y en Sistemas, Universidad Nacional Autónoma de México, Ciudad de México, Mexico
| | - José P. Ocelotl-Oviedo
- grid.9486.30000 0001 2159 0001Laboratorio Nacional de Microscopía Avanzada, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Morelos Mexico
| | - Yasel Garcés
- grid.9486.30000 0001 2159 0001Laboratorio Nacional de Microscopía Avanzada, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Morelos Mexico ,grid.9486.30000 0001 2159 0001Departamento de Genética del Desarrollo y Fisiología Molecular, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Morelos Mexico
| | - Marco Barchi
- grid.6530.00000 0001 2300 0941Department of Biomedicine and Prevention, Faculty of Medicine, University of Rome Tor Vergata, Rome, Italy
| | | | - Ana Bošković
- grid.418924.20000 0004 0627 3632Neurobiology and Epigenetics Unit, European Molecular Biology Laboratory, Monterotondo, Rome Italy
| | - Joseph G. Dubrovsky
- grid.9486.30000 0001 2159 0001Departamento de Biología Molecular de Plantas, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Morelos Mexico
| | - Alberto Darszon
- grid.9486.30000 0001 2159 0001Departamento de Genética del Desarrollo y Fisiología Molecular, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Morelos Mexico
| | - Mariano G. Buffone
- grid.464644.00000 0004 0637 7271Instituto de Biología y Medicina Experimental (IBYME‐CONICET), Buenos Aires, Argentina
| | - Roberto Rodríguez Morales
- grid.472559.80000 0004 0498 8706Instituto de Cibernética, Matemática y Física, Ciudad de la Habana, Cuba
| | - Juan Manuel Rendon-Mancha
- grid.412873.b0000 0004 0484 1712Centro de Investigación en Ciencias, Instituto de Investigación en Ciencias Básicas y Aplicadas, Universidad Autónoma del Estado de Morelos, Cuernavaca, Morelos Mexico
| | - Christopher D. Wood
- grid.9486.30000 0001 2159 0001Laboratorio Nacional de Microscopía Avanzada, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Morelos Mexico
| | - Armando Hernández-García
- grid.9486.30000 0001 2159 0001Departamento de Química de Biomacromoléculas, Instituto de Química. Universidad Nacional Autónoma de México, Ciudad de México, Mexico
| | - Diego Krapf
- grid.47894.360000 0004 1936 8083Electrical and Computer Engineering and School of Biomedical Engineering, Colorado State University, Fort Collins, CO USA
| | - Álvaro H. Crevenna
- grid.418924.20000 0004 0627 3632Neurobiology and Epigenetics Unit, European Molecular Biology Laboratory, Monterotondo, Rome Italy
| | - Adán Guerrero
- grid.9486.30000 0001 2159 0001Laboratorio Nacional de Microscopía Avanzada, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Morelos Mexico
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26
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Varol R, Karavelioglu Z, Omeroglu S, Aydemir G, Karadag A, Meco HE, Demircali AA, Yilmaz A, Kocal GC, Gencoglan G, Oruc ME, Esmer GB, Basbinar Y, Ozdemir SK, Uvet H. Acousto-holographic reconstruction of whole-cell stiffness maps. Nat Commun 2022; 13:7351. [PMID: 36446776 DOI: 10.1038/s41467-022-35075-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2021] [Accepted: 11/14/2022] [Indexed: 11/30/2022] Open
Abstract
Accurate assessment of cell stiffness distribution is essential due to the critical role of cell mechanobiology in regulation of vital cellular processes like proliferation, adhesion, migration, and motility. Stiffness provides critical information in understanding onset and progress of various diseases, including metastasis and differentiation of cancer. Atomic force microscopy and optical trapping set the gold standard in stiffness measurements. However, their widespread use has been hampered with long processing times, unreliable contact point determination, physical damage to cells, and unsuitability for multiple cell analysis. Here, we demonstrate a simple, fast, label-free, and high-resolution technique using acoustic stimulation and holographic imaging to reconstruct stiffness maps of single cells. We used this acousto-holographic method to determine stiffness maps of HCT116 and CTC-mimicking HCT116 cells and differentiate between them. Our system would enable widespread use of whole-cell stiffness measurements in clinical and research settings for cancer studies, disease modeling, drug testing, and diagnostics.
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27
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Kano F, Naik H, Keskin G, Couzin ID, Nagy M. Head-tracking of freely-behaving pigeons in a motion-capture system reveals the selective use of visual field regions. Sci Rep 2022; 12:19113. [PMID: 36352049 PMCID: PMC9646700 DOI: 10.1038/s41598-022-21931-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Accepted: 10/06/2022] [Indexed: 11/11/2022] Open
Abstract
Using a motion-capture system and custom head-calibration methods, we reconstructed the head-centric view of freely behaving pigeons and examined how they orient their head when presented with various types of attention-getting objects at various relative locations. Pigeons predominantly employed their retinal specializations to view a visual target, namely their foveas projecting laterally (at an azimuth of ± 75°) into the horizon, and their visually-sensitive "red areas" projecting broadly into the lower-frontal visual field. Pigeons used their foveas to view any distant object while they used their red areas to view a nearby object on the ground (< 50 cm). Pigeons "fixated" a visual target with their foveas; the intervals between head-saccades were longer when the visual target was viewed by birds' foveas compared to when it was viewed by any other region. Furthermore, pigeons showed a weak preference to use their right eye to examine small objects distinctive in detailed features and their left eye to view threat-related or social stimuli. Despite the known difficulty in identifying where a bird is attending, we show that it is possible to estimate the visual attention of freely-behaving birds by tracking the projections of their retinal specializations in their visual field with cutting-edge methods.
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Affiliation(s)
- Fumihiro Kano
- grid.9811.10000 0001 0658 7699Centre for the Advanced Study of Collective Behaviour, University of Konstanz, Universitätsstraße 10, 78464 Konstanz, Germany ,grid.507516.00000 0004 7661 536XDepartment of Collective Behaviour, Max-Planck Institute of Animal Behavior, Konstanz, Germany
| | - Hemal Naik
- grid.507516.00000 0004 7661 536XDepartment of Collective Behaviour, Max-Planck Institute of Animal Behavior, Konstanz, Germany ,grid.507516.00000 0004 7661 536XDepartment of Ecology of Animal Societies, Max-Planck Institute of Animal Behavior, Konstanz, Germany ,grid.5252.00000 0004 1936 973XComputer Aided Medical Procedures, Teschnische Universiät Munchen, Munich, Germany ,grid.9811.10000 0001 0658 7699Department of Biology, University of Konstanz, Konstanz, Germany
| | - Göksel Keskin
- grid.5018.c0000 0001 2149 4407MTA-ELTE Lendület Collective Behaviour Research Group, Hungarian Academy of Sciences, Budapest, Hungary ,grid.5591.80000 0001 2294 6276Department of Biological Physics, Eötvös Loránd University, Budapest, Hungary
| | - Iain D. Couzin
- grid.9811.10000 0001 0658 7699Centre for the Advanced Study of Collective Behaviour, University of Konstanz, Universitätsstraße 10, 78464 Konstanz, Germany ,grid.507516.00000 0004 7661 536XDepartment of Collective Behaviour, Max-Planck Institute of Animal Behavior, Konstanz, Germany ,grid.9811.10000 0001 0658 7699Department of Biology, University of Konstanz, Konstanz, Germany
| | - Máté Nagy
- grid.507516.00000 0004 7661 536XDepartment of Collective Behaviour, Max-Planck Institute of Animal Behavior, Konstanz, Germany ,grid.5018.c0000 0001 2149 4407MTA-ELTE Lendület Collective Behaviour Research Group, Hungarian Academy of Sciences, Budapest, Hungary ,grid.5591.80000 0001 2294 6276Department of Biological Physics, Eötvös Loránd University, Budapest, Hungary
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28
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Parsa S, Rodriguez A, Robertson DM, Bowman RW, Petroll WM. Temporal and Spatial Assessment of the Corneal Response to UV Cross-Linking Using 3-Dimensional In Vivo Confocal Microscopy. Eye Contact Lens 2022; 48:308-312. [PMID: 35333808 PMCID: PMC9232861 DOI: 10.1097/icl.0000000000000892] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/21/2021] [Indexed: 11/25/2022]
Abstract
ABSTRACT The goal of this study was to evaluate the temporal and spatial pattern of wound healing following UV corneal cross-linking (CXL) using 3-dimensional (3-D) confocal imaging in vivo. Using a modified Heidelberg Retinal Tomograph with Rostock Corneal Module confocal microscope, we performed 3-D scans on two patients at multiple time points after CXL. Patient 1 showed a normal post-CXL wound healing response, with initial subbasal nerve loss and keratocyte apoptosis in the anterior stroma, followed by partial restoration of both the nerve plexus and stromal keratocytes by 6 months. In patient 2, in addition to anterior corneal damage, pyknotic nuclei were observed in the posterior stroma 7 days after CXL. Acellular areas were present in the posterior stroma at 3 months, with only partial keratocyte repopulation at 6 months. Regeneration of the subbasal nerve plexus was also delayed. Three-dimensional confocal imaging allowed these unusual wound healing responses to be identified in the absence of any corresponding clinical observations.
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Affiliation(s)
- Shyon Parsa
- Southwestern Medical School, UT Southwestern Medical Center, Dallas, TX, USA
| | - Alejandro Rodriguez
- Southwestern Medical School, UT Southwestern Medical Center, Dallas, TX, USA
| | | | - R. Wayne Bowman
- Department of Ophthalmology, UT Southwestern Medical Center, Dallas, TX, USA
| | - W. Matthew Petroll
- Department of Ophthalmology, UT Southwestern Medical Center, Dallas, TX, USA
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29
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Lee JY, Mack AF, Shiozawa T, Longo R, Tromba G, Scheffler K, Hagberg GE. Microvascular imaging of the unstained human superior colliculus using synchrotron-radiation phase-contrast microtomography. Sci Rep 2022; 12:9238. [PMID: 35655082 PMCID: PMC9163179 DOI: 10.1038/s41598-022-13282-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2022] [Accepted: 05/23/2022] [Indexed: 12/05/2022] Open
Abstract
Characterizing the microvasculature of the human brain is critical to advance understanding of brain vascular function. Most methods rely on tissue staining and microscopy in two-dimensions, which pose several challenges to visualize the three-dimensional structure of microvessels. In this study, we used an edge-based segmentation method to extract the 3D vasculature from synchrotron radiation phase-contrast microtomography (PC-μCT) of two unstained, paraffin-embedded midbrain region of the human brain stem. Vascular structures identified in PC-μCT were validated with histology of the same specimen. Using the Deriche-Canny edge detector that was sensitive to the boundary between tissue and vascular space, we could segment the vessels independent of signal variations in PC-μCT images. From the segmented volumetric vasculature, we calculated vessel diameter, vessel length and volume fraction of the vasculature in the superior colliculi. From high resolution images, we found the most frequent vessel diameter to be between 8.6-10.2 µm. Our findings are consistent with the known anatomy showing two types of vessels with distinctive morphology: peripheral collicular vessels and central collicular vessels. The proposed method opens up new possibilities for vascular research of the central nervous system using synchrotron radiation PC-μCT of unstained human tissue.
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Affiliation(s)
- Ju Young Lee
- High Field Magnetic Resonance, Max Planck Institute for Biological Cybernetics, Tübingen, Germany.
- Graduate Training Centre of Neuroscience, Eberhard Karl's University of Tübingen, Tübingen, Germany.
| | - Andreas F Mack
- Institute of Clinical Anatomy and Cell Analysis, Eberhard Karl's University of Tübingen, Tübingen, Germany
| | - Thomas Shiozawa
- Institute of Clinical Anatomy and Cell Analysis, Eberhard Karl's University of Tübingen, Tübingen, Germany
| | - Renata Longo
- University of Trieste, Trieste, Italy
- Istituto Nazionale di Fisica Nucleare (INFN), Trieste, Italy
| | | | - Klaus Scheffler
- High Field Magnetic Resonance, Max Planck Institute for Biological Cybernetics, Tübingen, Germany
- Department of Biomedical Magnetic Resonance, University Hospital Tübingen, Tübingen, Germany
| | - Gisela E Hagberg
- High Field Magnetic Resonance, Max Planck Institute for Biological Cybernetics, Tübingen, Germany
- Department of Biomedical Magnetic Resonance, University Hospital Tübingen, Tübingen, Germany
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30
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Ajayi PT, Katti P, Zhang Y, Willingham TB, Sun Y, Bleck CKE, Glancy B. Regulation of the evolutionarily conserved muscle myofibrillar matrix by cell type dependent and independent mechanisms. Nat Commun 2022; 13:2661. [PMID: 35562354 PMCID: PMC9106682 DOI: 10.1038/s41467-022-30401-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2021] [Accepted: 04/29/2022] [Indexed: 12/29/2022] Open
Abstract
Skeletal muscles play a central role in human movement through forces transmitted by contraction of the sarcomere. We recently showed that mammalian sarcomeres are connected through frequent branches forming a singular, mesh-like myofibrillar matrix. However, the extent to which myofibrillar connectivity is evolutionarily conserved as well as mechanisms which regulate the specific architecture of sarcomere branching remain unclear. Here, we demonstrate the presence of a myofibrillar matrix in the tubular, but not indirect flight (IF) muscles within Drosophila melanogaster. Moreover, we find that loss of transcription factor H15 increases sarcomere branching frequency in the tubular jump muscles, and we show that sarcomere branching can be turned on in IF muscles by salm-mediated conversion to tubular muscles. Finally, we demonstrate that neurochondrin misexpression results in myofibrillar connectivity in IF muscles without conversion to tubular muscles. These data indicate an evolutionarily conserved myofibrillar matrix regulated by both cell-type dependent and independent mechanisms.
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Affiliation(s)
- Peter T Ajayi
- Muscle Energetics Laboratory, NHLBI, NIH, Bethesda, MD, 20892, USA
| | - Prasanna Katti
- Muscle Energetics Laboratory, NHLBI, NIH, Bethesda, MD, 20892, USA
| | - Yingfan Zhang
- Muscle Energetics Laboratory, NHLBI, NIH, Bethesda, MD, 20892, USA
| | | | - Ye Sun
- Electron Microscopy Core, NHLBI, NIH, Bethesda, MD, 20892, USA
| | | | - Brian Glancy
- Muscle Energetics Laboratory, NHLBI, NIH, Bethesda, MD, 20892, USA.
- NIAMS, NIH, Bethesda, MD, 20892, USA.
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31
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Adams JK, Yan D, Wu J, Boominathan V, Gao S, Rodriguez AV, Kim S, Carns J, Richards-Kortum R, Kemere C, Veeraraghavan A, Robinson JT. In vivo lensless microscopy via a phase mask generating diffraction patterns with high-contrast contours. Nat Biomed Eng 2022; 6:617-628. [PMID: 35256759 PMCID: PMC9142365 DOI: 10.1038/s41551-022-00851-z] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2021] [Accepted: 01/21/2022] [Indexed: 12/25/2022]
Abstract
The simple and compact optics of lensless microscopes and the associated computational algorithms allow for large fields of view and the refocusing of the captured images. However, existing lensless techniques cannot accurately reconstruct the typical low-contrast images of optically dense biological tissue. Here we show that lensless imaging of tissue in vivo can be achieved via an optical phase mask designed to create a point spread function consisting of high-contrast contours with a broad spectrum of spatial frequencies. We built a prototype lensless microscope incorporating the 'contour' phase mask and used it to image calcium dynamics in the cortex of live mice (over a field of view of about 16 mm2) and in freely moving Hydra vulgaris, as well as microvasculature in the oral mucosa of volunteers. The low cost, small form factor and computational refocusing capability of in vivo lensless microscopy may open it up to clinical uses, especially for imaging difficult-to-reach areas of the body.
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Affiliation(s)
- Jesse K Adams
- Applied Physics Program, Rice University, Houston, TX, USA
- Department of Electrical and Computer Engineering, Rice University, Houston, TX, USA
| | - Dong Yan
- Applied Physics Program, Rice University, Houston, TX, USA
- Department of Electrical and Computer Engineering, Rice University, Houston, TX, USA
| | - Jimin Wu
- Department of Bioengineering, Rice University, Houston, TX, USA
| | - Vivek Boominathan
- Department of Electrical and Computer Engineering, Rice University, Houston, TX, USA
| | - Sibo Gao
- Department of Electrical and Computer Engineering, Rice University, Houston, TX, USA
- Department of Neuroscience, Baylor College of Medicine, Houston, TX, USA
| | - Alex V Rodriguez
- Department of Electrical and Computer Engineering, Rice University, Houston, TX, USA
| | - Soonyoung Kim
- Department of Electrical and Computer Engineering, Rice University, Houston, TX, USA
| | - Jennifer Carns
- Department of Bioengineering, Rice University, Houston, TX, USA
| | - Rebecca Richards-Kortum
- Department of Electrical and Computer Engineering, Rice University, Houston, TX, USA
- Department of Bioengineering, Rice University, Houston, TX, USA
| | - Caleb Kemere
- Department of Electrical and Computer Engineering, Rice University, Houston, TX, USA
- Department of Bioengineering, Rice University, Houston, TX, USA
- Department of Neuroscience, Baylor College of Medicine, Houston, TX, USA
| | - Ashok Veeraraghavan
- Applied Physics Program, Rice University, Houston, TX, USA.
- Department of Electrical and Computer Engineering, Rice University, Houston, TX, USA.
- Department of Computer Science, Rice University, Houston, TX, USA.
| | - Jacob T Robinson
- Applied Physics Program, Rice University, Houston, TX, USA.
- Department of Electrical and Computer Engineering, Rice University, Houston, TX, USA.
- Department of Bioengineering, Rice University, Houston, TX, USA.
- Department of Neuroscience, Baylor College of Medicine, Houston, TX, USA.
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32
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Uceda-Castro R, van Asperen JV, Vennin C, Sluijs JA, van Bodegraven EJ, Margarido AS, Robe PAJ, van Rheenen J, Hol EM. GFAP splice variants fine-tune glioma cell invasion and tumour dynamics by modulating migration persistence. Sci Rep 2022; 12:424. [PMID: 35013418 PMCID: PMC8748899 DOI: 10.1038/s41598-021-04127-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2021] [Accepted: 12/16/2021] [Indexed: 12/26/2022] Open
Abstract
Glioma is the most common form of malignant primary brain tumours in adults. Their highly invasive nature makes the disease incurable to date, emphasizing the importance of better understanding the mechanisms driving glioma invasion. Glial fibrillary acidic protein (GFAP) is an intermediate filament protein that is characteristic for astrocyte- and neural stem cell-derived gliomas. Glioma malignancy is associated with changes in GFAP alternative splicing, as the canonical isoform GFAPα is downregulated in higher-grade tumours, leading to increased dominance of the GFAPδ isoform in the network. In this study, we used intravital imaging and an ex vivo brain slice invasion model. We show that the GFAPδ and GFAPα isoforms differentially regulate the tumour dynamics of glioma cells. Depletion of either isoform increases the migratory capacity of glioma cells. Remarkably, GFAPδ-depleted cells migrate randomly through the brain tissue, whereas GFAPα-depleted cells show a directionally persistent invasion into the brain parenchyma. This study shows that distinct compositions of the GFAPnetwork lead to specific migratory dynamics and behaviours of gliomas.
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Affiliation(s)
- Rebeca Uceda-Castro
- Division of Molecular Pathology, Oncode Institute, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Jessy V van Asperen
- Department of Translational Neuroscience, University Medical Center Utrecht Brain Center, Utrecht University, Utrecht, The Netherlands
| | - Claire Vennin
- Division of Molecular Pathology, Oncode Institute, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Jacqueline A Sluijs
- Department of Translational Neuroscience, University Medical Center Utrecht Brain Center, Utrecht University, Utrecht, The Netherlands
| | - Emma J van Bodegraven
- Department of Translational Neuroscience, University Medical Center Utrecht Brain Center, Utrecht University, Utrecht, The Netherlands
| | - Andreia S Margarido
- Division of Molecular Pathology, Oncode Institute, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Pierre A J Robe
- Department of Neurology and Neurosurgery, University Medical Center Utrecht Brain Center, University Utrecht, Utrecht, The Netherlands
| | - Jacco van Rheenen
- Division of Molecular Pathology, Oncode Institute, The Netherlands Cancer Institute, Amsterdam, The Netherlands.
| | - Elly M Hol
- Department of Translational Neuroscience, University Medical Center Utrecht Brain Center, Utrecht University, Utrecht, The Netherlands.
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33
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Quinn SE, Huang L, Kerkvliet JG, Swanson JA, Smith S, Hoppe AD, Anderson RB, Thiex NW, Scott BL. Author Correction: The structural dynamics of macropinosome formation and PI3-kinase-mediated sealing revealed by lattice light sheet microscopy. Nat Commun 2021; 12:7266. [PMID: 34880216 PMCID: PMC8655030 DOI: 10.1038/s41467-021-27411-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Affiliation(s)
- Shayne E Quinn
- Nanoscience and Nanoengineering, South Dakota School of Mines and Technology (South Dakota Mines), Rapid City, SD, USA
- BioSNTR, South Dakota Mines, Rapid City, SD, USA
| | - Lu Huang
- Department of Biology and Microbiology, South Dakota State University (SDSU), Brookings, SD, USA
- BioSNTR, SDSU, Brookings, SD, USA
| | - Jason G Kerkvliet
- BioSNTR, SDSU, Brookings, SD, USA
- Department of Chemistry and Biochemistry, SDSU, Brookings, SD, USA
| | - Joel A Swanson
- Department of Microbiology and Immunology, University of Michigan, Ann Arbor, MI, USA
| | - Steve Smith
- Nanoscience and Nanoengineering, South Dakota School of Mines and Technology (South Dakota Mines), Rapid City, SD, USA
- BioSNTR, South Dakota Mines, Rapid City, SD, USA
| | - Adam D Hoppe
- BioSNTR, SDSU, Brookings, SD, USA
- Department of Chemistry and Biochemistry, SDSU, Brookings, SD, USA
| | - Robert B Anderson
- Nanoscience and Nanoengineering, South Dakota School of Mines and Technology (South Dakota Mines), Rapid City, SD, USA.
- BioSNTR, South Dakota Mines, Rapid City, SD, USA.
| | - Natalie W Thiex
- Department of Biology and Microbiology, South Dakota State University (SDSU), Brookings, SD, USA.
- BioSNTR, SDSU, Brookings, SD, USA.
| | - Brandon L Scott
- Nanoscience and Nanoengineering, South Dakota School of Mines and Technology (South Dakota Mines), Rapid City, SD, USA.
- BioSNTR, South Dakota Mines, Rapid City, SD, USA.
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34
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Kanevche K, Burr DJ, Nürnberg DJ, Hass PK, Elsaesser A, Heberle J. Infrared nanoscopy and tomography of intracellular structures. Commun Biol 2021; 4:1341. [PMID: 34848821 DOI: 10.1038/s42003-021-02876-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2021] [Accepted: 11/09/2021] [Indexed: 11/08/2022] Open
Abstract
Although techniques such as fluorescence-based super-resolution imaging or confocal microscopy simultaneously gather both morphological and chemical data, these techniques often rely on the use of localized and chemically specific markers. To eliminate this flaw, we have developed a method of examining cellular cross sections using the imaging power of scattering-type scanning near-field optical microscopy and Fourier-transform infrared spectroscopy at a spatial resolution far beyond the diffraction limit. Herewith, nanoscale surface and volumetric chemical imaging is performed using the intrinsic contrast generated by the characteristic absorption of mid-infrared radiation by the covalent bonds. We employ infrared nanoscopy to study the subcellular structures of eukaryotic (Chlamydomonas reinhardtii) and prokaryotic (Escherichia coli) species, revealing chemically distinct regions within each cell such as the microtubular structure of the flagellum. Serial 100 nm-thick cellular cross-sections were compiled into a tomogram yielding a three-dimensional infrared image of subcellular structure distribution at 20 nm resolution. The presented methodology is able to image biological samples complementing current fluorescence nanoscopy but at less interference due to the low energy of infrared radiation and the absence of labeling.
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35
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Rindone AN, Liu X, Farhat S, Perdomo-Pantoja A, Witham TF, Coutu DL, Wan M, Grayson WL. Quantitative 3D imaging of the cranial microvascular environment at single-cell resolution. Nat Commun 2021; 12:6219. [PMID: 34711819 PMCID: PMC8553857 DOI: 10.1038/s41467-021-26455-w] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2020] [Accepted: 10/05/2021] [Indexed: 11/09/2022] Open
Abstract
Vascularization is critical for skull development, maintenance, and healing. Yet, there remains a significant knowledge gap in the relationship of blood vessels to cranial skeletal progenitors during these processes. Here, we introduce a quantitative 3D imaging platform to enable the visualization and analysis of high-resolution data sets (>100 GB) throughout the entire murine calvarium. Using this technique, we provide single-cell resolution 3D maps of vessel phenotypes and skeletal progenitors in the frontoparietal cranial bones. Through these high-resolution data sets, we demonstrate that CD31hiEmcnhi vessels are spatially correlated with both Osterix+ and Gli1+ skeletal progenitors during postnatal growth, healing, and stimulated remodeling, and are concentrated at transcortical canals and osteogenic fronts. Interestingly, we find that this relationship is weakened in mice with a conditional knockout of PDGF-BB in TRAP+ osteoclasts, suggesting a potential role for osteoclasts in maintaining the native cranial microvascular environment. Our findings provide a foundational framework for understanding how blood vessels and skeletal progenitors spatially interact in cranial bone, and will enable more targeted studies into the mechanisms of skull disease pathologies and treatments. Additionally, our technique can be readily adapted to study numerous cell types and investigate other elusive phenomena in cranial bone biology.
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Affiliation(s)
- Alexandra N Rindone
- Department of Biomedical Engineering, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Translational Tissue Engineering Center, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Xiaonan Liu
- Department of Orthopaedic Surgery, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Division of Orthopaedics and Traumatology, Department of Orthopaedics, Nanfang Hospital, Southern Medical University, Guangzhou, Guangdong, China
| | - Stephanie Farhat
- Regenerative Medicine Program, Ottawa Hospital Research Institute, Ottawa, ON, Canada
- Department of Cellular and Molecular Medicine, University of Ottawa, Ottawa, ON, Canada
- Division of Orthopaedic Surgery, The Ottawa Hospital, Ottawa, ON, Canada
| | | | - Timothy F Witham
- Department of Neurosurgery, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Daniel L Coutu
- Regenerative Medicine Program, Ottawa Hospital Research Institute, Ottawa, ON, Canada
- Department of Cellular and Molecular Medicine, University of Ottawa, Ottawa, ON, Canada
- Division of Orthopaedic Surgery, The Ottawa Hospital, Ottawa, ON, Canada
| | - Mei Wan
- Department of Orthopaedic Surgery, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Warren L Grayson
- Department of Biomedical Engineering, Johns Hopkins University School of Medicine, Baltimore, MD, USA.
- Translational Tissue Engineering Center, Johns Hopkins University School of Medicine, Baltimore, MD, USA.
- Department of Materials Science and Engineering, Johns Hopkins University, Baltimore, MD, USA.
- Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, MD, USA.
- Institute for NanoBioTechnology, Johns Hopkins University, Baltimore, MD, USA.
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36
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Quinn SE, Huang L, Kerkvliet JG, Swanson JA, Smith S, Hoppe AD, Anderson RB, Thiex NW, Scott BL. The structural dynamics of macropinosome formation and PI3-kinase-mediated sealing revealed by lattice light sheet microscopy. Nat Commun 2021; 12:4838. [PMID: 34376698 PMCID: PMC8355319 DOI: 10.1038/s41467-021-25187-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2020] [Accepted: 07/22/2021] [Indexed: 12/11/2022] Open
Abstract
Macropinosomes are formed by shaping actin-rich plasma membrane ruffles into large intracellular organelles in a phosphatidylinositol 3-kinase (PI3K)-coordinated manner. Here, we utilize lattice lightsheet microscopy and image visualization methods to map the three-dimensional structure and dynamics of macropinosome formation relative to PI3K activity. We show that multiple ruffling morphologies produce macropinosomes and that the majority form through collisions of adjacent PI3K-rich ruffles. By combining multiple volumetric representations of the plasma membrane structure and PI3K products, we show that PI3K activity begins early throughout the entire ruffle volume and continues to increase until peak activity concentrates at the base of the ruffle after the macropinosome closes. Additionally, areas of the plasma membrane rich in ruffling had increased PI3K activity and produced many macropinosomes of various sizes. Pharmacologic inhibition of PI3K activity had little effect on the rate and morphology of membrane ruffling, demonstrating that early production of 3'-phosphoinositides within ruffles plays a minor role in regulating their morphology. However, 3'-phosphoinositides are critical for the fusogenic activity that seals ruffles into macropinosomes. Taken together, these data indicate that local PI3K activity is amplified in ruffles and serves as a priming mechanism for closure and sealing of ruffles into macropinosomes.
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Affiliation(s)
- Shayne E Quinn
- Nanoscience and Nanoengineering, South Dakota School of Mines and Technology (South Dakota Mines), Rapid City, SD, USA
- BioSNTR, South Dakota Mines, Rapid City, SD, USA
| | - Lu Huang
- Department of Biology and Microbiology, South Dakota State University (SDSU), Brookings, SD, USA
- BioSNTR, SDSU, Brookings, SD, USA
| | - Jason G Kerkvliet
- BioSNTR, SDSU, Brookings, SD, USA
- Department of Chemistry and Biochemistry, SDSU, Brookings, SD, USA
| | - Joel A Swanson
- Department of Microbiology and Immunology, University of Michigan, Ann Arbor, MI, USA
| | - Steve Smith
- Nanoscience and Nanoengineering, South Dakota School of Mines and Technology (South Dakota Mines), Rapid City, SD, USA
- BioSNTR, South Dakota Mines, Rapid City, SD, USA
| | - Adam D Hoppe
- BioSNTR, SDSU, Brookings, SD, USA
- Department of Chemistry and Biochemistry, SDSU, Brookings, SD, USA
| | - Robert B Anderson
- Nanoscience and Nanoengineering, South Dakota School of Mines and Technology (South Dakota Mines), Rapid City, SD, USA.
- BioSNTR, South Dakota Mines, Rapid City, SD, USA.
| | - Natalie W Thiex
- Department of Biology and Microbiology, South Dakota State University (SDSU), Brookings, SD, USA.
- BioSNTR, SDSU, Brookings, SD, USA.
| | - Brandon L Scott
- Nanoscience and Nanoengineering, South Dakota School of Mines and Technology (South Dakota Mines), Rapid City, SD, USA.
- BioSNTR, South Dakota Mines, Rapid City, SD, USA.
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37
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Hansen JN, Gong A, Wachten D, Pascal R, Turpin A, Jikeli JF, Kaupp UB, Alvarez L. Multifocal imaging for precise, label-free tracking of fast biological processes in 3D. Nat Commun 2021; 12:4574. [PMID: 34321468 PMCID: PMC8319204 DOI: 10.1038/s41467-021-24768-4] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2020] [Accepted: 07/06/2021] [Indexed: 11/22/2022] Open
Abstract
Many biological processes happen on a nano- to millimeter scale and within milliseconds. Established methods such as confocal microscopy are suitable for precise 3D recordings but lack the temporal or spatial resolution to resolve fast 3D processes and require labeled samples. Multifocal imaging (MFI) allows high-speed 3D imaging but is limited by the compromise between high spatial resolution and large field-of-view (FOV), and the requirement for bright fluorescent labels. Here, we provide an open-source 3D reconstruction algorithm for multi-focal images that allows using MFI for fast, precise, label-free tracking spherical and filamentous structures in a large FOV and across a high depth. We characterize fluid flow and flagellar beating of human and sea urchin sperm with a z-precision of 0.15 µm, in a volume of 240 × 260 × 21 µm, and at high speed (500 Hz). The sampling volume allowed to follow sperm trajectories while simultaneously recording their flagellar beat. Our MFI concept is cost-effective, can be easily implemented, and does not rely on object labeling, which renders it broadly applicable.
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Affiliation(s)
- Jan N Hansen
- Institute of Innate Immunity, Biophysical Imaging, Medical Faculty, University of Bonn, Bonn, Germany.
| | - An Gong
- Center of Advanced European Studies and Research (caesar), Molecular Sensory Systems, Bonn, Germany
| | - Dagmar Wachten
- Institute of Innate Immunity, Biophysical Imaging, Medical Faculty, University of Bonn, Bonn, Germany
| | - René Pascal
- Center of Advanced European Studies and Research (caesar), Molecular Sensory Systems, Bonn, Germany
| | - Alex Turpin
- School of Computing Science, University of Glasgow, Glasgow, UK
| | - Jan F Jikeli
- Institute of Innate Immunity, Biophysical Imaging, Medical Faculty, University of Bonn, Bonn, Germany
| | - U Benjamin Kaupp
- Center of Advanced European Studies and Research (caesar), Molecular Sensory Systems, Bonn, Germany
- Life & Medical Sciences Institute (LIMES), University of Bonn, Bonn, Germany
| | - Luis Alvarez
- Center of Advanced European Studies and Research (caesar), Molecular Sensory Systems, Bonn, Germany.
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38
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Kim YH, Shin JY, Lee A, Park S, Han SS, Hwang HJ. Automated cortical thickness measurement of the mandibular condyle head on CBCT images using a deep learning method. Sci Rep 2021; 11:14852. [PMID: 34290333 PMCID: PMC8295413 DOI: 10.1038/s41598-021-94362-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2020] [Accepted: 07/05/2021] [Indexed: 11/09/2022] Open
Abstract
This study proposes a deep learning model for cortical bone segmentation in the mandibular condyle head using cone-beam computed tomography (CBCT) and an automated method for measuring cortical thickness with a color display based on the segmentation results. In total, 12,800 CBCT images from 25 normal subjects, manually labeled by an oral radiologist, served as the gold-standard. The segmentation model combined a modified U-Net and a convolutional neural network for target region classification. Model performance was evaluated using intersection over union (IoU) and the Hausdorff distance in comparison with the gold standard. The second automated model measured the cortical thickness based on a three-dimensional (3D) model rendered from the segmentation results and presented a color visualization of the measurements. The IoU and Hausdorff distance showed high accuracy (0.870 and 0.928 for marrow bone and 0.734 and 1.247 for cortical bone, respectively). A visual comparison of the 3D color maps showed a similar trend to the gold standard. This algorithm for automatic segmentation of the mandibular condyle head and visualization of the measured cortical thickness as a 3D-rendered model with a color map may contribute to the automated quantification of bone thickness changes of the temporomandibular joint complex on CBCT.
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Affiliation(s)
- Young Hyun Kim
- Department of Oral and Maxillofacial Radiology, Yonsei University College of Dentistry, 50-1 Yonsei-ro Seodaemun-gu, Seoul, 03722, South Korea
| | - Jin Young Shin
- Department of Mathematics, Pohang University of Science and Technology, 150 Jigok-ro Nam-gu, Pohang-si, Gyeongsangbuk-do, 37666, South Korea
| | - Ari Lee
- Department of Oral and Maxillofacial Radiology, Yonsei University College of Dentistry, 50-1 Yonsei-ro Seodaemun-gu, Seoul, 03722, South Korea
| | - Seungtae Park
- Department of Mathematics, Pohang University of Science and Technology, 150 Jigok-ro Nam-gu, Pohang-si, Gyeongsangbuk-do, 37666, South Korea
| | - Sang-Sun Han
- Department of Oral and Maxillofacial Radiology, Yonsei University College of Dentistry, 50-1 Yonsei-ro Seodaemun-gu, Seoul, 03722, South Korea.
| | - Hyung Ju Hwang
- Department of Mathematics, Pohang University of Science and Technology, 150 Jigok-ro Nam-gu, Pohang-si, Gyeongsangbuk-do, 37666, South Korea.
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39
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Masuyama K, Higo T, Lee JK, Matsuura R, Jones I, Bakal C, Higo S, Morimoto S, Miyagawa S, Sawa Y, Sakata Y. Homogeneous 2D and 3D alignment of cardiomyocyte in dilated cardiomyopathy revealed by intravital heart imaging. Sci Rep 2021; 11:14698. [PMID: 34282197 PMCID: PMC8289833 DOI: 10.1038/s41598-021-94100-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2020] [Accepted: 07/01/2021] [Indexed: 01/15/2023] Open
Abstract
In contrast to hypertrophic cardiomyopathy, there has been reported no specific pattern of cardiomyocyte array in dilated cardiomyopathy (DCM), partially because lack of alignment assessment in a three-dimensional (3D) manner. Here we have established a novel method to evaluate cardiomyocyte alignment in 3D using intravital heart imaging and demonstrated homogeneous alignment in DCM mice. Whilst cardiomyocytes of control mice changed their alignment by every layer in 3D and position twistedly even in a single layer, termed myocyte twist, cardiomyocytes of DCM mice aligned homogeneously both in two-dimensional (2D) and in 3D and lost myocyte twist. Manipulation of cultured cardiomyocyte toward homogeneously aligned increased their contractility, suggesting that homogeneous alignment in DCM mice is due to a sort of alignment remodelling as a way to compensate cardiac dysfunction. Our findings provide the first intravital evidence of cardiomyocyte alignment and will bring new insights into understanding the mechanism of heart failure.
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MESH Headings
- Animals
- Animals, Newborn
- Cardiomyopathy, Dilated/diagnostic imaging
- Cardiomyopathy, Dilated/pathology
- Cardiomyopathy, Hypertrophic/diagnostic imaging
- Cardiomyopathy, Hypertrophic/pathology
- Cell Movement/physiology
- Cells, Cultured
- Diagnostic Imaging/methods
- Male
- Mice
- Mice, Transgenic
- Myocytes, Cardiac/cytology
- Myocytes, Cardiac/physiology
- Rats
- Rats, Wistar
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Affiliation(s)
- Kiyoshi Masuyama
- Department of Cardiovascular Medicine, Osaka University Graduate School of Medicine, 2-2 Yamadaoka, Suita, 565-0871, Japan
| | - Tomoaki Higo
- Department of Cardiovascular Medicine, Osaka University Graduate School of Medicine, 2-2 Yamadaoka, Suita, 565-0871, Japan.
- The Institute of Cancer Research, London, Chester Beatty Laboratories, 237 Fulham Road, London, SW3 6JB, UK.
| | - Jong-Kook Lee
- Department of Cardiovascular Regenerative Medicine, Osaka University Graduate School of Medicine, 2-2 Yamadaoka, Suita, 565-0871, Japan
| | - Ryohei Matsuura
- Department of Cardiovascular Surgery, Osaka University Graduate School of Medicine, 2-2 Yamadaoka, Suita, 565-0871, Japan
| | - Ian Jones
- The Institute of Cancer Research, London, Chester Beatty Laboratories, 237 Fulham Road, London, SW3 6JB, UK
| | - Chris Bakal
- The Institute of Cancer Research, London, Chester Beatty Laboratories, 237 Fulham Road, London, SW3 6JB, UK
| | - Shuichiro Higo
- Department of Cardiovascular Medicine, Osaka University Graduate School of Medicine, 2-2 Yamadaoka, Suita, 565-0871, Japan
- Department of Medical Therapeutics for Heart Failure, Osaka University Graduate School of Medicine, 2-2 Yamadaoka, Suita, 565-0871, Japan
| | - Sachio Morimoto
- Department of Health and Medical Care, International University of Health and Welfare, Okawa, Fukuoka, 831-8501, Japan
| | - Shigeru Miyagawa
- Department of Cardiovascular Surgery, Osaka University Graduate School of Medicine, 2-2 Yamadaoka, Suita, 565-0871, Japan
| | - Yoshiki Sawa
- Department of Cardiovascular Surgery, Osaka University Graduate School of Medicine, 2-2 Yamadaoka, Suita, 565-0871, Japan
| | - Yasushi Sakata
- Department of Cardiovascular Medicine, Osaka University Graduate School of Medicine, 2-2 Yamadaoka, Suita, 565-0871, Japan
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40
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Liu Y, Feng X, Liu H, McComb DW, Breuer CK, Sacks MS. On the shape and structure of the murine pulmonary heart valve. Sci Rep 2021; 11:14078. [PMID: 34234231 PMCID: PMC8263753 DOI: 10.1038/s41598-021-93513-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2020] [Accepted: 06/10/2021] [Indexed: 11/20/2022] Open
Abstract
Murine animal models are an established standard in translational research and provides a potential platform for studying heart valve disease. To date, studies on heart valve disease using murine models have been hindered by a lack of appropriate methodologies due to their small scale. In the present study, we developed a multi-scale, imaging-based approach to extract the functional structure and geometry for the murine heart valve. We chose the pulmonary valve (PV) to study, due to its importance in congenital heart valve disease. Excised pulmonary outflow tracts from eleven 1-year old C57BL/6J mice were fixed at 10, 20, and 30 mmHg to simulate physiological loading. Micro-computed tomography was used to reconstruct the 3D organ-level PV geometry, which was then spatially correlated with serial en-face scanning electron microscopy imaging to quantify local collagen fiber distributions. From the acquired volume renderings, we obtained the geometric descriptors of the murine PV under increasing transvalvular pressures, which demonstrated remarkable consistency. Results to date suggest that the preferred collagen orientation was predominantly in the circumferential direction, as in larger mammalian valves. The present study represents a first step in establishing organ-level murine models for the study of heart valve disease.
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Affiliation(s)
- Yifei Liu
- Center for Electron Microscopy and Analysis, The Ohio State University, Columbus, OH, 43210, USA
- Department of Materials Science and Engineering, The Ohio State University, Columbus, OH, 43210, USA
| | - Xinzeng Feng
- Willerson Center, Oden Institute for Computational Engineering and Sciences, The University of Texas At Austin, Austin, TX, 78712, USA
| | - Hao Liu
- Willerson Center, Oden Institute for Computational Engineering and Sciences, The University of Texas At Austin, Austin, TX, 78712, USA
- Department of Biomedical Engineering, The University of Texas At Austin, Austin, TX, 78712, USA
| | - David W McComb
- Center for Electron Microscopy and Analysis, The Ohio State University, Columbus, OH, 43210, USA
- Department of Materials Science and Engineering, The Ohio State University, Columbus, OH, 43210, USA
| | - Christopher K Breuer
- Center for Regenerative Medicine, Abigail Wexner Research Institute, Nationwide Children's Hospital, Columbus, OH, 43205, USA
- Department of Pediatric Surgery, Nationwide Children's Hospital, Columbus, OH, 43205, USA
| | - Michael S Sacks
- Willerson Center, Oden Institute for Computational Engineering and Sciences, The University of Texas At Austin, Austin, TX, 78712, USA.
- Department of Biomedical Engineering, The University of Texas At Austin, Austin, TX, 78712, USA.
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41
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Kapsokalyvas D, Rosas R, Janssen RWA, Vanoevelen JM, Nabben M, Strauch M, Merhof D, van Zandvoort MAMJ. Multiview deconvolution approximation multiphoton microscopy of tissues and zebrafish larvae. Sci Rep 2021; 11:10160. [PMID: 33980963 PMCID: PMC8115086 DOI: 10.1038/s41598-021-89566-w] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2020] [Accepted: 03/30/2021] [Indexed: 02/03/2023] Open
Abstract
Imaging in three dimensions is necessary for thick tissues and small organisms. This is possible with tomographic optical microscopy techniques such as confocal, multiphoton and light sheet microscopy. All these techniques suffer from anisotropic resolution and limited penetration depth. In the past, Multiview microscopy-imaging the sample from different angles followed by 3D image reconstruction-was developed to address this issue for light sheet microscopy based on fluorescence signal. In this study we applied this methodology to accomplish Multiview imaging with multiphoton microscopy based on fluorescence and additionally second harmonic signal from myosin and collagen. It was shown that isotropic resolution was achieved, the entirety of the sample was visualized, and interference artifacts were suppressed allowing clear visualization of collagen fibrils and myofibrils. This method can be applied to any scanning microscopy technique without microscope modifications. It can be used for imaging tissue and whole mount small organisms such as heart tissue, and zebrafish larva in 3D, label-free or stained, with at least threefold axial resolution improvement which can be significant for the accurate quantification of small 3D structures.
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Affiliation(s)
- Dimitrios Kapsokalyvas
- grid.5012.60000 0001 0481 6099Department of Genetics and Cell Biology, Faculty of Health, Medicine and Life Sciences (FHML), Maastricht University, Maastricht, the Netherlands ,grid.412301.50000 0000 8653 1507Institute for Molecular Cardiovascular Research (IMCAR), University Hospital RWTH Aachen University, Aachen, Germany
| | - Rodrigo Rosas
- grid.5012.60000 0001 0481 6099Department of Genetics and Cell Biology, Faculty of Health, Medicine and Life Sciences (FHML), Maastricht University, Maastricht, the Netherlands
| | - Rob W. A. Janssen
- grid.5012.60000 0001 0481 6099Department of Genetics and Cell Biology, Faculty of Health, Medicine and Life Sciences (FHML), Maastricht University, Maastricht, the Netherlands
| | - Jo M. Vanoevelen
- grid.5012.60000 0001 0481 6099Department of Genetics and Cell Biology, Faculty of Health, Medicine and Life Sciences (FHML), Maastricht University, Maastricht, the Netherlands
| | - Miranda Nabben
- grid.5012.60000 0001 0481 6099Department of Genetics and Cell Biology, Faculty of Health, Medicine and Life Sciences (FHML), Maastricht University, Maastricht, the Netherlands
| | - Martin Strauch
- grid.1957.a0000 0001 0728 696XInstitute of Imaging and Computer Vision, RWTH Aachen University, Aachen, Germany
| | - Dorit Merhof
- grid.1957.a0000 0001 0728 696XInstitute of Imaging and Computer Vision, RWTH Aachen University, Aachen, Germany
| | - Marc A. M. J. van Zandvoort
- grid.5012.60000 0001 0481 6099Department of Genetics and Cell Biology, Faculty of Health, Medicine and Life Sciences (FHML), Maastricht University, Maastricht, the Netherlands ,grid.412301.50000 0000 8653 1507Institute for Molecular Cardiovascular Research (IMCAR), University Hospital RWTH Aachen University, Aachen, Germany
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42
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Ozturk MS, Montero MG, Wang L, Chaible LM, Jechlinger M, Prevedel R. Intravital mesoscopic fluorescence molecular tomography allows non-invasive in vivo monitoring and quantification of breast cancer growth dynamics. Commun Biol 2021; 4:556. [PMID: 33976362 DOI: 10.1038/s42003-021-02063-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2020] [Accepted: 03/31/2021] [Indexed: 02/03/2023] Open
Abstract
Preclinical breast tumor models are an invaluable tool to systematically study tumor progression and treatment response, yet methods to non-invasively monitor the involved molecular and mechanistic properties under physiologically relevant conditions are limited. Here we present an intravital mesoscopic fluorescence molecular tomography (henceforth IFT) approach that is capable of tracking fluorescently labeled tumor cells in a quantitative manner inside the mammary gland of living mice. Our mesoscopic approach is entirely non-invasive and thus permits prolonged observational periods of several months. The relatively high sensitivity and spatial resolution further enable inferring the overall number of oncogene-expressing tumor cells as well as their tumor volume over the entire cycle from early tumor growth to residual disease following the treatment phase. Our IFT approach is a promising method for studying tumor growth dynamics in a quantitative and longitudinal fashion in-vivo.
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43
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Asadi Zarch ME, Afshar A, Rahmanifar F, Jafarzadeh Shirazi MR, Baghban M, Dadpasand M, Mohammad Rezazadeh F, Khoradmehr A, Baharvand H, Tamadon A. Three-dimensional and two-dimensional relationships of gangliogenesis with folliculogenesis in mature mouse ovary: a Golgi-Cox staining approach. Sci Rep 2021; 11:5547. [PMID: 33692376 PMCID: PMC7970916 DOI: 10.1038/s41598-021-84835-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2020] [Accepted: 02/19/2021] [Indexed: 01/31/2023] Open
Abstract
The present study was set out to investigate two-dimensional (2D) and three-dimensional (3D) evaluations of ovarian nervous network development and the structural relationship between folliculogenesis and gangliogenesis in mouse ovaries. Adult mice ovarian tissue samples were collected from follicular and luteal phases after cardiac perfusion. Ovarian samples were stained by a Golgi-Cox protocol. Following staining, tissues were serially sectioned for imaging. Neural filaments and ganglia were present in the ovaries. In both 2D and 3D studies, an increase in the number and area of ganglia was seen during the follicular growth. The same pattern was also seen in corpora lutea development. However, in some cases such as ratio of ganglia number to follicle area, the ratio of ganglia area to follicular area, 2D findings were different compared with the 3D results. 3D analysis of ovarian gangliogenesis showed the possible direct effect of them on folliculogenesis. Golgi-Cox staining was used in this study for 3D evaluation in non-brain tissue. The results of 3D analysis of the present study showed that, in some cases, the information provided by 2D analysis does not match the reality of ovarian neuronal function. This confirmed the importance of 3D analysis for evaluation of ovarian function.
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Affiliation(s)
| | - Alireza Afshar
- The Persian Gulf Marine Biotechnology Research Center, The Persian Gulf Biomedical Sciences Research Institute, Bushehr University of Medical Sciences, 75146-33196, Bushehr, Iran
| | - Farhad Rahmanifar
- Department of Basic Sciences, School of Veterinary Medicine, Shiraz University, Shiraz, Iran
| | | | - Mandana Baghban
- Department of Obstetrics and Gynecology, School of Medicine, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Mohammad Dadpasand
- Department of Animal Sciences, College of Agriculture, Shiraz University, 71441-65186, Shiraz, Iran
| | | | - Arezoo Khoradmehr
- The Persian Gulf Marine Biotechnology Research Center, The Persian Gulf Biomedical Sciences Research Institute, Bushehr University of Medical Sciences, 75146-33196, Bushehr, Iran
| | - Hossein Baharvand
- Department of Stem Cells and Developmental Biology, Cell Science Research Center, Royan Institute for Stem Cell Biology and Technology, ACECR, Tehran, Iran
- Department of Developmental Biology, University of Science and Culture, Tehran, Iran
| | - Amin Tamadon
- The Persian Gulf Marine Biotechnology Research Center, The Persian Gulf Biomedical Sciences Research Institute, Bushehr University of Medical Sciences, 75146-33196, Bushehr, Iran.
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44
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Kubota SI, Takahashi K, Mano T, Matsumoto K, Katsumata T, Shi S, Tainaka K, Ueda HR, Ehata S, Miyazono K. Whole-organ analysis of TGF-β-mediated remodelling of the tumour microenvironment by tissue clearing. Commun Biol 2021; 4:294. [PMID: 33674758 PMCID: PMC7935961 DOI: 10.1038/s42003-021-01786-y] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2020] [Accepted: 02/02/2021] [Indexed: 01/06/2023] Open
Abstract
Tissue clearing is one of the most powerful strategies for a comprehensive analysis of disease progression. Here, we established an integrated pipeline that combines tissue clearing, 3D imaging, and machine learning and applied to a mouse tumour model of experimental lung metastasis using human lung adenocarcinoma A549 cells. This pipeline provided the spatial information of the tumour microenvironment. We further explored the role of transforming growth factor-β (TGF-β) in cancer metastasis. TGF-β-stimulated cancer cells enhanced metastatic colonization of unstimulated-cancer cells in vivo when both cells were mixed. RNA-sequencing analysis showed that expression of the genes related to coagulation and inflammation were up-regulated in TGF-β-stimulated cancer cells. Further, whole-organ analysis revealed accumulation of platelets or macrophages with TGF-β-stimulated cancer cells, suggesting that TGF-β might promote remodelling of the tumour microenvironment, enhancing the colonization of cancer cells. Hence, our integrated pipeline for 3D profiling will help the understanding of the tumour microenvironment.
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Affiliation(s)
- Shimpei I Kubota
- Department of Molecular Pathology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Kei Takahashi
- Department of Molecular Pathology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Tomoyuki Mano
- Department of Systems Pharmacology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Katsuhiko Matsumoto
- Laboratory for Synthetic Biology, RIKEN Quantitative Biology Center, Osaka, Japan
| | - Takahiro Katsumata
- Department of Systems Pharmacology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Shoi Shi
- Department of Systems Pharmacology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Kazuki Tainaka
- Brain Research Institute, Niigata University, Niigata, Japan
| | - Hiroki R Ueda
- Department of Systems Pharmacology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
- Laboratory for Synthetic Biology, RIKEN Quantitative Biology Center, Osaka, Japan
| | - Shogo Ehata
- Department of Molecular Pathology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan.
- Environmental Science Center, The University of Tokyo, Tokyo, Japan.
| | - Kohei Miyazono
- Department of Molecular Pathology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan.
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45
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Ushenko VA, Hogan BT, Dubolazov A, Piavchenko G, Kuznetsov SL, Ushenko AG, Ushenko YO, Gorsky M, Bykov A, Meglinski I. 3D Mueller matrix mapping of layered distributions of depolarisation degree for analysis of prostate adenoma and carcinoma diffuse tissues. Sci Rep 2021; 11:5162. [PMID: 33664274 PMCID: PMC7933337 DOI: 10.1038/s41598-021-83986-4] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2020] [Accepted: 02/10/2021] [Indexed: 11/17/2022] Open
Abstract
Prostate cancer is the second most common cancer globally in men, and in some countries is now the most diagnosed form of cancer. It is necessary to differentiate between benign and malignant prostate conditions to give accurate diagnoses. We aim to demonstrate the use of a 3D Mueller matrix method to allow quick and easy clinical differentiation between prostate adenoma and carcinoma tissues with different grades and Gleason scores. Histological sections of benign and malignant prostate tumours, obtained by radical prostatectomy, were investigated. We map the degree of depolarisation in the different prostate tumour tissues using a Mueller matrix polarimeter set-up, based on the superposition of a reference laser beam with the interference pattern of the sample in the image plane. The depolarisation distributions can be directly related to the morphology of the biological tissues. The dependences of the magnitude of the 1st to 4th order statistical moments of the depolarisation distribution are determined, which characterise the distributions of the depolarisation values. To determine the diagnostic potential of the method three groups of histological sections of prostate tumour biopsies were formed. The first group contained 36 adenoma tissue samples, while the second contained 36 carcinoma tissue samples of a high grade (grade 4: poorly differentiated-4 + 4 Gleason score), and the third group contained 36 carcinoma tissue samples of a low grade (grade 1: moderately differentiated-3 + 3 Gleason score). Using the calculated values of the statistical moments, tumour tissues are categorised as either adenoma or carcinoma. A high level (> 90%) accuracy of differentiation between adenoma and carcinoma samples was achieved for each group. Differentiation between the high-grade and low-grade carcinoma samples was achieved with an accuracy of 87.5%. The results demonstrate that Mueller matrix mapping of the depolarisation distribution of prostate tumour tissues can accurately differentiate between adenoma and carcinoma, and between different grades of carcinoma. This represents a first step towards the implementation of 3D Mueller matrix mapping for clinical analysis and diagnosis of prostate tumours.
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Affiliation(s)
- Volodymyr A Ushenko
- Optics and Publishing Department, Chernivtsi National University, 2 Kotsiubynskyi Str., Chernivtsi, 58012, Ukraine
| | - Benjamin T Hogan
- Optoelectronics and Measurement Techniques Laboratory, University of Oulu, 90014, Oulu, Finland
| | - Alexander Dubolazov
- Optics and Publishing Department, Chernivtsi National University, 2 Kotsiubynskyi Str., Chernivtsi, 58012, Ukraine
| | - Gennadii Piavchenko
- Institute of Clinical Medicine N.V. Sklifosovsky, I.M. Sechenov First Moscow State Medical University, Moscow, Russia, 129090
| | - Sergey L Kuznetsov
- Institute of Clinical Medicine N.V. Sklifosovsky, I.M. Sechenov First Moscow State Medical University, Moscow, Russia, 129090
| | - Alexander G Ushenko
- Optics and Publishing Department, Chernivtsi National University, 2 Kotsiubynskyi Str., Chernivtsi, 58012, Ukraine
| | - Yuriy O Ushenko
- Optics and Publishing Department, Chernivtsi National University, 2 Kotsiubynskyi Str., Chernivtsi, 58012, Ukraine
| | - Mykhailo Gorsky
- Optics and Publishing Department, Chernivtsi National University, 2 Kotsiubynskyi Str., Chernivtsi, 58012, Ukraine
| | - Alexander Bykov
- Optoelectronics and Measurement Techniques Laboratory, University of Oulu, 90014, Oulu, Finland
| | - Igor Meglinski
- Optoelectronics and Measurement Techniques Laboratory, University of Oulu, 90014, Oulu, Finland.
- Institute of Clinical Medicine N.V. Sklifosovsky, I.M. Sechenov First Moscow State Medical University, Moscow, Russia, 129090.
- Institute of Engineering Physics for Biomedicine (PhysBio), National Research Nuclear University (MEPhI), Moscow, Russia, 115409.
- College of Engineering and Physical Sciences, Aston University, Birmingham, B4 7ET, UK.
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46
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Roostalu U, Thisted L, Skytte JL, Salinas CG, Pedersen PJ, Hecksher-Sørensen J, Rolin B, Hansen HH, MacKrell JG, Christie RM, Vrang N, Jelsing J, Zois NE. Effect of captopril on post-infarction remodelling visualized by light sheet microscopy and echocardiography. Sci Rep 2021; 11:5241. [PMID: 33664407 DOI: 10.1038/s41598-021-84812-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2021] [Accepted: 02/22/2021] [Indexed: 02/08/2023] Open
Abstract
Angiotensin converting enzyme inhibitors, among them captopril, improve survival following myocardial infarction (MI). The mechanisms of captopril action remain inadequately understood due to its diverse effects on multiple signalling pathways at different time periods following MI. Here we aimed to establish the role of captopril in late-stage post-MI remodelling. Left anterior descending artery (LAD) ligation or sham surgery was carried out in male C57BL/6J mice. Seven days post-surgery LAD ligated mice were allocated to daily vehicle or captopril treatment continued over four weeks. To provide comprehensive characterization of the changes in mouse heart following MI a 3D light sheet imaging method was established together with automated image analysis workflow. The combination of echocardiography and light sheet imaging enabled to assess cardiac function and the underlying morphological changes. We show that delayed captopril treatment does not affect infarct size but prevents left ventricle dilation and hypertrophy, resulting in improved ejection fraction. Quantification of lectin perfused blood vessels showed improved vascular density in the infarct border zone in captopril treated mice in comparison to vehicle dosed control mice. These results validate the applicability of combined echocardiographic and light sheet assessment of drug mode of action in preclinical cardiovascular research.
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47
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Polilov AA, Makarova AA, Pang S, Shan Xu C, Hess H. Protocol for preparation of heterogeneous biological samples for 3D electron microscopy: a case study for insects. Sci Rep 2021; 11:4717. [PMID: 33633143 PMCID: PMC7907262 DOI: 10.1038/s41598-021-83936-0] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2020] [Accepted: 02/08/2021] [Indexed: 11/25/2022] Open
Abstract
Modern morphological and structural studies are coming to a new level by incorporating the latest methods of three-dimensional electron microscopy (3D-EM). One of the key problems for the wide usage of these methods is posed by difficulties with sample preparation, since the methods work poorly with heterogeneous (consisting of tissues different in structure and in chemical composition) samples and require expensive equipment and usually much time. We have developed a simple protocol allows preparing heterogeneous biological samples suitable for 3D-EM in a laboratory that has a standard supply of equipment and reagents for electron microscopy. This protocol, combined with focused ion-beam scanning electron microscopy, makes it possible to study 3D ultrastructure of complex biological samples, e.g., whole insect heads, over their entire volume at the cellular and subcellular levels. The protocol provides new opportunities for many areas of study, including connectomics.
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Affiliation(s)
- Alexey A Polilov
- Department of Entomology, Faculty of Biology, Moscow State University, Moscow, Russia.
| | - Anastasia A Makarova
- Department of Entomology, Faculty of Biology, Moscow State University, Moscow, Russia
| | - Song Pang
- Janelia Research Campus of the Howard Hughes Medical Institute, Ashburn, USA
| | - C Shan Xu
- Janelia Research Campus of the Howard Hughes Medical Institute, Ashburn, USA
| | - Harald Hess
- Janelia Research Campus of the Howard Hughes Medical Institute, Ashburn, USA
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48
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Chen C, Gu Y, Philippe J, Zhang P, Bachman H, Zhang J, Mai J, Rufo J, Rawls JF, Davis EE, Katsanis N, Huang TJ. Acoustofluidic rotational tweezing enables high-speed contactless morphological phenotyping of zebrafish larvae. Nat Commun 2021; 12:1118. [PMID: 33602914 PMCID: PMC7892888 DOI: 10.1038/s41467-021-21373-3] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2020] [Accepted: 01/08/2021] [Indexed: 01/31/2023] Open
Abstract
Modern biomedical research and preclinical pharmaceutical development rely heavily on the phenotyping of small vertebrate models for various diseases prior to human testing. In this article, we demonstrate an acoustofluidic rotational tweezing platform that enables contactless, high-speed, 3D multispectral imaging and digital reconstruction of zebrafish larvae for quantitative phenotypic analysis. The acoustic-induced polarized vortex streaming achieves contactless and rapid (~1 s/rotation) rotation of zebrafish larvae. This enables multispectral imaging of the zebrafish body and internal organs from different viewing perspectives. Moreover, we develop a 3D reconstruction pipeline that yields accurate 3D models based on the multi-view images for quantitative evaluation of basic morphological characteristics and advanced combinations of metrics. With its contactless nature and advantages in speed and automation, our acoustofluidic rotational tweezing system has the potential to be a valuable asset in numerous fields, especially for developmental biology, small molecule screening in biochemistry, and pre-clinical drug development in pharmacology.
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Affiliation(s)
- Chuyi Chen
- Department of Mechanical Engineering and Material Science, Duke University, Durham, NC, USA
| | - Yuyang Gu
- Department of Mechanical Engineering and Material Science, Duke University, Durham, NC, USA
| | - Julien Philippe
- Center for Human Disease Modeling, Duke University Medical Center, Durham, NC, USA
| | - Peiran Zhang
- Department of Mechanical Engineering and Material Science, Duke University, Durham, NC, USA
| | - Hunter Bachman
- Department of Mechanical Engineering and Material Science, Duke University, Durham, NC, USA
| | - Jinxin Zhang
- Department of Mechanical Engineering and Material Science, Duke University, Durham, NC, USA
| | - John Mai
- Alfred E. Mann Institute for Biomedical Engineering, University of Southern California, Los Angeles, CA, USA
| | - Joseph Rufo
- Department of Mechanical Engineering and Material Science, Duke University, Durham, NC, USA
| | - John F Rawls
- Department of Molecular Genetics and Microbiology, Duke University, Durham, NC, USA
| | - Erica E Davis
- Center for Human Disease Modeling, Duke University Medical Center, Durham, NC, USA
- Advanced Center for Translational and Genetic Medicine (ACT-GeM), Stanley Manne Children's Research Institute, Ann & Robert H. Lurie Children's Hospital of Chicago, Chicago, IL, USA
- Department of Pediatrics, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Nicholas Katsanis
- Center for Human Disease Modeling, Duke University Medical Center, Durham, NC, USA
- Advanced Center for Translational and Genetic Medicine (ACT-GeM), Stanley Manne Children's Research Institute, Ann & Robert H. Lurie Children's Hospital of Chicago, Chicago, IL, USA
- Department of Pediatrics, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Tony Jun Huang
- Department of Mechanical Engineering and Material Science, Duke University, Durham, NC, USA.
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49
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Coskun AF, Han G, Ganesh S, Chen SY, Clavé XR, Harmsen S, Jiang S, Schürch CM, Bai Y, Hitzman C, Nolan GP. Nanoscopic subcellular imaging enabled by ion beam tomography. Nat Commun 2021; 12:789. [PMID: 33542220 PMCID: PMC7862654 DOI: 10.1038/s41467-020-20753-5] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2020] [Accepted: 12/08/2020] [Indexed: 01/30/2023] Open
Abstract
Multiplexed ion beam imaging (MIBI) has been previously used to profile multiple parameters in two dimensions in single cells within tissue slices. Here, a mathematical and technical framework for three-dimensional (3D) subcellular MIBI is presented. Ion-beam tomography (IBT) compiles ion beam images that are acquired iteratively across successive, multiple scans, and later assembled into a 3D format without loss of depth resolution. Algorithmic deconvolution, tailored for ion beams, is then applied to the transformed ion image series, yielding 4-fold enhanced ion beam data cubes. To further generate 3D sub-ion-beam-width precision visuals, isolated ion molecules are localized in the raw ion beam images, creating an approach coined as SILM, secondary ion beam localization microscopy, providing sub-25 nm accuracy in original ion images. Using deep learning, a parameter-free reconstruction method for ion beam tomograms with high accuracy is developed for low-density targets. In cultured cancer cells and tissues, IBT enables accessible visualization of 3D volumetric distributions of genomic regions, RNA transcripts, and protein factors with 5 nm axial resolution using isotope-enrichments and label-free elemental analyses. Multiparameter imaging of subcellular features at near macromolecular resolution is implemented by the IBT tools as a general biocomputation pipeline for imaging mass spectrometry.
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Affiliation(s)
- Ahmet F. Coskun
- grid.168010.e0000000419368956Baxter Laboratory, Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA USA ,grid.168010.e0000000419368956Department of Radiology, Molecular Imaging Program at Stanford, Stanford University School of Medicine, Stanford, CA USA ,grid.213917.f0000 0001 2097 4943Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, GA USA
| | - Guojun Han
- grid.168010.e0000000419368956Baxter Laboratory, Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA USA
| | - Shambavi Ganesh
- grid.213917.f0000 0001 2097 4943Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, GA USA ,grid.213917.f0000 0001 2097 4943School of Electrical and Computer Engineering, Georgia Institute of Technology, Atlanta, GA USA
| | - Shih-Yu Chen
- grid.168010.e0000000419368956Baxter Laboratory, Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA USA
| | - Xavier Rovira Clavé
- grid.168010.e0000000419368956Baxter Laboratory, Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA USA
| | - Stefan Harmsen
- grid.168010.e0000000419368956Department of Radiology, Molecular Imaging Program at Stanford, Stanford University School of Medicine, Stanford, CA USA ,grid.25879.310000 0004 1936 8972Present Address: Department of Radiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA USA
| | - Sizun Jiang
- grid.168010.e0000000419368956Baxter Laboratory, Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA USA
| | - Christian M. Schürch
- grid.168010.e0000000419368956Baxter Laboratory, Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA USA ,grid.411544.10000 0001 0196 8249Present Address: Department of Pathology and Neuropathology, University Hospital and Comprehensive Cancer Center Tübingen, Tübingen, Germany
| | - Yunhao Bai
- grid.168010.e0000000419368956Department of Chemistry, Stanford University, Stanford, CA USA
| | - Chuck Hitzman
- grid.168010.e0000000419368956Department of Materials Science and Engineering, Stanford University, Stanford, CA USA
| | - Garry P. Nolan
- grid.168010.e0000000419368956Baxter Laboratory, Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA USA
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50
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Mulligan JA, Ling L, Leartprapun N, Fischbach C, Adie SG. Computational 4D-OCM for label-free imaging of collective cell invasion and force-mediated deformations in collagen. Sci Rep 2021; 11:2814. [PMID: 33531512 PMCID: PMC7854660 DOI: 10.1038/s41598-021-81470-7] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2020] [Accepted: 12/29/2020] [Indexed: 02/06/2023] Open
Abstract
Traction force microscopy (TFM) is an important family of techniques used to measure and study the role of cellular traction forces (CTFs) associated with many biological processes. However, current standard TFM methods rely on imaging techniques that do not provide the experimental capabilities necessary to study CTFs within 3D collective and dynamic systems embedded within optically scattering media. Traction force optical coherence microscopy (TF-OCM) was developed to address these needs, but has only been demonstrated for the study of isolated cells embedded within optically clear media. Here, we present computational 4D-OCM methods that enable the study of dynamic invasion behavior of large tumor spheroids embedded in collagen. Our multi-day, time-lapse imaging data provided detailed visualizations of evolving spheroid morphology, collagen degradation, and collagen deformation, all using label-free scattering contrast. These capabilities, which provided insights into how stromal cells affect cancer progression, significantly expand access to critical data about biophysical interactions of cells with their environment, and lay the foundation for future efforts toward volumetric, time-lapse reconstructions of collective CTFs with TF-OCM.
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Affiliation(s)
- Jeffrey A. Mulligan
- School of Electrical and Computer Engineering, Cornell University, Ithaca, NY 14853 USA
- Nancy E. and Peter C. Meinig School of Biomedical Engineering, Cornell University, Ithaca, NY 14853 USA
| | - Lu Ling
- Nancy E. and Peter C. Meinig School of Biomedical Engineering, Cornell University, Ithaca, NY 14853 USA
| | - Nichaluk Leartprapun
- Nancy E. and Peter C. Meinig School of Biomedical Engineering, Cornell University, Ithaca, NY 14853 USA
| | - Claudia Fischbach
- Nancy E. and Peter C. Meinig School of Biomedical Engineering, Cornell University, Ithaca, NY 14853 USA
- Kavli Institute at Cornell for Nanoscale Science, Cornell University, Ithaca, NY 14853 USA
| | - Steven G. Adie
- Nancy E. and Peter C. Meinig School of Biomedical Engineering, Cornell University, Ithaca, NY 14853 USA
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