1
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Blackie L, Gaspar P, Mosleh S, Lushchak O, Kong L, Jin Y, Zielinska AP, Cao B, Mineo A, Silva B, Ameku T, Lim SE, Mao Y, Prieto-Godino L, Schoborg T, Varela M, Mahadevan L, Miguel-Aliaga I. The sex of organ geometry. Nature 2024; 630:392-400. [PMID: 38811741 PMCID: PMC11168936 DOI: 10.1038/s41586-024-07463-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2023] [Accepted: 04/24/2024] [Indexed: 05/31/2024]
Abstract
Organs have a distinctive yet often overlooked spatial arrangement in the body1-5. We propose that there is a logic to the shape of an organ and its proximity to its neighbours. Here, by using volumetric scans of many Drosophila melanogaster flies, we develop methods to quantify three-dimensional features of organ shape, position and interindividual variability. We find that both the shapes of organs and their relative arrangement are consistent yet differ between the sexes, and identify unexpected interorgan adjacencies and left-right organ asymmetries. Focusing on the intestine, which traverses the entire body, we investigate how sex differences in three-dimensional organ geometry arise. The configuration of the adult intestine is only partially determined by physical constraints imposed by adjacent organs; its sex-specific shape is actively maintained by mechanochemical crosstalk between gut muscles and vascular-like trachea. Indeed, sex-biased expression of a muscle-derived fibroblast growth factor-like ligand renders trachea sexually dimorphic. In turn, tracheal branches hold gut loops together into a male or female shape, with physiological consequences. Interorgan geometry represents a previously unrecognized level of biological complexity which might enable or confine communication across organs and could help explain sex or species differences in organ function.
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Affiliation(s)
- Laura Blackie
- MRC Laboratory of Medical Sciences, London, UK
- Institute of Clinical Sciences, Faculty of Medicine, Imperial College London, London, UK
- The Francis Crick Institute, London, UK
| | - Pedro Gaspar
- MRC Laboratory of Medical Sciences, London, UK
- Institute of Clinical Sciences, Faculty of Medicine, Imperial College London, London, UK
- The Francis Crick Institute, London, UK
| | - Salem Mosleh
- School of Engineering and Applied Sciences, Harvard University, Cambridge, MA, USA
- Department of Natural Sciences, University of Maryland Eastern Shore, Princess Anne, MD, USA
| | | | - Lingjin Kong
- MRC Laboratory of Medical Sciences, London, UK
- Institute of Clinical Sciences, Faculty of Medicine, Imperial College London, London, UK
| | - Yuhong Jin
- MRC Laboratory of Medical Sciences, London, UK
- Institute of Clinical Sciences, Faculty of Medicine, Imperial College London, London, UK
| | - Agata P Zielinska
- MRC Laboratory of Medical Sciences, London, UK
- Institute of Clinical Sciences, Faculty of Medicine, Imperial College London, London, UK
| | - Boxuan Cao
- MRC Laboratory of Medical Sciences, London, UK
- Institute of Clinical Sciences, Faculty of Medicine, Imperial College London, London, UK
| | - Alessandro Mineo
- MRC Laboratory of Medical Sciences, London, UK
- Institute of Clinical Sciences, Faculty of Medicine, Imperial College London, London, UK
- The Francis Crick Institute, London, UK
| | - Bryon Silva
- MRC Laboratory of Medical Sciences, London, UK
- Institute of Clinical Sciences, Faculty of Medicine, Imperial College London, London, UK
- The Francis Crick Institute, London, UK
| | - Tomotsune Ameku
- MRC Laboratory of Medical Sciences, London, UK
- Institute of Clinical Sciences, Faculty of Medicine, Imperial College London, London, UK
- The Francis Crick Institute, London, UK
| | - Shu En Lim
- MRC Laboratory for Molecular Cell Biology, University College London, London, UK
- Institute for the Physics of Living Systems, University College London, London, UK
| | - Yanlan Mao
- MRC Laboratory for Molecular Cell Biology, University College London, London, UK
- Institute for the Physics of Living Systems, University College London, London, UK
| | | | - Todd Schoborg
- Department of Molecular Biology, University of Wyoming, Laramie, WY, USA
| | - Marta Varela
- Faculty of Medicine, National Heart & Lung Institute, Imperial College London, London, UK
| | - L Mahadevan
- School of Engineering and Applied Sciences, Harvard University, Cambridge, MA, USA
- Departments of Physics and Organismic and Evolutionary Biology, Harvard University, Cambridge, MA, USA
| | - Irene Miguel-Aliaga
- MRC Laboratory of Medical Sciences, London, UK.
- Institute of Clinical Sciences, Faculty of Medicine, Imperial College London, London, UK.
- The Francis Crick Institute, London, UK.
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2
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Winkel EAB, Kristiansen R, Møller PR, Lauridsen H. Interactive three-dimensional atlas of the mineralized skeleton of the sand tiger shark Carcharias taurus. ROYAL SOCIETY OPEN SCIENCE 2024; 11:240287. [PMID: 38725522 PMCID: PMC11081003 DOI: 10.1098/rsos.240287] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/03/2023] [Accepted: 03/09/2024] [Indexed: 05/12/2024]
Abstract
Non-invasive computed tomography (CT) of an adult sand tiger shark Carcharias taurus Rafinesque, 1810 is used to provide an interactive three-dimensional 'general' shark (Selachimorpha) anatomy atlas. Given its post-cranial body morphology, the sand tiger shark appeared to be a well-chosen candidate and through comparison of the sand tiger shark with several other representatives of all eight established orders of sharks, we confirm that the relatively large degree of mineralization of the endoskeleton, along with the overall size, makes the sand tiger shark an ideal candidate for skeletal segmentation and construction of a skeletal atlas using conventional CT. This atlas both increases accessibility to the internal morphological features of the sand tiger shark and provides a more generalized overview of the skeletal anatomy of sharks and can aid as a supplement to destructive fresh dissection of specimens in the future and the construction of future skeletal atlases of other less mineralized sharks.
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Affiliation(s)
- Emil Alexander Byriel Winkel
- Department of Clinical Medicine, Aarhus University, Aarhus N8200, Denmark
- Department of Forensic Medicine, Aarhus University, Aarhus N8200, Denmark
| | | | - Peter Rask Møller
- Natural History Museum of Denmark, University of Copenhagen, København Ø, Denmark
| | - Henrik Lauridsen
- Department of Clinical Medicine, Aarhus University, Aarhus N8200, Denmark
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Parobková V, Kompaníková P, Lázňovský J, Kavková M, Hampl M, Buchtová M, Zikmund T, Kaiser J, Bryja V. Ch OP-CT: quantitative morphometrical analysis of the Hindbrain Choroid Plexus by X-ray micro-computed tomography. Fluids Barriers CNS 2024; 21:9. [PMID: 38268040 DOI: 10.1186/s12987-023-00502-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2023] [Accepted: 12/11/2023] [Indexed: 01/26/2024] Open
Abstract
The Hindbrain Choroid Plexus is a complex, cerebrospinal fluid-secreting tissue that projects into the 4th vertebrate brain ventricle. Despite its irreplaceability in the development and homeostasis of the entire central nervous system, the research of Hindbrain Choroid Plexus and other Choroid Plexuses has been neglected by neuroscientists for decades. One of the obstacles is the lack of tools that describe the complex shape of the Hindbrain Choroid Plexus in the context of brain ventricles. Here we introduce an effective tool, termed ChOP-CT, for the noninvasive, X-ray micro-computed tomography-based, three-dimensional visualization and subsequent quantitative spatial morphological analysis of developing mouse Hindbrain Choroid Plexus. ChOP-CT can reliably quantify Hindbrain Choroid Plexus volume, surface area, length, outgrowth angle, the proportion of the ventricular space occupied, asymmetries and general shape alterations in mouse embryos from embryonic day 13.5 onwards. We provide evidence that ChOP-CT is suitable for the unbiased evaluation and detection of the Hindbrain Choroid Plexus alterations within various mutant embryos. We believe, that thanks to its versatility, quantitative nature and the possibility of automation, ChOP-CT will facilitate the analysis of the Hindbrain Choroid Plexus in the mouse models. This will ultimately accelerate the screening of the candidate genes and mechanisms involved in the onset of various Hindbrain Choroid Plexus-related diseases.
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Affiliation(s)
- Viktória Parobková
- Central European Institute of Technology, Brno University of Technology, Brno, Czech Republic
| | - Petra Kompaníková
- Department of Experimental Biology, Faculty of Science, Masaryk University, 625 00, Brno, Czech Republic
| | - Jakub Lázňovský
- Central European Institute of Technology, Brno University of Technology, Brno, Czech Republic
| | - Michaela Kavková
- Central European Institute of Technology, Brno University of Technology, Brno, Czech Republic
| | - Marek Hampl
- Department of Experimental Biology, Faculty of Science, Masaryk University, 625 00, Brno, Czech Republic
- Laboratory of Molecular Morphogenesis, Institute of Animal Physiology and Genetics, Czech Academy of Sciences, 602 00, Brno, Czech Republic
| | - Marcela Buchtová
- Department of Experimental Biology, Faculty of Science, Masaryk University, 625 00, Brno, Czech Republic
- Laboratory of Molecular Morphogenesis, Institute of Animal Physiology and Genetics, Czech Academy of Sciences, 602 00, Brno, Czech Republic
| | - Tomáš Zikmund
- Central European Institute of Technology, Brno University of Technology, Brno, Czech Republic.
| | - Jozef Kaiser
- Central European Institute of Technology, Brno University of Technology, Brno, Czech Republic
| | - Vítězslav Bryja
- Department of Experimental Biology, Faculty of Science, Masaryk University, 625 00, Brno, Czech Republic.
- Department of Cytokinetics, Institute of Biophysics, Academy of Sciences of the Czech Republic, Brno, Czech Republic.
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4
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Lamouroux A, Cardoso M, Bottero C, Gallo M, Duraes M, Salerno J, Bertrand M, Rigau V, Fuchs F, Mousty E, Genevieve D, Subsol G, Goze-Bac C, Captier G. Micro-CT and high-field MRI for studying very early post-mortem human fetal anatomy at 8 weeks of gestation. Prenat Diagn 2024; 44:3-14. [PMID: 38161284 DOI: 10.1002/pd.6489] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2023] [Revised: 10/19/2023] [Accepted: 12/02/2023] [Indexed: 01/03/2024]
Abstract
OBJECTIVE This study involved very early post-mortem (PM) examination of human fetal anatomy at 8 weeks of gestation (WG) using whole-body multimodal micro-imaging: micro-CT and high-field MRI (HF-MRI). We discuss the potential place of this imaging in early first-trimester virtual autopsy. METHODS We performed micro-CT after different contrast-bath protocols including diffusible iodine-based contrast-enhanced (dice) and HF-MRI with a 9.4 T machine with qualitative and quantitative evaluation and obtained histological sections. RESULTS Nine fetuses were included: the crown-rump length was 10-24 mm and corresponded to 7 and 9 WG according to the Robinson formula. The Carnegie stages were 17-21. Dice micro-CT and HF-MRI presented high signal to noise ratio, >5, according to the Rose criterion, and for allowed anatomical phenotyping in these specimens. Imaging did not alter the histology, allowing immunostaining and pathological examination. CONCLUSION PM non-destructive whole-body multimodal micro-imaging: dice micro-CT and HF-MRI allows for PM human fetal anatomy study as early as 8 WG. It paves the way to virtual autopsy in the very early first trimester. Obtaining a precision phenotype, even regarding miscarriage products, allows a reverse phenotyping to select variants of interest in genome-wide analysis, offering potential genetic counseling for bereaved parents.
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Affiliation(s)
- Audrey Lamouroux
- Clinical Genetics Department, Montpellier University Hospital, University of Montpellier, Montpellier, France
- Obstetrical Gynaecology Department, Nîmes University Hospital, University of Montpellier, Nîmes, France
- Charles Coulomb Laboratory, UMR 5221 CNRS-UM, BNIF User Facility Imaging, University of Montpellier, CNRS, Montpellier, France
- ICAR Research Team, LIRMM, University of Montpellier, CNRS, Montpellier, France
- Univ. Montpellier, Montpellier, France
| | - Maïda Cardoso
- Charles Coulomb Laboratory, UMR 5221 CNRS-UM, BNIF User Facility Imaging, University of Montpellier, CNRS, Montpellier, France
- Univ. Montpellier, Montpellier, France
| | - Célia Bottero
- Obstetrical Gynaecology Department, Nîmes University Hospital, University of Montpellier, Nîmes, France
- Univ. Montpellier, Montpellier, France
| | - Mathieu Gallo
- Univ. Montpellier, Montpellier, France
- Pathology Department, Montpellier University Hospital, University of Montpellier, Montpellier, France
| | - Martha Duraes
- ICAR Research Team, LIRMM, University of Montpellier, CNRS, Montpellier, France
- Univ. Montpellier, Montpellier, France
- Anatomy Laboratory, Faculty of Medicine Montpellier-Nimes, University of Montpellier, Montpellier, France
- Obstetrical Gynaecology Department, Montpellier University Hospital, University of Montpellier, Montpellier, France
| | - Jennifer Salerno
- Obstetrical Gynaecology Department, Nîmes University Hospital, University of Montpellier, Nîmes, France
- Univ. Montpellier, Montpellier, France
- Gynaecology and Gynaecology Surgery Department, Clinique Beau Soleil, Montpellier, France
| | - Martin Bertrand
- Univ. Montpellier, Montpellier, France
- Experimental Anatomy Department, Faculty of Medicine Montpellier-Nimes, University Montpellier, Nîmes, France
- Digestive Surgery Department, Nimes University Hospital, Nîmes, France
| | - Valérie Rigau
- Univ. Montpellier, Montpellier, France
- Pathology Department, Montpellier University Hospital, University of Montpellier, Montpellier, France
| | - Florent Fuchs
- Univ. Montpellier, Montpellier, France
- Obstetrical Gynaecology Department, Montpellier University Hospital, University of Montpellier, Montpellier, France
- Inserm, CESP Center for Research in Epidemiology and Population Health, U1018, Reproduction and Child Development, Villejuif, France
- Desbrest Institute of Epidemiology and Public Health (IDESP), University of Montpellier, INSERM, Montpellier, France
| | - Eve Mousty
- Obstetrical Gynaecology Department, Nîmes University Hospital, University of Montpellier, Nîmes, France
- Univ. Montpellier, Montpellier, France
| | - David Genevieve
- Clinical Genetics Department, Montpellier University Hospital, University of Montpellier, Montpellier, France
- Univ. Montpellier, Montpellier, France
- Center for Rare Disease Development Anomaly and Malformative Syndromes, Montpellier University Hospital, Montpellier, France
| | - Gérard Subsol
- ICAR Research Team, LIRMM, University of Montpellier, CNRS, Montpellier, France
- Univ. Montpellier, Montpellier, France
| | - Christophe Goze-Bac
- Charles Coulomb Laboratory, UMR 5221 CNRS-UM, BNIF User Facility Imaging, University of Montpellier, CNRS, Montpellier, France
- Univ. Montpellier, Montpellier, France
| | - Guillaume Captier
- ICAR Research Team, LIRMM, University of Montpellier, CNRS, Montpellier, France
- Univ. Montpellier, Montpellier, France
- Anatomy Laboratory, Faculty of Medicine Montpellier-Nimes, University of Montpellier, Montpellier, France
- Paediatric Surgery Department, Montpellier University Hospital, University of Montpellier, Montpellier, France
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5
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Ishii R, Yoshida M, Suzuki N, Ogino H, Suzuki M. X-ray micro-computed tomography of Xenopus tadpole reveals changes in brain ventricular morphology during telencephalon regeneration. Dev Growth Differ 2023; 65:300-310. [PMID: 37477433 DOI: 10.1111/dgd.12881] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2023] [Revised: 06/26/2023] [Accepted: 06/30/2023] [Indexed: 07/22/2023]
Abstract
Xenopus tadpoles serve as an exceptional model organism for studying post-embryonic development in vertebrates. During post-embryonic development, large-scale changes in tissue morphology, including organ regeneration and metamorphosis, occur at the organ level. However, understanding these processes in a three-dimensional manner remains challenging. In this study, the use of X-ray micro-computed tomography (microCT) for the three-dimensional observation of the soft tissues of Xenopus tadpoles was explored. The findings revealed that major organs, such as the brain, heart, and kidneys, could be visualized with high contrast by phosphotungstic acid staining following fixation with Bouin's solution. Then, the changes in brain shape during telencephalon regeneration were analyzed as the first example of utilizing microCT to study organ regeneration in Xenopus tadpoles, and it was found that the size of the amputated telencephalon recovered to >80% of its original length within approximately 1 week. It was also observed that the ventricles tended to shrink after amputation and maintained this state for at least 3 days. This shrinkage was transient, as the ventricles expanded to exceed their original size within the following week. Temporary shrinkage and expansion of the ventricles, which were also observed in transgenic or fluorescent dye-injected tadpoles with telencephalon amputation, may be significant in tissue homeostasis in response to massive brain injury and subsequent repair and regeneration. This established method will improve experimental analyses in developmental biology and medical science using Xenopus tadpoles.
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Affiliation(s)
- Riona Ishii
- Amphibian Research Center, Graduate School of Integrated Sciences for Life, Hiroshima University, Hiroshima, Japan
| | - Mana Yoshida
- Amphibian Research Center, Graduate School of Integrated Sciences for Life, Hiroshima University, Hiroshima, Japan
| | - Nanoka Suzuki
- Amphibian Research Center, Graduate School of Integrated Sciences for Life, Hiroshima University, Hiroshima, Japan
| | - Hajime Ogino
- Amphibian Research Center, Graduate School of Integrated Sciences for Life, Hiroshima University, Hiroshima, Japan
| | - Makoto Suzuki
- Amphibian Research Center, Graduate School of Integrated Sciences for Life, Hiroshima University, Hiroshima, Japan
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6
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Li-Villarreal N, Rasmussen TL, Christiansen AE, Dickinson ME, Hsu CW. Three-dimensional microCT imaging of mouse heart development from early post-implantation to late fetal stages. Mamm Genome 2023; 34:156-165. [PMID: 36595063 PMCID: PMC10290591 DOI: 10.1007/s00335-022-09976-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2022] [Accepted: 12/15/2022] [Indexed: 01/04/2023]
Abstract
Comprehensive detailed characterization of new mouse models can be challenging due to the individual focus involved in developing these models. Often models are engineered to test a specific hypothesis in a limited number of tissues, stages, and/or other contexts. Whether or not the model produces the desired phenotypes, phenotyping beyond the desired context can be extremely work intensive and these studies are often not undertaken. However, the general information resulting from broader phenotyping can be invaluable to the wider scientific community. The International Mouse Phenotyping Consortium (IMPC) and its subsidiaries, like the Knockout Mouse Project (KOMP), has made great strides in streamlining this process. In particular, the use of microCT has been an invaluable resource in examining internal organ systems throughout fetal/developmental stages. Here, we provide several novel vignettes demonstrating the utility of microCT in uncovering cardiac phenotypes both based on human disease correlations and those that are unpredicted.
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Affiliation(s)
- Nanbing Li-Villarreal
- Department of Integrative Physiology, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA
| | - Tara L Rasmussen
- Department of Integrative Physiology, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA
- Cardiovascular Research Institute, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA
| | - Audrey E Christiansen
- Department of Integrative Physiology, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA
| | - Mary E Dickinson
- Department of Integrative Physiology, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA
- Cardiovascular Research Institute, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA
| | - Chih-Wei Hsu
- Department of Integrative Physiology, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA.
- Cardiovascular Research Institute, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA.
- Department of Education, Innovation and Technology, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA.
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7
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Muratore IB, Garnier S. Ontogeny of collective behaviour. Philos Trans R Soc Lond B Biol Sci 2023; 378:20220065. [PMID: 36802780 PMCID: PMC9939274 DOI: 10.1098/rstb.2022.0065] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2022] [Accepted: 10/21/2022] [Indexed: 02/21/2023] Open
Abstract
During their lifetime, superorganisms, like unitary organisms, undergo transformations that change the machinery of their collective behaviour. Here, we suggest that these transformations are largely understudied and propose that more systematic research into the ontogeny of collective behaviours is needed if we hope to better understand the link between proximate behavioural mechanisms and the development of collective adaptive functions. In particular, certain social insects engage in self-assemblage, forming dynamic and physically connected architectures with striking similarities to developing multicellular organisms, making them good model systems for ontogenetic studies of collective behaviour. However, exhaustive time series and three-dimensional data are required to thoroughly characterize the different life stages of the collective structures and the transitions between these stages. The well-established fields of embryology and developmental biology offer practical tools and theoretical frameworks that could speed up the acquisition of new knowledge about the formation, development, maturity and dissolution of social insect self-assemblages and, by extension, other superorganismal behaviours. We hope that this review will encourage an expansion of the ontogenetic perspective in the field of collective behaviour and, in particular, in self-assemblage research, which has far-reaching applications in robotics, computer science and regenerative medicine. This article is part of a discussion meeting issue 'Collective behaviour through time'.
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Affiliation(s)
| | - Simon Garnier
- Department of Biological Sciences, New Jersey Institute of Technology, Newark, NJ 07102, USA
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8
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Rolfe SM, Whikehart SM, Maga AM. Deep learning enabled multi-organ segmentation of mouse embryos. Biol Open 2023; 12:bio059698. [PMID: 36802342 PMCID: PMC9990908 DOI: 10.1242/bio.059698] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2023] [Accepted: 01/13/2023] [Indexed: 02/23/2023] Open
Abstract
The International Mouse Phenotyping Consortium (IMPC) has generated a large repository of three-dimensional (3D) imaging data from mouse embryos, providing a rich resource for investigating phenotype/genotype interactions. While the data is freely available, the computing resources and human effort required to segment these images for analysis of individual structures can create a significant hurdle for research. In this paper, we present an open source, deep learning-enabled tool, Mouse Embryo Multi-Organ Segmentation (MEMOS), that estimates a segmentation of 50 anatomical structures with a support for manually reviewing, editing, and analyzing the estimated segmentation in a single application. MEMOS is implemented as an extension on the 3D Slicer platform and is designed to be accessible to researchers without coding experience. We validate the performance of MEMOS-generated segmentations through comparison to state-of-the-art atlas-based segmentation and quantification of previously reported anatomical abnormalities in a Cbx4 knockout strain. This article has an associated First Person interview with the first author of the paper.
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Affiliation(s)
- S. M. Rolfe
- Center for Developmental Biology and Regenerative Medicine, Seattle Children's Research Institute, Seattle, WA 98101, USA
| | - S. M. Whikehart
- Center for Developmental Biology and Regenerative Medicine, Seattle Children's Research Institute, Seattle, WA 98101, USA
| | - A. M. Maga
- Center for Developmental Biology and Regenerative Medicine, Seattle Children's Research Institute, Seattle, WA 98101, USA
- Department of Pediatrics, University of Washington, Seattle, WA 98105, USA
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9
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Sutrisno AA, Katano W, Kawamura H, Tajika Y, Koshiba-Takeuchi K. Combined method of whole mount and block-face imaging: Acquisition of 3D data of gene expression pattern from conventional in situ hybridization. Dev Growth Differ 2023; 65:56-64. [PMID: 36450660 DOI: 10.1111/dgd.12827] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2022] [Revised: 10/29/2022] [Accepted: 11/20/2022] [Indexed: 12/02/2022]
Abstract
Visualization of spatiotemporal expression of a gene of interest is a fundamental technique for analyzing the involvements of genes in organ development. In situ hybridization (ISH) is one of the most popular methods for visualizing gene expression. When conventional ISH is performed on sections or whole-mount specimens, the gene expression pattern is represented in 2-dimensional (2D) microscopic images or in the surface view of the specimen. To obtain 3-dimensional (3D) data of gene expression from conventional ISH, the "serial section method" has traditionally been employed. However, this method requires an extensive amount of time and labor because it requires researchers to collect a tremendous number of sections, label all sections by ISH, and image them before 3D reconstruction. Here, we proposed a rapid and low-cost 3D imaging method that can create 3D gene expression patterns from conventional ISH-labeled specimens. Our method consists of a combination of whole-mount ISH and Correlative Microscopy and Blockface imaging (CoMBI). The whole-mount ISH-labeled specimens were sliced using a microtome or cryostat, and all block-faces were imaged and used to reconstruct 3D images by CoMBI. The 3D data acquired using our method showed sufficient quality to analyze the morphology and gene expression patterns in the developing mouse heart. In addition, 2D microscopic images of the sections can be obtained when needed. Correlating 2D microscopic images and 3D data can help annotate gene expression patterns and understand the anatomy of developing organs. These results indicated that our method can be useful in the field of developmental biology.
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Affiliation(s)
| | - Wataru Katano
- Graduate School of Life Sciences, Toyo University, Gunma, Japan
| | - Hayata Kawamura
- Graduate School of Life Sciences, Toyo University, Gunma, Japan
| | - Yuki Tajika
- Graduate School of Medicine, Gunma University, Maebashi, Gunma, Japan
| | - Kazuko Koshiba-Takeuchi
- Faculty of Life Sciences, Department of Applied Biosciences, Toyo University, Gunma, Japan.,Graduate School of Life Sciences, Toyo University, Gunma, Japan
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10
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Aristizábal O, Qiu Z, Gallego E, Aristizábal M, Mamou J, Wang Y, Ketterling JA, Turnbull DH. Longitudinal in Utero Analysis of Engrailed-1 Knockout Mouse Embryonic Phenotypes Using High-Frequency Ultrasound. ULTRASOUND IN MEDICINE & BIOLOGY 2023; 49:356-367. [PMID: 36283941 PMCID: PMC9712241 DOI: 10.1016/j.ultrasmedbio.2022.09.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/28/2022] [Revised: 09/08/2022] [Accepted: 09/11/2022] [Indexed: 06/16/2023]
Abstract
Large-scale international efforts to generate and analyze loss-of-function mutations in each of the approximately 20,000 protein-encoding gene mutations are ongoing using the "knockout" mouse as a model organism. Because one-third of gene knockouts are expected to result in embryonic lethality, it is important to develop non-invasive in utero imaging methods to detect and monitor mutant phenotypes in mouse embryos. We describe the utility of 3-D high-frequency (40-MHz) ultrasound (HFU) for longitudinal in utero imaging of mouse embryos between embryonic days (E) 11.5 and E14.5, which represent critical stages of brain and organ development. Engrailed-1 knockout (En1-ko) mouse embryos and their normal control littermates were imaged with HFU in 3-D, enabling visualization of morphological phenotypes in the developing brains, limbs and heads of the En1-ko embryos. Recently developed deep learning approaches were used to automatically segment the embryonic brain ventricles and bodies from the 3-D HFU images, allowing quantitative volumetric analyses of the En1-ko brain phenotypes. Taken together, these results show great promise for the application of longitudinal 3-D HFU to analyze knockout mouse embryos in utero.
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Affiliation(s)
- Orlando Aristizábal
- Skirball Institute of Biomolecular Medicine and Department of Radiology, New York University Grossman School of Medicine, New York, New York, USA
| | - Ziming Qiu
- Department of Electrical and Computer Engineering, New York University Tandon School of Engineering, New York, New York, USA
| | - Estefania Gallego
- Skirball Institute of Biomolecular Medicine and Department of Radiology, New York University Grossman School of Medicine, New York, New York, USA
| | - Matias Aristizábal
- Skirball Institute of Biomolecular Medicine and Department of Radiology, New York University Grossman School of Medicine, New York, New York, USA
| | - Jonathan Mamou
- Department of Radiology, Weill Cornell Medicine, New York, New York, USA
| | - Yao Wang
- Department of Electrical and Computer Engineering, New York University Tandon School of Engineering, New York, New York, USA
| | | | - Daniel H Turnbull
- Skirball Institute of Biomolecular Medicine and Department of Radiology, New York University Grossman School of Medicine, New York, New York, USA.
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11
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Tsurugizawa T, Kumamoto T, Yoshioka Y. Utilization of potato starch suspension for MR-microimaging in ex vivo mouse embryos. iScience 2022; 25:105694. [PMID: 36567713 PMCID: PMC9768372 DOI: 10.1016/j.isci.2022.105694] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2022] [Revised: 07/31/2022] [Accepted: 11/24/2022] [Indexed: 12/05/2022] Open
Abstract
Magnetic resonance (MR) microimaging of the mouse embryo is a promising tool to noninvasively investigate the microstructure of the brain of a developing mouse. The proton-free fluid is used for the liquid surrounding the specimen in MR microimaging, but the potential issue of image quality remains due to the air bubbles on the specimen and the retained water proton in the curvature of the embryo. Furthermore, the specimen may move during the scanning, resulting in motion artifact. Here, we developed the new concept of the ex vivo microimaging protocol with the robust method using the potato starch-containing biological polymers. Potato starch suspension with PBS significantly reduced T1 and T2 signal intensity of the suspension and strongly suppressed the motion of the embryo. Furthermore, potato starch-PBS suspension is stable for long-time scanning at room temperature. These results indicate the utility of potato starch suspension for MR microimaging in mouse embryos.
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Affiliation(s)
- Tomokazu Tsurugizawa
- Human Informatics and Interaction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), 1-1-1 Higashi, Tsukuba 305-8568, Japan,Faculty of Engineering, Information and Systems, University of Tsukuba, Tsukuba 305-8573, Japan,Jikei University School of Medicine, 3-25-8 Nishishinbashi, Tokyo 105-8461, Japan,Graduate School of Frontier Biosciences, Osaka University, Suita 565-0871, Japan,Center for Information and Neural Networks (CiNet), Osaka University and National Institute of Information and Communications Technology (NICT), Suita 565-0871, Japan,Corresponding author
| | - Takuma Kumamoto
- Developmental Neuroscience Project, Department of Brain & Neurosciences, Tokyo Metropolitan Institute of Medical Science, Tokyo 156-8506, Japan
| | - Yoshichika Yoshioka
- Graduate School of Frontier Biosciences, Osaka University, Suita 565-0871, Japan,Center for Information and Neural Networks (CiNet), Osaka University and National Institute of Information and Communications Technology (NICT), Suita 565-0871, Japan,Corresponding author
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12
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Profiling development of abdominal organs in the pig. Sci Rep 2022; 12:16245. [PMID: 36171243 PMCID: PMC9519580 DOI: 10.1038/s41598-022-19960-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2022] [Accepted: 09/07/2022] [Indexed: 11/25/2022] Open
Abstract
The pig is an ideal model system for studying human development and disease due to its similarities to human anatomy, physiology, size, and genome. Further, advances in CRISPR gene editing have made genetically engineered pigs viable models for the study of human pathologies and congenital anomalies. However, a detailed atlas illustrating pig development is necessary for identifying and modeling developmental defects. Here we describe normal development of the pig abdominal system and show examples of congenital defects that can arise in CRISPR gene edited SAP130 mutant pigs. Normal pigs at different gestational ages from day 20 (D20) to term were examined and the configuration of the abdominal organs was studied using 3D histological reconstructions with episcopic confocal microscopy, magnetic resonance imaging (MRI) and necropsy. This revealed prominent mesonephros, a transient embryonic organ present only during embryogenesis, at D20, while the developing metanephros that will form the permanent kidney are noted at D26. By D64 the mesonephroi are absent and only the metanephroi remain. The formation of the liver and pancreas was observed by D20 and complete by D30 and D35 respectively. The spleen and adrenal glands are first identified at D26 and completed by D42. The developing bowel and the gonads are identified at D20. The bowel appears completely rotated by D42, and testes in the male were descended at D64. This atlas and the methods used are excellent tools for identifying developmental pathologies of the abdominal organs in the pig at different stages of development.
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13
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Handschuh S, Glösmann M. Mouse embryo phenotyping using X-ray microCT. Front Cell Dev Biol 2022; 10:949184. [PMID: 36187491 PMCID: PMC9523164 DOI: 10.3389/fcell.2022.949184] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2022] [Accepted: 08/22/2022] [Indexed: 11/30/2022] Open
Abstract
Microscopic X-ray computed tomography (microCT) is a structural ex vivo imaging technique providing genuine isotropic 3D images from biological samples at micron resolution. MicroCT imaging is non-destructive and combines well with other modalities such as light and electron microscopy in correlative imaging workflows. Protocols for staining embryos with X-ray dense contrast agents enable the acquisition of high-contrast and high-resolution datasets of whole embryos and specific organ systems. High sample throughput is achieved with dedicated setups. Consequently, microCT has gained enormous importance for both qualitative and quantitative phenotyping of mouse development. We here summarize state-of-the-art protocols of sample preparation and imaging procedures, showcase contemporary applications, and discuss possible pitfalls and sources for artefacts. In addition, we give an outlook on phenotyping workflows using microscopic dual energy CT (microDECT) and tissue-specific contrast agents.
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14
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Dalmasso G, Musy M, Niksic M, Robert-Moreno A, Badía-Careaga C, Sanz-Ezquerro JJ, Sharpe J. 4D reconstruction of murine developmental trajectories using spherical harmonics. Dev Cell 2022; 57:2140-2150.e5. [PMID: 36055247 PMCID: PMC9481268 DOI: 10.1016/j.devcel.2022.08.005] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2021] [Revised: 05/02/2022] [Accepted: 08/11/2022] [Indexed: 11/30/2022]
Abstract
Normal organogenesis cannot be recapitulated in vitro for mammalian organs, unlike in species including Drosophila and zebrafish. Available 3D data in the form of ex vivo images only provide discrete snapshots of the development of an organ morphology. Here, we propose a computer-based approach to recreate its continuous evolution in time and space from a set of 3D volumetric images. Our method is based on the remapping of shape data into the space of the coefficients of a spherical harmonics expansion where a smooth interpolation over time is simpler. We tested our approach on mouse limb buds and embryonic hearts. A key advantage of this method is that the resulting 4D trajectory can take advantage of all the available data while also being able to interpolate well through time intervals for which there are little or no data. This allows for a quantitative, data-driven 4D description of mouse limb morphogenesis. Computer-based method recreating a 3D plus time evolution of a set of volumetric images Technique based on the interpolation of the coefficients of spherical harmonics Data-driven quantitative 4D description of limb and heart morphogenesis Quantitatively reliable baseline description of organ development
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Affiliation(s)
- Giovanni Dalmasso
- European Molecular Biology Laboratory (EMBL-Barcelona), 08003 Barcelona, Spain.
| | - Marco Musy
- European Molecular Biology Laboratory (EMBL-Barcelona), 08003 Barcelona, Spain
| | - Martina Niksic
- Centre for Genomic Regulation (CRG), 08003 Barcelona, Spain
| | | | | | - Juan Jose Sanz-Ezquerro
- Centro Nacional de Investigaciones Cardiovasculares (CNIC), 28029 Madrid, Spain; Centro Nacional de Biotecnologia (CSIC Madrid), 28049 Madrid, Spain
| | - James Sharpe
- European Molecular Biology Laboratory (EMBL-Barcelona), 08003 Barcelona, Spain; Institució Catalana de Recerca i Estudis Avançats (ICREA), 08010 Barcelona, Spain.
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15
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MusMorph, a database of standardized mouse morphology data for morphometric meta-analyses. Sci Data 2022; 9:230. [PMID: 35614082 PMCID: PMC9133120 DOI: 10.1038/s41597-022-01338-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2021] [Accepted: 04/13/2022] [Indexed: 11/08/2022] Open
Abstract
Complex morphological traits are the product of many genes with transient or lasting developmental effects that interact in anatomical context. Mouse models are a key resource for disentangling such effects, because they offer myriad tools for manipulating the genome in a controlled environment. Unfortunately, phenotypic data are often obtained using laboratory-specific protocols, resulting in self-contained datasets that are difficult to relate to one another for larger scale analyses. To enable meta-analyses of morphological variation, particularly in the craniofacial complex and brain, we created MusMorph, a database of standardized mouse morphology data spanning numerous genotypes and developmental stages, including E10.5, E11.5, E14.5, E15.5, E18.5, and adulthood. To standardize data collection, we implemented an atlas-based phenotyping pipeline that combines techniques from image registration, deep learning, and morphometrics. Alongside stage-specific atlases, we provide aligned micro-computed tomography images, dense anatomical landmarks, and segmentations (if available) for each specimen (N = 10,056). Our workflow is open-source to encourage transparency and reproducible data collection. The MusMorph data and scripts are available on FaceBase ( www.facebase.org , https://doi.org/10.25550/3-HXMC ) and GitHub ( https://github.com/jaydevine/MusMorph ).
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16
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Yakovlev MA, Vanselow DJ, Ngu MS, Zaino CR, Katz SR, Ding Y, Parkinson D, Wang SY, Ang KC, La Riviere P, Cheng KC. A wide-field micro-computed tomography detector: micron resolution at half-centimetre scale. JOURNAL OF SYNCHROTRON RADIATION 2022; 29:505-514. [PMID: 35254315 PMCID: PMC8900834 DOI: 10.1107/s160057752101287x] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/20/2021] [Accepted: 12/03/2021] [Indexed: 06/14/2023]
Abstract
Ideal three-dimensional imaging of complex samples made up of micron-scale structures extending over mm to cm, such as biological tissues, requires both wide field of view and high resolution. For existing optics and detectors used for micro-CT (computed tomography) imaging, sub-micron pixel resolution can only be achieved for fields of view of <2 mm. This article presents a unique detector system with a 6 mm field-of-view image circle and 0.5 µm pixel size that can be used in micro-CT units utilizing both synchrotron and commercial X-ray sources. A resolution-test pattern with linear microstructures and whole adult Daphnia magna were imaged at beamline 8.3.2 of the Berkeley Advanced Light Source. Volumes of 10000 × 10000 × 7096 isotropic 0.5 µm voxels were reconstructed over a 5.0 mm × 3.5 mm field of view. Measurements in the projection domain confirmed a 0.90 µm measured spatial resolution that is largely Nyquist-limited. This unprecedented combination of field of view and resolution dramatically reduces the need for sectional scans and computational stitching for large samples, ultimately offering the means to elucidate changes in tissue and cellular morphology in the context of larger, whole, intact model organisms and specimens. This system is also anticipated to benefit micro-CT imaging in materials science, microelectronics, agricultural science and biomedical engineering.
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Affiliation(s)
- Maksim A. Yakovlev
- Department of Pathology, Penn State College of Medicine, Hershey, Pennsylvania, USA
- The Jake Gittlen Laboratories for Cancer Research, Penn State College of Medicine, Hershey, Pennsylvania, USA
- Biomedical Sciences PhD Program, Penn State College of Medicine, Hershey, Pennsylvania, USA
| | - Daniel J. Vanselow
- Department of Pathology, Penn State College of Medicine, Hershey, Pennsylvania, USA
- The Jake Gittlen Laboratories for Cancer Research, Penn State College of Medicine, Hershey, Pennsylvania, USA
| | - Mee Siing Ngu
- Department of Pathology, Penn State College of Medicine, Hershey, Pennsylvania, USA
- The Jake Gittlen Laboratories for Cancer Research, Penn State College of Medicine, Hershey, Pennsylvania, USA
| | - Carolyn R. Zaino
- Department of Pathology, Penn State College of Medicine, Hershey, Pennsylvania, USA
- The Jake Gittlen Laboratories for Cancer Research, Penn State College of Medicine, Hershey, Pennsylvania, USA
| | - Spencer R. Katz
- Department of Pathology, Penn State College of Medicine, Hershey, Pennsylvania, USA
- The Jake Gittlen Laboratories for Cancer Research, Penn State College of Medicine, Hershey, Pennsylvania, USA
- Medical Scientist Training Program, Penn State College of Medicine, Hershey, Pennsylvania, USA
| | - Yifu Ding
- Department of Pathology, Penn State College of Medicine, Hershey, Pennsylvania, USA
- The Jake Gittlen Laboratories for Cancer Research, Penn State College of Medicine, Hershey, Pennsylvania, USA
- Medical Scientist Training Program, Penn State College of Medicine, Hershey, Pennsylvania, USA
| | - Dula Parkinson
- Advanced Light Source, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | | | - Khai Chung Ang
- Department of Pathology, Penn State College of Medicine, Hershey, Pennsylvania, USA
- The Jake Gittlen Laboratories for Cancer Research, Penn State College of Medicine, Hershey, Pennsylvania, USA
- Penn State Zebrafish Functional Genomics Core, Penn State College of Medicine, Hershey, Pennsylvania, USA
| | | | - Keith C. Cheng
- Department of Pathology, Penn State College of Medicine, Hershey, Pennsylvania, USA
- The Jake Gittlen Laboratories for Cancer Research, Penn State College of Medicine, Hershey, Pennsylvania, USA
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17
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A diffusion MRI-based spatiotemporal continuum of the embryonic mouse brain for probing gene-neuroanatomy connections. Proc Natl Acad Sci U S A 2022; 119:2111869119. [PMID: 35165149 PMCID: PMC8851557 DOI: 10.1073/pnas.2111869119] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/07/2021] [Indexed: 11/18/2022] Open
Abstract
We established an ultra high-resolution diffusion MRI atlas of the embryonic mouse brains from E10.5 to E15.5, which characterizes the continuous changes of brain morphology and microstructures at mesoscopic scale. By integrating gene-expression data into the spatiotemporal continuum, we can navigate the evolving landscape of gene expression and neuroanatomy across both spatial and temporal dimensions to visualize their interactions in normal and abnormal embryonic brain development. We also identified regional clusters with distinct developmental trajectories and identified gene-expression profiles that matched to these regional domains. The diffusion MRI–based continuum of the embryonic brain and the computational techniques presented in this study offer a valuable tool for systematic study of the genetic control of brain development. The embryonic mouse brain undergoes drastic changes in establishing basic anatomical compartments and laying out major axonal connections of the developing brain. Correlating anatomical changes with gene-expression patterns is an essential step toward understanding the mechanisms regulating brain development. Traditionally, this is done in a cross-sectional manner, but the dynamic nature of development calls for probing gene–neuroanatomy interactions in a combined spatiotemporal domain. Here, we present a four-dimensional (4D) spatiotemporal continuum of the embryonic mouse brain from E10.5 to E15.5 reconstructed from diffusion magnetic resonance microscopy (dMRM) data. This study achieved unprecedented high-definition dMRM at 30- to 35-µm isotropic resolution, and together with computational neuroanatomy techniques, we revealed both morphological and microscopic changes in the developing brain. We transformed selected gene-expression data to this continuum and correlated them with the dMRM-based neuroanatomical changes in embryonic brains. Within the continuum, we identified distinct developmental modes comprising regional clusters that shared developmental trajectories and similar gene-expression profiles. Our results demonstrate how this 4D continuum can be used to examine spatiotemporal gene–neuroanatomical interactions by connecting upstream genetic events with anatomical changes that emerge later in development. This approach would be useful for large-scale analysis of the cooperative roles of key genes in shaping the developing brain.
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18
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Qiu Q, Huang Y, Zhang B, Huang D, Chen X, Fan Z, Lin J, Yang W, Wang K, Qu N, Li J, Li Z, Huang J, Li S, Zhang J, Liu G, Rui G, Chen X, Zhao Q. Noninvasive Dual-Modality Photoacoustic-Ultrasonic Imaging to Detect Mammalian Embryo Abnormalities after Prenatal Exposure to Methylmercury Chloride (MMC): A Mouse Study. ENVIRONMENTAL HEALTH PERSPECTIVES 2022; 130:27002. [PMID: 35108087 PMCID: PMC8809665 DOI: 10.1289/ehp8907] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/31/2020] [Revised: 01/05/2022] [Accepted: 01/05/2022] [Indexed: 06/14/2023]
Abstract
BACKGROUND Severe environmental pollution and contaminants left in the environment due to the abuse of chemicals, such as methylmercury, are associated with an increasing number of embryonic disorders. Ultrasound imaging has been widely used to investigate embryonic development malformation and dysorganoplasia in both research and clinics. However, this technique is limited by its low contrast and lacking functional parameters such as the ability to measure blood oxygen saturation (SaO 2 ) and hemoglobin content (HbT) in tissues, measures that could be early vital indicators for embryonic development abnormality. Herein, we proposed combining two highly complementary techniques into a photoacoustic-ultrasound (PA-US) dual-modality imaging approach to noninvasively detect early mouse embryo abnormalities caused by methylmercury chloride (MMC) in real time. OBJECTIVES This study aimed to assess the use of PA-US dual-modality imaging for noninvasive detection of embryonic toxicity at different stages of growth following prenatal MMC exposure. Additionally, we compared the PA-US imagining results to traditional histological methods to determine whether this noninvasive method could detect early developmental defects in utero. METHODS Different dosages of MMC were administrated to pregnant mice by gavage to establish models of different levels of embryonic malformation. Ultrasound, photoacoustic signal intensity (PSI), blood oxygen saturation (SaO 2 ), and hemoglobin content (HbT) were quantified in all experimental groups. Furthermore, the embryos were sectioned and examined for pathological changes. RESULTS Using PA-US imaging, we detected differences in PSI, SaO 2 , HbT, and heart volume at embryonic day (E)14.5 and E11.5 for low and high dosages of MMC, respectively. More important, our results showed that differences between control and treated embryos identified by in utero PA-US imaging were consistent with those identified in ex vivo embryos using histological methods. CONCLUSION Our results suggest that noninvasive dual-modality PA-US is a promising strategy for detecting developmental toxicology in the uterus. Overall, this study presents a new approach for detecting embryonic toxicities, which could be crucial in clinics when diagnosing aberrant embryonic development. https://doi.org/10.1289/EHP8907.
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Affiliation(s)
- Qi Qiu
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, Center for Molecular Imaging and Translational Medicine, Department of Laboratory Medicine, School of Public Health, Xiamen University, Xiamen, China
| | - Yali Huang
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, Center for Molecular Imaging and Translational Medicine, Department of Laboratory Medicine, School of Public Health, Xiamen University, Xiamen, China
| | - Bei Zhang
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, Center for Molecular Imaging and Translational Medicine, Department of Laboratory Medicine, School of Public Health, Xiamen University, Xiamen, China
| | - Doudou Huang
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, Center for Molecular Imaging and Translational Medicine, Department of Laboratory Medicine, School of Public Health, Xiamen University, Xiamen, China
| | - Xin Chen
- Department of Orthopedics, The First Affiliated Hospital of Xiamen University, Xiamen, China
| | - Zhongxiong Fan
- Department of Biomaterials, College of Materials, Research Center of Biomedical Engineering of Xiamen & Key Laboratory of Biomedical Engineering of Fujian Province & Fujian Provincial Key Laboratory for Soft Functional Materials Research, Xiamen University, Xiamen, China
| | - Jinpei Lin
- Department of Integrated TCM & Western Medicine Department, Fujian Cancer Hospital & Fujian Medical University Cancer Hospital, Fuzhou, China
| | - Wensheng Yang
- Department of Pathology Affiliated Chenggong Hospital, Xiamen University, Xiamen, China
| | - Kai Wang
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, Center for Molecular Imaging and Translational Medicine, Department of Laboratory Medicine, School of Public Health, Xiamen University, Xiamen, China
| | - Ning Qu
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, Center for Molecular Imaging and Translational Medicine, Department of Laboratory Medicine, School of Public Health, Xiamen University, Xiamen, China
| | - Juan Li
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, Center for Molecular Imaging and Translational Medicine, Department of Laboratory Medicine, School of Public Health, Xiamen University, Xiamen, China
| | - Zhihong Li
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, Center for Molecular Imaging and Translational Medicine, Department of Laboratory Medicine, School of Public Health, Xiamen University, Xiamen, China
| | - Jingyu Huang
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, Center for Molecular Imaging and Translational Medicine, Department of Laboratory Medicine, School of Public Health, Xiamen University, Xiamen, China
| | - Shenrui Li
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, Center for Molecular Imaging and Translational Medicine, Department of Laboratory Medicine, School of Public Health, Xiamen University, Xiamen, China
| | - Jiaxing Zhang
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, Center for Molecular Imaging and Translational Medicine, Department of Laboratory Medicine, School of Public Health, Xiamen University, Xiamen, China
| | - Gang Liu
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, Center for Molecular Imaging and Translational Medicine, Department of Laboratory Medicine, School of Public Health, Xiamen University, Xiamen, China
| | - Gang Rui
- Department of Orthopedics, The First Affiliated Hospital of Xiamen University, Xiamen, China
| | - Xiaoyuan Chen
- Yong Loo Lin School of Medicine and Faculty of Engineering, National University of Singapore, Singapore, Singapore
| | - Qingliang Zhao
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, Center for Molecular Imaging and Translational Medicine, Department of Laboratory Medicine, School of Public Health, Xiamen University, Xiamen, China
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19
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PEG-modified gadolinium nanoparticles as contrast agents for in vivo micro-CT. Sci Rep 2021; 11:16603. [PMID: 34400681 PMCID: PMC8367985 DOI: 10.1038/s41598-021-95716-x] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2021] [Accepted: 07/09/2021] [Indexed: 12/30/2022] Open
Abstract
Vascular research is largely performed in rodents with the goal of developing treatments for human disease. Micro-computed tomography (micro-CT) provides non-destructive three-dimensional imaging that can be used to study the vasculature of rodents. However, to distinguish vasculature from other soft tissues, long-circulating contrast agents are required. In this study, we demonstrated that poly(ethylene glycol) (PEG)-coated gadolinium nanoparticles can be used as a vascular contrast agent in micro-CT. The coated particles could be lyophilized and then redispersed in an aqueous solution to achieve 100 mg/mL of gadolinium. After an intravenous injection of the contrast agent into mice, micro-CT scans showed blood pool contrast enhancements of at least 200 HU for 30 min. Imaging and quantitative analysis of gadolinium in tissues showed the presence of contrast agent in clearance organs including the liver and spleen and very low amounts in other organs. In vitro cell culture experiments, subcutaneous injections, and analysis of mouse body weight suggested that the agents exhibited low toxicity. Histological analysis of tissues 5 days after injection of the contrast agent showed cytotoxicity in the spleen, but no abnormalities were observed in the liver, lungs, kidneys, and bladder.
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20
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Rolfe S, Pieper S, Porto A, Diamond K, Winchester J, Shan S, Kirveslahti H, Boyer D, Summers A, Maga AM. SlicerMorph: An open and extensible platform to retrieve, visualize and analyse 3D morphology. Methods Ecol Evol 2021. [DOI: 10.1111/2041-210x.13669] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Sara Rolfe
- Friday Harbor Marine LaboratoriesUniversity of Washington San Juan WA USA
- Seattle Children's Research Institute Center for Developmental Biology and Regenerative Medicine Seattle WA USA
| | | | - Arthur Porto
- Department of Biological Sciences Louisiana State University Baton Rouge LA USA
- Center for Computation and Technology Louisiana State University Baton Rouge LA USA
| | - Kelly Diamond
- Seattle Children's Research Institute Center for Developmental Biology and Regenerative Medicine Seattle WA USA
| | - Julie Winchester
- Department of Evolutionary Anthropology Duke University Durham NC USA
| | - Shan Shan
- Department of Mathematics Mount Holyoke College South Hadley MA USA
| | | | - Doug Boyer
- Department of Biological Sciences Louisiana State University Baton Rouge LA USA
| | - Adam Summers
- Friday Harbor Marine LaboratoriesUniversity of Washington San Juan WA USA
| | - A. Murat Maga
- Seattle Children's Research Institute Center for Developmental Biology and Regenerative Medicine Seattle WA USA
- Department of Pediatrics Division of Craniofacial Medicine University of Washington Seattle WA USA
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21
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Wendling O, Hentsch D, Jacobs H, Lemercier N, Taubert S, Pertuy F, Vonesch JL, Sorg T, Di Michele M, Le Cam L, Rosahl T, Carballo-Jane E, Liu M, Mu J, Mark M, Herault Y. High Resolution Episcopic Microscopy for Qualitative and Quantitative Data in Phenotyping Altered Embryos and Adult Mice Using the New "Histo3D" System. Biomedicines 2021; 9:767. [PMID: 34356832 PMCID: PMC8301480 DOI: 10.3390/biomedicines9070767] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2021] [Revised: 06/21/2021] [Accepted: 06/23/2021] [Indexed: 12/27/2022] Open
Abstract
3D imaging in animal models, during development or in adults, facilitates the identification of structural morphological changes that cannot be achieved with traditional 2D histological staining. Through the reconstruction of whole embryos or a region-of-interest, specific changes are better delimited and can be easily quantified. We focused here on high-resolution episcopic microscopy (HREM), and its potential for visualizing and quantifying the organ systems of normal and genetically altered embryos and adult organisms. Although the technique is based on episcopic images, these are of high resolution and are close to histological quality. The images reflect the tissue structure and densities revealed by histology, albeit in a grayscale color map. HREM technology permits researchers to take advantage of serial 2D aligned stacks of images to perform 3D reconstructions. Three-dimensional visualization allows for an appreciation of topology and morphology that is difficult to achieve with classical histological studies. The nature of the data lends itself to novel forms of computational analysis that permit the accurate quantitation and comparison of individual embryos in a manner that is impossible with histology. Here, we have developed a new HREM prototype consisting of the assembly of a Leica Biosystems Nanocut rotary microtome with optics and a camera. We describe some examples of applications in the prenatal and adult lifestage of the mouse to show the added value of HREM for phenotyping experimental cohorts to compare and quantify structure volumes. At prenatal stages, segmentations and 3D reconstructions allowed the quantification of neural tissue and ventricular system volumes of normal brains at E14.5 and E16.5 stages. 3D representations of normal cranial and peripheric nerves at E15.5 and of the normal urogenital system from stages E11.5 to E14.5 were also performed. We also present a methodology to quantify the volume of the atherosclerotic plaques of ApoEtm1Unc/tm1Unc mutant mice and illustrate a 3D reconstruction of knee ligaments in adult mice.
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Affiliation(s)
- Olivia Wendling
- CNRS, INSERM, CELPHEDIA, PHENOMIN-Institut Clinique de la Souris (ICS), Université de Strasbourg, 1 Rue Laurent Fries, 67404 Illkirch Graffenstaden, France; (O.W.); (H.J.); (F.P.); (T.S.); (M.M.)
- CNRS, INSERM, Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), Université de Strasbourg, 1 Rue Laurent Fries, 67404 Illkirch Graffenstaden, France; (D.H.); (S.T.); (J.-L.V.)
| | - Didier Hentsch
- CNRS, INSERM, Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), Université de Strasbourg, 1 Rue Laurent Fries, 67404 Illkirch Graffenstaden, France; (D.H.); (S.T.); (J.-L.V.)
| | - Hugues Jacobs
- CNRS, INSERM, CELPHEDIA, PHENOMIN-Institut Clinique de la Souris (ICS), Université de Strasbourg, 1 Rue Laurent Fries, 67404 Illkirch Graffenstaden, France; (O.W.); (H.J.); (F.P.); (T.S.); (M.M.)
| | | | - Serge Taubert
- CNRS, INSERM, Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), Université de Strasbourg, 1 Rue Laurent Fries, 67404 Illkirch Graffenstaden, France; (D.H.); (S.T.); (J.-L.V.)
| | - Fabien Pertuy
- CNRS, INSERM, CELPHEDIA, PHENOMIN-Institut Clinique de la Souris (ICS), Université de Strasbourg, 1 Rue Laurent Fries, 67404 Illkirch Graffenstaden, France; (O.W.); (H.J.); (F.P.); (T.S.); (M.M.)
| | - Jean-Luc Vonesch
- CNRS, INSERM, Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), Université de Strasbourg, 1 Rue Laurent Fries, 67404 Illkirch Graffenstaden, France; (D.H.); (S.T.); (J.-L.V.)
| | - Tania Sorg
- CNRS, INSERM, CELPHEDIA, PHENOMIN-Institut Clinique de la Souris (ICS), Université de Strasbourg, 1 Rue Laurent Fries, 67404 Illkirch Graffenstaden, France; (O.W.); (H.J.); (F.P.); (T.S.); (M.M.)
| | - Michela Di Michele
- Institut de Recherche en Cancérologie de Montpellier (IRCM), INSERM U1194, Université Montpellier, 34298 Montpellier, France; (M.D.M.); (L.L.C.)
- Institut Régional du Cancer de Montpellier (ICM), Université Montpellier, 34298 Montpellier, France
| | - Laurent Le Cam
- Institut de Recherche en Cancérologie de Montpellier (IRCM), INSERM U1194, Université Montpellier, 34298 Montpellier, France; (M.D.M.); (L.L.C.)
- Institut Régional du Cancer de Montpellier (ICM), Université Montpellier, 34298 Montpellier, France
| | - Thomas Rosahl
- Merck & Co. Inc., Kenilworth, NJ 07033, USA; (T.R.); (E.C.-J.); (M.L.); (J.M.)
| | - Ester Carballo-Jane
- Merck & Co. Inc., Kenilworth, NJ 07033, USA; (T.R.); (E.C.-J.); (M.L.); (J.M.)
| | - Mindy Liu
- Merck & Co. Inc., Kenilworth, NJ 07033, USA; (T.R.); (E.C.-J.); (M.L.); (J.M.)
| | - James Mu
- Merck & Co. Inc., Kenilworth, NJ 07033, USA; (T.R.); (E.C.-J.); (M.L.); (J.M.)
| | - Manuel Mark
- CNRS, INSERM, CELPHEDIA, PHENOMIN-Institut Clinique de la Souris (ICS), Université de Strasbourg, 1 Rue Laurent Fries, 67404 Illkirch Graffenstaden, France; (O.W.); (H.J.); (F.P.); (T.S.); (M.M.)
- CNRS, INSERM, Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), Université de Strasbourg, 1 Rue Laurent Fries, 67404 Illkirch Graffenstaden, France; (D.H.); (S.T.); (J.-L.V.)
- Service de Biologie de la Reproduction, Hôpitaux Universitaires de Strasbourg (HUS), CEDEX, 67091 Strasbourg, France
| | - Yann Herault
- CNRS, INSERM, CELPHEDIA, PHENOMIN-Institut Clinique de la Souris (ICS), Université de Strasbourg, 1 Rue Laurent Fries, 67404 Illkirch Graffenstaden, France; (O.W.); (H.J.); (F.P.); (T.S.); (M.M.)
- CNRS, INSERM, Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), Université de Strasbourg, 1 Rue Laurent Fries, 67404 Illkirch Graffenstaden, France; (D.H.); (S.T.); (J.-L.V.)
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22
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Mark M, Teletin M, Wendling O, Vonesch JL, Féret B, Hérault Y, Ghyselinck NB. Pathogenesis of Anorectal Malformations in Retinoic Acid Receptor Knockout Mice Studied by HREM. Biomedicines 2021; 9:742. [PMID: 34203310 PMCID: PMC8301324 DOI: 10.3390/biomedicines9070742] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2021] [Revised: 06/22/2021] [Accepted: 06/23/2021] [Indexed: 12/12/2022] Open
Abstract
Anorectal malformations (ARMs) are relatively common congenital abnormalities, but their pathogenesis is poorly understood. Previous gene knockout studies indicated that the signalling pathway mediated by the retinoic acid receptors (RAR) is instrumental to the formation of the anorectal canal and of various urogenital structures. Here, we show that simultaneous ablation of the three RARs in the mouse embryo results in a spectrum of malformations of the pelvic organs in which anorectal and urinary bladder ageneses are consistently associated. We found that these ageneses could be accounted for by defects in the processes of growth and migration of the cloaca, the embryonic structure from which the anorectal canal and urinary bladder originate. We further show that these defects are preceded by a failure of the lateral shift of the umbilical arteries and propose vascular abnormalities as a possible cause of ARM. Through the comparisons of these phenotypes with those of other mutant mice and of human patients, we would like to suggest that morphological data may provide a solid base to test molecular as well as clinical hypotheses.
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Affiliation(s)
- Manuel Mark
- CNRS, INSERM, Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), Université de Strasbourg, 1 rue Laurent Fries, 67404 Illkirch Graffenstaden, France; (M.T.); (O.W.); (J.-L.V.); (B.F.); (Y.H.); (N.B.G.)
- Service de Biologie de la Reproduction, Hôpitaux Universitaires de Strasbourg (HUS), 67300 Schiltigheim, France
- CNRS, INSERM, CELPHEDIA, PHENOMIN-Institut Clinique de la Souris (ICS), Université de Strasbourg, 1 rue Laurent Fries, 67404 Illkirch Graffenstaden, France
| | - Marius Teletin
- CNRS, INSERM, Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), Université de Strasbourg, 1 rue Laurent Fries, 67404 Illkirch Graffenstaden, France; (M.T.); (O.W.); (J.-L.V.); (B.F.); (Y.H.); (N.B.G.)
- Service de Biologie de la Reproduction, Hôpitaux Universitaires de Strasbourg (HUS), 67300 Schiltigheim, France
| | - Olivia Wendling
- CNRS, INSERM, Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), Université de Strasbourg, 1 rue Laurent Fries, 67404 Illkirch Graffenstaden, France; (M.T.); (O.W.); (J.-L.V.); (B.F.); (Y.H.); (N.B.G.)
- CNRS, INSERM, CELPHEDIA, PHENOMIN-Institut Clinique de la Souris (ICS), Université de Strasbourg, 1 rue Laurent Fries, 67404 Illkirch Graffenstaden, France
| | - Jean-Luc Vonesch
- CNRS, INSERM, Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), Université de Strasbourg, 1 rue Laurent Fries, 67404 Illkirch Graffenstaden, France; (M.T.); (O.W.); (J.-L.V.); (B.F.); (Y.H.); (N.B.G.)
| | - Betty Féret
- CNRS, INSERM, Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), Université de Strasbourg, 1 rue Laurent Fries, 67404 Illkirch Graffenstaden, France; (M.T.); (O.W.); (J.-L.V.); (B.F.); (Y.H.); (N.B.G.)
| | - Yann Hérault
- CNRS, INSERM, Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), Université de Strasbourg, 1 rue Laurent Fries, 67404 Illkirch Graffenstaden, France; (M.T.); (O.W.); (J.-L.V.); (B.F.); (Y.H.); (N.B.G.)
- CNRS, INSERM, CELPHEDIA, PHENOMIN-Institut Clinique de la Souris (ICS), Université de Strasbourg, 1 rue Laurent Fries, 67404 Illkirch Graffenstaden, France
| | - Norbert B. Ghyselinck
- CNRS, INSERM, Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), Université de Strasbourg, 1 rue Laurent Fries, 67404 Illkirch Graffenstaden, France; (M.T.); (O.W.); (J.-L.V.); (B.F.); (Y.H.); (N.B.G.)
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23
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Yi W, Rücklin M, Poelmann RE, Aldridge DC, Richardson MK. Normal stages of embryonic development of a brood parasite, the rosy bitterling Rhodeus ocellatus (Teleostei: Cypriniformes). J Morphol 2021; 282:783-819. [PMID: 33583089 PMCID: PMC8252481 DOI: 10.1002/jmor.21335] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2020] [Revised: 02/10/2021] [Accepted: 02/10/2021] [Indexed: 12/14/2022]
Abstract
Bitterlings, a group of freshwater teleosts, provide a fascinating example among vertebrates of the evolution of brood parasitism. Their eggs are laid inside the gill chamber of their freshwater mussel hosts where they develop as brood parasites. Studies of the embryonic development of bitterlings are crucial in deciphering the evolution of their distinct early life-history. Here, we have studied 255 embryos and larvae of the rosy bitterling (Rhodeus ocellatus) using in vitro fertilization and X-ray microtomography (microCT). We describe 11 pre-hatching and 13 post-hatching developmental stages spanning the first 14 days of development, from fertilization to the free-swimming stage. In contrast to previous developmental studies of various bitterling species, the staging system we describe is character-based and therefore more compatible with the widely-used stages described for zebrafish. Our bitterling data provide new insights into to the polarity of the chorion, and into notochord vacuolization and yolk sac extension in relation to body straightening. This study represents the first application of microCT scanning to bitterling development and provides one of the most detailed systematic descriptions of development in any teleost. Our staging series will be an important tool for heterochrony analysis and other comparative studies of teleost development, and may provide insight into the co-evolution of brood parasitism.
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Affiliation(s)
- Wenjing Yi
- Institute of BiologyUniversity of Leiden, Sylvius LaboratoryLeidenthe Netherlands
- The Key Laboratory of Aquatic Biodiversity and Conservation, Institute of HydrobiologyChinese Academy of SciencesHubeiChina
| | - Martin Rücklin
- Vertebrate Evolution, Development and EcologyNaturalis Biodiversity CenterLeidenThe Netherlands
| | - Robert E. Poelmann
- Institute of BiologyUniversity of Leiden, Sylvius LaboratoryLeidenthe Netherlands
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24
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Shreeve N, Depierreux D, Hawkes D, Traherne JA, Sovio U, Huhn O, Jayaraman J, Horowitz A, Ghadially H, Perry JRB, Moffett A, Sled JG, Sharkey AM, Colucci F. The CD94/NKG2A inhibitory receptor educates uterine NK cells to optimize pregnancy outcomes in humans and mice. Immunity 2021; 54:1231-1244.e4. [PMID: 33887202 PMCID: PMC8211638 DOI: 10.1016/j.immuni.2021.03.021] [Citation(s) in RCA: 37] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2019] [Revised: 12/13/2020] [Accepted: 03/25/2021] [Indexed: 12/13/2022]
Abstract
The conserved CD94/NKG2A inhibitory receptor is expressed by nearly all human and ∼50% of mouse uterine natural killer (uNK) cells. Binding human HLA-E and mouse Qa-1, NKG2A drives NK cell education, a process of unknown physiological importance influenced by HLA-B alleles. Here, we show that NKG2A genetic ablation in dams mated with wild-type males caused suboptimal maternal vascular responses in pregnancy, accompanied by perturbed placental gene expression, reduced fetal weight, greater rates of smaller fetuses with asymmetric growth, and abnormal brain development. These are features of the human syndrome pre-eclampsia. In a genome-wide association study of 7,219 pre-eclampsia cases, we found a 7% greater relative risk associated with the maternal HLA-B allele that does not favor NKG2A education. These results show that the maternal HLA-B→HLA-E→NKG2A pathway contributes to healthy pregnancy and may have repercussions on offspring health, thus establishing the physiological relevance for NK cell education. Video Abstract
CD94/NKG2A educates uterine NK cells NKG2A-deficient dams display reduced utero-placental hemodynamic adaptations Asymmetric growth restriction and abnormal brain development in NKG2A-deficient dams Non-functional HLA-B→HLA-E→NKG2A pathway exposes women to greater pre-eclampsia risk
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Affiliation(s)
- Norman Shreeve
- Department of Obstetrics & Gynaecology, University of Cambridge, National Institute for Health Research Cambridge Biomedical Research Centre, Cambridge CB2 0SW, UK; University of Cambridge Centre for Trophoblast Research, Cambridge, UK
| | - Delphine Depierreux
- Department of Obstetrics & Gynaecology, University of Cambridge, National Institute for Health Research Cambridge Biomedical Research Centre, Cambridge CB2 0SW, UK; University of Cambridge Centre for Trophoblast Research, Cambridge, UK
| | - Delia Hawkes
- Department of Obstetrics & Gynaecology, University of Cambridge, National Institute for Health Research Cambridge Biomedical Research Centre, Cambridge CB2 0SW, UK
| | | | - Ulla Sovio
- Department of Obstetrics & Gynaecology, University of Cambridge, National Institute for Health Research Cambridge Biomedical Research Centre, Cambridge CB2 0SW, UK; University of Cambridge Centre for Trophoblast Research, Cambridge, UK
| | - Oisin Huhn
- Department of Obstetrics & Gynaecology, University of Cambridge, National Institute for Health Research Cambridge Biomedical Research Centre, Cambridge CB2 0SW, UK; University of Cambridge Centre for Trophoblast Research, Cambridge, UK; Department of Pathology, University of Cambridge, Cambridge, UK; AstraZeneca, Granta Park, Cambridge CB21 6GH, UK
| | - Jyothi Jayaraman
- University of Cambridge Centre for Trophoblast Research, Cambridge, UK; Department of Pathology, University of Cambridge, Cambridge, UK; Department of Physiology, Development and Neurobiology, University of Cambridge, Cambridge, UK
| | - Amir Horowitz
- Department of Oncological Sciences, Precision Immunology Institute and Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | | | - John R B Perry
- MRC Epidemiology Unit, University of Cambridge, Cambridge UK
| | - Ashley Moffett
- University of Cambridge Centre for Trophoblast Research, Cambridge, UK; Department of Pathology, University of Cambridge, Cambridge, UK
| | - John G Sled
- Department of Medical Biophysics, University of Toronto, Toronto, Canada; Translational Medicine, Hospital for Sick Children, Toronto, Canada
| | - Andrew M Sharkey
- University of Cambridge Centre for Trophoblast Research, Cambridge, UK; Department of Pathology, University of Cambridge, Cambridge, UK
| | - Francesco Colucci
- Department of Obstetrics & Gynaecology, University of Cambridge, National Institute for Health Research Cambridge Biomedical Research Centre, Cambridge CB2 0SW, UK; University of Cambridge Centre for Trophoblast Research, Cambridge, UK.
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25
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Horner NR, Venkataraman S, Armit C, Casero R, Brown JM, Wong MD, van Eede MC, Henkelman RM, Johnson S, Teboul L, Wells S, Brown SD, Westerberg H, Mallon AM. LAMA: automated image analysis for the developmental phenotyping of mouse embryos. Development 2021; 148:dev192955. [PMID: 33574040 PMCID: PMC8015254 DOI: 10.1242/dev.192955] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2020] [Accepted: 12/21/2020] [Indexed: 11/20/2022]
Abstract
Advanced 3D imaging modalities, such as micro-computed tomography (micro-CT), have been incorporated into the high-throughput embryo pipeline of the International Mouse Phenotyping Consortium (IMPC). This project generates large volumes of raw data that cannot be immediately exploited without significant resources of personnel and expertise. Thus, rapid automated annotation is crucial to ensure that 3D imaging data can be integrated with other multi-dimensional phenotyping data. We present an automated computational mouse embryo phenotyping pipeline that harnesses the large amount of wild-type control data available in the IMPC embryo pipeline in order to address issues of low mutant sample number as well as incomplete penetrance and variable expressivity. We also investigate the effect of developmental substage on automated phenotyping results. Designed primarily for developmental biologists, our software performs image pre-processing, registration, statistical analysis and segmentation of embryo images. We also present a novel anatomical E14.5 embryo atlas average and, using it with LAMA, show that we can uncover known and novel dysmorphology from two IMPC knockout lines.
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Affiliation(s)
- Neil R Horner
- Medical Research Council Harwell Institute, Harwell OX11 0RD, UK
| | - Shanmugasundaram Venkataraman
- MRC Human Genetics Unit, MRC Institute of Genetics and Molecular Medicine (IGMM), University of Edinburgh, Edinburgh EH4 2XU, UK
| | - Chris Armit
- MRC Human Genetics Unit, MRC Institute of Genetics and Molecular Medicine (IGMM), University of Edinburgh, Edinburgh EH4 2XU, UK
- BGI Hong Kong, 26/F, Kings Wing Plaza 2, 1 On Kwan Street, Shek Mun, New Territories, Hong Kong
| | - Ramón Casero
- Medical Research Council Harwell Institute, Harwell OX11 0RD, UK
| | - James M Brown
- School of Computer Science, University of Lincoln, Lincoln LN6 7TS
| | - Michael D Wong
- Mouse Imaging Centre, Hospital for Sick Children, Toronto, Ontario M5T 3H7, Canada
| | - Matthijs C van Eede
- Mouse Imaging Centre, Hospital for Sick Children, Toronto, Ontario M5T 3H7, Canada
| | - R Mark Henkelman
- Mouse Imaging Centre, Hospital for Sick Children, Toronto, Ontario M5T 3H7, Canada
| | - Sara Johnson
- Medical Research Council Harwell Institute, Harwell OX11 0RD, UK
| | - Lydia Teboul
- Medical Research Council Harwell Institute, Harwell OX11 0RD, UK
| | - Sara Wells
- Medical Research Council Harwell Institute, Harwell OX11 0RD, UK
| | - Steve D Brown
- Medical Research Council Harwell Institute, Harwell OX11 0RD, UK
| | | | - Ann-Marie Mallon
- Medical Research Council Harwell Institute, Harwell OX11 0RD, UK
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26
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Markel M, Ginzel M, Peukert N, Schneider H, Haak R, Mayer S, Suttkus A, Lacher M, Kluth D, Gosemann J. High resolution three-dimensional imaging and measurement of lung, heart, liver, and diaphragmatic development in the fetal rat based on micro-computed tomography (micro-CT). J Anat 2020; 238:1042-1054. [PMID: 33289078 PMCID: PMC7930770 DOI: 10.1111/joa.13355] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2020] [Revised: 10/21/2020] [Accepted: 10/21/2020] [Indexed: 11/30/2022] Open
Abstract
Understanding of normal fetal organ development is crucial for the evaluation of the pathogenesis of congenital anomalies. Various techniques have been used to generate imaging of fetal rat organogenesis, such as histological dissection with 3-dimensional reconstruction and scanning electron microscopy. However, these techniques did not imply quantitative measurements of developing organs (volumes, surface areas of organs). Furthermore, a partial or total destruction of the embryos prior to analysis was inevitable. Recently, micro-computed tomography (micro-CT) has been established as a novel tool to investigate embryonic development in non-dissected embryos of rodents. In this study, we used the micro-CT technique to generate 4D datasets of rat embryos aged between embryonic day 15-22 and newborns. Lungs, hearts, diaphragms, and livers were digitally segmented in order to measure organ volumes and analyze organ development as well as generate high-resolution 3D images. These data provide objective values compiling a 4D atlas of pulmonary, cardiac, diaphragmatic, and hepatic development in the fetal rat.
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Affiliation(s)
- Moritz Markel
- Department of Pediatric SurgeryUniversity of LeipzigLeipzigGermany
| | - Marco Ginzel
- Department of Pediatric SurgeryUniversity of LeipzigLeipzigGermany
- Department of NeonatologyUniversity of TübingenTübingenGermany
| | - Nicole Peukert
- Department of Pediatric SurgeryUniversity of LeipzigLeipzigGermany
| | - Hartmut Schneider
- Department of Cariology, Endodontology and PeriodontologyUniversity of LeipzigLeipzigGermany
| | - Rainer Haak
- Department of Cariology, Endodontology and PeriodontologyUniversity of LeipzigLeipzigGermany
| | - Steffi Mayer
- Department of Pediatric SurgeryUniversity of LeipzigLeipzigGermany
| | - Anne Suttkus
- Department of Pediatric SurgeryUniversity of LeipzigLeipzigGermany
| | - Martin Lacher
- Department of Pediatric SurgeryUniversity of LeipzigLeipzigGermany
| | - Dietrich Kluth
- Department of Pediatric SurgeryUniversity of LeipzigLeipzigGermany
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27
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Llambrich S, Wouters J, Himmelreich U, Dierssen M, Sharpe J, Gsell W, Martínez-Abadías N, Vande Velde G. ViceCT and whiceCT for simultaneous high-resolution visualization of craniofacial, brain and ventricular anatomy from micro-computed tomography. Sci Rep 2020; 10:18772. [PMID: 33128010 PMCID: PMC7599226 DOI: 10.1038/s41598-020-75720-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2020] [Accepted: 10/13/2020] [Indexed: 02/07/2023] Open
Abstract
Up to 40% of congenital diseases present disturbances of brain and craniofacial development resulting in simultaneous alterations of both systems. Currently, the best available method to preclinically visualize the brain and the bones simultaneously is to co-register micro-magnetic resonance (µMR) and micro-computed tomography (µCT) scans of the same specimen. However, this requires expertise and access to both imaging techniques, dedicated software and post-processing knowhow. To provide a more affordable, reliable and accessible alternative, recent research has focused on optimizing a contrast-enhanced µCT protocol using iodine as contrast agent that delivers brain and bone images from a single scan. However, the available methods still cannot provide the complete visualization of both the brain and whole craniofacial complex. In this study, we have established an optimized protocol to diffuse the contrast into the brain that allows visualizing the brain parenchyma and the complete craniofacial structure in a single ex vivo µCT scan (whiceCT). In addition, we have developed a new technique that allows visualizing the brain ventricles using a bilateral stereotactic injection of iodine-based contrast (viceCT). Finally, we have tested both techniques in a mouse model of Down syndrome, as it is a neurodevelopmental disorder with craniofacial, brain and ventricle defects. The combined use of viceCT and whiceCT provides a complete visualization of the brain and bones with intact craniofacial structure of an adult mouse ex vivo using a single imaging modality.
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Affiliation(s)
- Sergi Llambrich
- Biomedical Imaging, Department of Imaging and Pathology, Faculty of Medicine, KU Leuven, Herestraat 49 O&N1 box 505, 3000, Leuven, Belgium.,Molecular Small Animal Imaging Centre (MoSAIC), KU Leuven, Leuven, Belgium
| | - Jens Wouters
- Biomedical Imaging, Department of Imaging and Pathology, Faculty of Medicine, KU Leuven, Herestraat 49 O&N1 box 505, 3000, Leuven, Belgium.,Molecular Small Animal Imaging Centre (MoSAIC), KU Leuven, Leuven, Belgium
| | - Uwe Himmelreich
- Biomedical Imaging, Department of Imaging and Pathology, Faculty of Medicine, KU Leuven, Herestraat 49 O&N1 box 505, 3000, Leuven, Belgium.,Molecular Small Animal Imaging Centre (MoSAIC), KU Leuven, Leuven, Belgium
| | - Mara Dierssen
- Centre for Genomic Regulation (CRG, The Barcelona Institute of Science and Technology, 08003, Barcelona, Spain.,Universitat Pompeu Fabra (UPF), 08003, Barcelona, Spain
| | - James Sharpe
- EMBL Barcelona, European Molecular Biology Laboratory, Barcelona, Spain Institució Catalana de Recerca I Estudis Avançats (ICREA), Barcelona, Spain
| | - Willy Gsell
- Biomedical Imaging, Department of Imaging and Pathology, Faculty of Medicine, KU Leuven, Herestraat 49 O&N1 box 505, 3000, Leuven, Belgium.,Molecular Small Animal Imaging Centre (MoSAIC), KU Leuven, Leuven, Belgium
| | - Neus Martínez-Abadías
- GREAB-Research Group in Biological Anthropology. Department of Evolutionary Biology, Ecology and Environmental Sciences, BEECA. Universitat de Barcelona, Barcelona, Spain
| | - Greetje Vande Velde
- Biomedical Imaging, Department of Imaging and Pathology, Faculty of Medicine, KU Leuven, Herestraat 49 O&N1 box 505, 3000, Leuven, Belgium. .,Molecular Small Animal Imaging Centre (MoSAIC), KU Leuven, Leuven, Belgium.
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28
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Schoborg TA. Whole Animal Imaging of Drosophila melanogaster using Microcomputed Tomography. J Vis Exp 2020. [PMID: 32955492 DOI: 10.3791/61515] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023] Open
Abstract
Biomedical imaging tools permit investigation of molecular mechanisms across spatial scales, from genes to organisms. Drosophila melanogaster, a well-characterized model organism, has benefited from the use of light and electron microscopy to understand gene function at the level of cells and tissues. The application of imaging platforms that allow for an understanding of gene function at the level of the entire intact organism would further enhance our knowledge of genetic mechanisms. Here a whole animal imaging method is presented that outlines the steps needed to visualize Drosophila at any developmental stage using microcomputed tomography (µ-CT). The advantages of µ-CT include commercially available instrumentation and minimal hands-on time to produce accurate 3D information at micron-level resolution without the need for tissue dissection or clearing methods. Paired with software that accelerate image analysis and 3D rendering, detailed morphometric analysis of any tissue or organ system can be performed to better understand mechanisms of development, physiology, and anatomy for both descriptive and hypothesis testing studies. By utilizing an imaging workflow that incorporates the use of electron microscopy, light microscopy, and µ-CT, a thorough evaluation of gene function can be performed, thus furthering the usefulness of this powerful model organism.
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29
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Charvet CJ. Closing the gap from transcription to the structural connectome enhances the study of connections in the human brain. Dev Dyn 2020; 249:1047-1061. [PMID: 32562584 DOI: 10.1002/dvdy.218] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2020] [Revised: 06/02/2020] [Accepted: 06/09/2020] [Indexed: 12/11/2022] Open
Abstract
The brain is composed of a complex web of networks but we have yet to map the structural connections of the human brain in detail. Diffusion MR imaging is a high-throughput method that relies on the principle of diffusion to reconstruct tracts (ie, pathways) across the brain. Although diffusion MR tractography is an exciting method to explore the structural connectivity of the brain in development and across species, the tractography has at times led to questionable interpretations. There are at present few if any alternative methods to trace structural pathways in the human brain. Given these limitations and the potential of diffusion MR imaging to map the human connectome, it is imperative that we develop new approaches to validate neuroimaging techniques. I discuss our recent studies integrating neuroimaging with transcriptional and anatomical variation across humans and other species over the course of development and in adulthood. Developing a novel framework to harness the potential of diffusion MR tractography provides new and exciting opportunities to study the evolution of developmental mechanisms generating variation in connections and bridge the gap between model systems to humans.
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30
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Gabner S, Böck P, Fink D, Glösmann M, Handschuh S. The visible skeleton 2.0: phenotyping of cartilage and bone in fixed vertebrate embryos and foetuses based on X-ray microCT. Development 2020; 147:dev187633. [PMID: 32439754 DOI: 10.1242/dev.187633] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2020] [Accepted: 04/23/2020] [Indexed: 01/14/2023]
Abstract
For decades, clearing and staining with Alcian Blue and Alizarin Red has been the gold standard to image vertebrate skeletal development. Here, we present an alternate approach to visualise bone and cartilage based on X-ray microCT imaging, which allows the collection of genuine 3D data of the entire developing skeleton at micron resolution. Our novel protocol is based on ethanol fixation and staining with Ruthenium Red, and efficiently contrasts cartilage matrix, as demonstrated in whole E16.5 mouse foetuses and limbs of E14 chicken embryos. Bone mineral is well preserved during staining, thus the entire embryonic skeleton can be imaged at high contrast. Differences in X-ray attenuation of ruthenium and calcium enable the spectral separation of cartilage matrix and bone by dual energy microCT (microDECT). Clearing of specimens is not required. The protocol is simple and reproducible. We demonstrate that cartilage contrast in E16.5 mouse foetuses is adequate for fast visual phenotyping. Morphometric skeletal parameters are easily extracted. We consider the presented workflow to be a powerful and versatile extension to the toolkit currently available for qualitative and quantitative phenotyping of vertebrate skeletal development.
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Affiliation(s)
- Simone Gabner
- Histology and Embryology, Department for Pathobiology, University of Veterinary Medicine Vienna, Veterinärplatz 1, A-1210 Vienna, Austria
| | - Peter Böck
- Histology and Embryology, Department for Pathobiology, University of Veterinary Medicine Vienna, Veterinärplatz 1, A-1210 Vienna, Austria
| | - Dieter Fink
- Institute of Laboratory Animal Science, University of Veterinary Medicine Vienna, Veterinaärplatz 1, A-1210 Vienna, Austria
| | - Martin Glösmann
- VetCore Facility for Research/Imaging Unit, University of Veterinary Medicine Vienna, Veterinärplatz 1, A-1210 Vienna, Austria
| | - Stephan Handschuh
- VetCore Facility for Research/Imaging Unit, University of Veterinary Medicine Vienna, Veterinärplatz 1, A-1210 Vienna, Austria
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31
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Gonzaga-Jauregui C, Yesil G, Nistala H, Gezdirici A, Bayram Y, Nannuru KC, Pehlivan D, Yuan B, Jimenez J, Sahin Y, Paine IS, Akdemir ZC, Rajamani S, Staples J, Dronzek J, Howell K, Fatih JM, Smaldone S, Schlesinger AE, Ramírez N, Cornier AS, Kelly MA, Haber R, Chim SM, Nieman K, Wu N, Walls J, Poueymirou W, Siao CJ, Sutton VR, Williams MS, Posey JE, Gibbs RA, Carlo S, Tegay DH, Economides AN, Lupski JR. Functional biology of the Steel syndrome founder allele and evidence for clan genomics derivation of COL27A1 pathogenic alleles worldwide. Eur J Hum Genet 2020; 28:1243-1264. [PMID: 32376988 PMCID: PMC7608441 DOI: 10.1038/s41431-020-0632-x] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2019] [Revised: 03/31/2020] [Accepted: 04/07/2020] [Indexed: 01/20/2023] Open
Abstract
Previously we reported the identification of a homozygous COL27A1 (c.2089G>C; p.Gly697Arg) missense variant and proposed it as a founder allele in Puerto Rico segregating with Steel syndrome (STLS, MIM #615155); a rare osteochondrodysplasia characterized by short stature, congenital bilateral hip dysplasia, carpal coalitions, and scoliosis. We now report segregation of this variant in five probands from the initial clinical report defining the syndrome and an additional family of Puerto Rican descent with multiple affected adult individuals. We modeled the orthologous variant in murine Col27a1 and found it recapitulates some of the major Steel syndrome associated skeletal features including reduced body length, scoliosis, and a more rounded skull shape. Characterization of the in vivo murine model shows abnormal collagen deposition in the extracellular matrix and disorganization of the proliferative zone of the growth plate. We report additional COL27A1 pathogenic variant alleles identified in unrelated consanguineous Turkish kindreds suggesting Clan Genomics and identity-by-descent homozygosity contributing to disease in this population. The hypothesis that carrier states for this autosomal recessive osteochondrodysplasia may contribute to common complex traits is further explored in a large clinical population cohort. Our findings augment our understanding of COL27A1 biology and its role in skeletal development; and expand the functional allelic architecture in this gene underlying both rare and common disease phenotypes.
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Affiliation(s)
| | - Gozde Yesil
- Istanbul Faculty of Medicine Department of Medical Genetics, Istanbul University, 34093, Istanbul, Turkey
| | - Harikiran Nistala
- Regeneron Genetics Center, Regeneron Pharmaceuticals Inc., Tarrytown, NY, 10591, USA
| | - Alper Gezdirici
- Department of Medical Genetics, Kanuni Sultan Suleyman Training and Research Hospital, 34303, Istanbul, Turkey
| | - Yavuz Bayram
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA.,Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | | | - Davut Pehlivan
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA.,Department of Pediatrics, Division of Pediatric Neurology, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Bo Yuan
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA
| | | | - Yavuz Sahin
- Medical Genetics, Genoks Genetics Center, 06570, Ankara, Turkey
| | - Ingrid S Paine
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Zeynep Coban Akdemir
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA
| | | | - Jeffrey Staples
- Regeneron Genetics Center, Regeneron Pharmaceuticals Inc., Tarrytown, NY, 10591, USA
| | - John Dronzek
- Regeneron Genetics Center, Regeneron Pharmaceuticals Inc., Tarrytown, NY, 10591, USA
| | - Kristen Howell
- Regeneron Genetics Center, Regeneron Pharmaceuticals Inc., Tarrytown, NY, 10591, USA
| | - Jawid M Fatih
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA
| | | | - Alan E Schlesinger
- Texas Children's Hospital, Houston, TX, 77030, USA.,Department of Radiology, Baylor College of Medicine, Houston, TX, 77030, USA
| | | | - Alberto S Cornier
- Genetics Section, San Jorge Children's Hospital, San Juan, PR, 00912, USA.,Ponce Health Sciences University, Ponce, PR, 00716, USA.,Department of Pediatrics, Universidad Central del Caribe School of Medicine, Bayamon, PR, 00960, USA
| | | | - Robert Haber
- Regeneron Genetics Center, Regeneron Pharmaceuticals Inc., Tarrytown, NY, 10591, USA
| | - Shek Man Chim
- Regeneron Genetics Center, Regeneron Pharmaceuticals Inc., Tarrytown, NY, 10591, USA
| | - Kristy Nieman
- Regeneron Pharmaceuticals Inc., Tarrytown, NY, 10591, USA
| | - Nan Wu
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA.,Department of Orthopedic Surgery, Beijing Key Laboratory for Genetic Research of Skeletal Deformity, and Medical Research Center of Orthopedics, Peking Union Medical College Hospital, Peking Union Medical College & Chinese Academy of Medical Sciences, 100730, Beijing, China
| | | | | | | | - Chia-Jen Siao
- Regeneron Pharmaceuticals Inc., Tarrytown, NY, 10591, USA
| | - V Reid Sutton
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA.,Texas Children's Hospital, Houston, TX, 77030, USA
| | | | - Jennifer E Posey
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Richard A Gibbs
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA.,Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Simon Carlo
- Mayagüez Medical Center, Mayagüez, PR, 00681, USA.,Ponce Health Sciences University, Ponce, PR, 00716, USA
| | - David H Tegay
- Department of Pediatrics, Division of Medical Genetics, Cohen Children's Medical Center of Northwell Health, New Hyde Park, NY, 11040, USA
| | - Aris N Economides
- Regeneron Genetics Center, Regeneron Pharmaceuticals Inc., Tarrytown, NY, 10591, USA.,Regeneron Pharmaceuticals Inc., Tarrytown, NY, 10591, USA
| | - James R Lupski
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA. .,Texas Children's Hospital, Houston, TX, 77030, USA.
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32
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Choi WJ, Maga AM, Kim ES, Wang RK. A feasibility study of OCT for anatomical and vascular phenotyping of mouse embryo. JOURNAL OF BIOPHOTONICS 2020; 13:e201960225. [PMID: 32067352 DOI: 10.1002/jbio.201960225] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/17/2019] [Revised: 01/31/2020] [Accepted: 02/14/2020] [Indexed: 06/10/2023]
Abstract
The embryo phenotyping of genetic murine model is invaluable when investigating functions of genes underlying embryonic development and birth defect. Although traditional imaging technologies such as ultrasound are very useful for evaluating phenotype of murine embryos, the use of advanced techniques for phenotyping is desirable to obtain more information from genetic research. This letter tests the feasibility of optical coherence tomography (OCT) as a high-throughput phenotyping tool for murine embryos. Three-dimensional OCT imaging is performed for live and cleared mouse embryos in the late developmental stage (embryonic day 17.5). By using a dynamic focusing method and OCT angiography (OCTA) approach, our OCT imaging of the embryo exhibits rapid and clean visualization of organ structures deeper than 5 mm and complex microvasculature of perfused blood vessels in the murine embryonic body. This demonstration suggests that OCT imaging can be useful for comprehensively assessing embryo anatomy and angiography of genetically engineered mice.
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Affiliation(s)
- Woo J Choi
- School of Electrical and Electronics Engineering, College of ICT Engineering, Chung-Ang University, Seoul, Republic of Korea
| | - A M Maga
- Division of Craniofacial Medicine, Department of Pediatrics, University of Washington, Seattle, Washington
- Center for Development Biology and Regenerative Medicine, Seattle Children's Hospital, Seattle, Washington
| | - Eun S Kim
- School of Electrical and Electronics Engineering, College of ICT Engineering, Chung-Ang University, Seoul, Republic of Korea
| | - Ruikang K Wang
- Department of Bioengineering, University of Washington, Seattle, Washington
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33
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de Bournonville S, Vangrunderbeeck S, Ly HGT, Geeroms C, De Borggraeve WM, Parac-Vogt TN, Kerckhofs G. Exploring polyoxometalates as non-destructive staining agents for contrast-enhanced microfocus computed tomography of biological tissues. Acta Biomater 2020; 105:253-262. [PMID: 31996331 DOI: 10.1016/j.actbio.2020.01.038] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2019] [Revised: 01/08/2020] [Accepted: 01/22/2020] [Indexed: 11/28/2022]
Abstract
To advance clinical translation of regenerative medicine, there is, amongst others, still need for better insights in tissue development and disease. For this purpose, more precise imaging of the 3D microstructure and spatial interrelationships of the different tissues within organs is crucial. Despite being destructive towards the sample, conventional histology still is the gold standard for structural analysis of biological tissues. It is, however, limited by 2D sections of a 3D object, prohibiting full 3D structural analysis. MicroCT has proven to provide full 3D structural information of mineralized tissues and dense biomaterials. However, the intrinsic low X-ray absorption of soft tissues requires contrast-enhancing staining agents (CESAs). In a previous study, we showed that hafnium-substituted Wells-Dawson polyoxometalate (Hf-WD POM) allows simultaneous contrast-enhanced microCT (CE-CT) visualization of bone and its marrow vascularization and adiposity. In this study, other POM species have been examined for their potential as soft tissue CESAs. Four Wells-Dawson POMs, differing in structure and overall charge, were used to stain murine long bones and kidneys. Their staining potential and diffusion rate were compared to those of Hf-WD POM and phosphotungstic acid (PTA), a frequently used but destructive CESA. Monolacunary Wells-Dawson POM (Mono-WD POM) showed similar soft tissue enhancement as Hf-WD POM and PTA. Moreover, Mono-WD POM is less destructive, shows a better diffusion than PTA, and its synthesis requires less time and cost than Hf-WD POM. Finally, the solubility of Mono-WD POM was improved by addition of lithium chloride (LiCl) to the staining solution, enhancing further the soft tissue contrast. STATEMENT OF SIGNIFICANCE: To advance clinical translation of regenerative medicine, there is, amongst others, still need for better insights in tissue development and disease. For this purpose, more precise imaging of the 3D microstructure and spatial interrelationships of the different tissues within organs is crucial. Current standard structural analysis techniques (e.g. 2D histomorphometry), however, do not allow full 3D assessment. Contrast-enhanced X-ray computed tomography has emerged as a powerful 3D structural characterization tool of soft biological tissues. In this study, from a library of Wells Dawson polyoxometalates (WD POMs), we identified monolacunary WD POM together with lithium chloride, dissolved in phosphate buffered saline, as the most suitable contrast-enhancing staining agent solution for different biological tissues without tissue shrinkage.
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Affiliation(s)
- Sébastien de Bournonville
- Prometheus, Division of Skeletal Tissue Engineering, KU Leuven, Leuven, Belgium; Biomechanics Section, Department of Mechanical Engineering, KU Leuven, Leuven, Belgium
| | - Sarah Vangrunderbeeck
- Molecular Design and Synthesis, Department of Chemistry, KU Leuven, Leuven, Belgium; Biomechanics Lab, Institute of Mechanics, Materials, and Civil Engineering, UCLouvain, Louvain-la-Neuve, Belgium
| | - Hong Giang T Ly
- Molecular Design and Synthesis, Department of Chemistry, KU Leuven, Leuven, Belgium; Department of Chemistry, College of Natural Sciences, Can Tho University, Can Tho, Vietnam
| | - Carla Geeroms
- Prometheus, Division of Skeletal Tissue Engineering, KU Leuven, Leuven, Belgium; Skeletal Biology and Engineering Research Center, Department Development and Regeneration, KU Leuven, Leuven, Belgium
| | - Wim M De Borggraeve
- Molecular Design and Synthesis, Department of Chemistry, KU Leuven, Leuven, Belgium
| | - Tatjana N Parac-Vogt
- Molecular Design and Synthesis, Department of Chemistry, KU Leuven, Leuven, Belgium
| | - Greet Kerckhofs
- Prometheus, Division of Skeletal Tissue Engineering, KU Leuven, Leuven, Belgium; Biomechanics Lab, Institute of Mechanics, Materials, and Civil Engineering, UCLouvain, Louvain-la-Neuve, Belgium; IREC, Institute of Experimental and Clinical Research, UCLouvain, Woluwé-Saint-Lambert, Belgium; Department Materials Engineering, KU Leuven, Leuven, Belgium.
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34
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Zdora MC, Zanette I, Walker T, Phillips NW, Smith R, Deyhle H, Ahmed S, Thibault P. X-ray phase imaging with the unified modulated pattern analysis of near-field speckles at a laboratory source. APPLIED OPTICS 2020; 59:2270-2275. [PMID: 32225757 DOI: 10.1364/ao.384531] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/27/2019] [Accepted: 01/30/2020] [Indexed: 06/10/2023]
Abstract
X-ray phase-contrast techniques are powerful methods for discerning features with similar densities, which are normally indistinguishable with conventional absorption contrast. While these techniques are well-established tools at large-scale synchrotron facilities, efforts have increasingly focused on implementations at laboratory sources for widespread use. X-ray speckle-based imaging is one of the phase-contrast techniques with high potential for translation to conventional x-ray systems. It yields phase-contrast, transmission, and dark-field images with high sensitivity using a relatively simple and cost-effective setup tolerant to divergent and polychromatic beams. Recently, we have introduced the unified modulated pattern analysis (UMPA) [Phys. Rev. Lett.118, 203903 (2017)PRLTAO0031-900710.1103/PhysRevLett.118.203903], which further simplifies the translation of x-ray speckle-based imaging to low-brilliance sources. Here, we present the proof-of-principle implementation of UMPA speckle-based imaging at a microfocus liquid-metal-jet x-ray laboratory source.
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35
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Schoborg TA, Smith SL, Smith LN, Morris HD, Rusan NM. Micro-computed tomography as a platform for exploring Drosophila development. Development 2019; 146:dev.176685. [PMID: 31722883 DOI: 10.1242/dev.176685] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2019] [Accepted: 11/07/2019] [Indexed: 12/20/2022]
Abstract
Understanding how events at the molecular and cellular scales contribute to tissue form and function is key to uncovering the mechanisms driving animal development, physiology and disease. Elucidating these mechanisms has been enhanced through the study of model organisms and the use of sophisticated genetic, biochemical and imaging tools. Here, we present an accessible method for non-invasive imaging of Drosophila melanogaster at high resolution using micro-computed tomography (µ-CT). We show how rapid processing of intact animals, at any developmental stage, provides precise quantitative assessment of tissue size and morphology, and permits analysis of inter-organ relationships. We then use µ-CT imaging to study growth defects in the Drosophila brain through the characterization of a bnormal spindle (asp) and WD repeat domain 62 (W dr62), orthologs of the two most commonly mutated genes in human microcephaly patients. Our work demonstrates the power of combining µ-CT with traditional genetic, cellular and developmental biology tools available in model organisms to address novel biological mechanisms that control animal development and disease.
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Affiliation(s)
- Todd A Schoborg
- Cell Biology and Physiology Center, National Heart, Lung and Blood Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Samantha L Smith
- Cell Biology and Physiology Center, National Heart, Lung and Blood Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Lauren N Smith
- Cell Biology and Physiology Center, National Heart, Lung and Blood Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - H Douglas Morris
- Mouse Imaging Facility, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD 20892, USA
| | - Nasser M Rusan
- Cell Biology and Physiology Center, National Heart, Lung and Blood Institute, National Institutes of Health, Bethesda, MD 20892, USA
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36
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Vallejo Ramirez PP, Zammit J, Vanderpoorten O, Riche F, Blé FX, Zhou XH, Spiridon B, Valentine C, Spasov SE, Oluwasanya PW, Goodfellow G, Fantham MJ, Siddiqui O, Alimagham F, Robbins M, Stretton A, Simatos D, Hadeler O, Rees EJ, Ströhl F, Laine RF, Kaminski CF. OptiJ: Open-source optical projection tomography of large organ samples. Sci Rep 2019; 9:15693. [PMID: 31666606 PMCID: PMC6821862 DOI: 10.1038/s41598-019-52065-0] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2019] [Accepted: 10/09/2019] [Indexed: 12/20/2022] Open
Abstract
The three-dimensional imaging of mesoscopic samples with Optical Projection Tomography (OPT) has become a powerful tool for biomedical phenotyping studies. OPT uses visible light to visualize the 3D morphology of large transparent samples. To enable a wider application of OPT, we present OptiJ, a low-cost, fully open-source OPT system capable of imaging large transparent specimens up to 13 mm tall and 8 mm deep with 50 µm resolution. OptiJ is based on off-the-shelf, easy-to-assemble optical components and an ImageJ plugin library for OPT data reconstruction. The software includes novel correction routines for uneven illumination and sample jitter in addition to CPU/GPU accelerated reconstruction for large datasets. We demonstrate the use of OptiJ to image and reconstruct cleared lung lobes from adult mice. We provide a detailed set of instructions to set up and use the OptiJ framework. Our hardware and software design are modular and easy to implement, allowing for further open microscopy developments for imaging large organ samples.
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Affiliation(s)
- Pedro P Vallejo Ramirez
- Laser Analytics Group, Department of Chemical Engineering and Biotechnology, University of Cambridge, Cambridge, UK
| | - Joseph Zammit
- Sensor CDT 2015-2016 student cohort, University of Cambridge, Cambridge, UK
| | - Oliver Vanderpoorten
- Laser Analytics Group, Department of Chemical Engineering and Biotechnology, University of Cambridge, Cambridge, UK
- Sensor CDT 2015-2016 student cohort, University of Cambridge, Cambridge, UK
| | - Fergus Riche
- Sensor CDT 2015-2016 student cohort, University of Cambridge, Cambridge, UK
| | - Francois-Xavier Blé
- Clinical Discovery Unit, Early Clinical Development, IMED Biotech Unit, AstraZeneca, Cambridge, UK
| | - Xiao-Hong Zhou
- Bioscience, Respiratory, Inflammation and Autoimmunity, IMED Biotech Unit, AstraZeneca, Gothenburg, Sweden
| | - Bogdan Spiridon
- Sensor CDT 2015-2016 student cohort, University of Cambridge, Cambridge, UK
| | | | - Simeon E Spasov
- Sensor CDT 2015-2016 student cohort, University of Cambridge, Cambridge, UK
| | | | - Gemma Goodfellow
- Sensor CDT 2015-2016 student cohort, University of Cambridge, Cambridge, UK
| | - Marcus J Fantham
- Laser Analytics Group, Department of Chemical Engineering and Biotechnology, University of Cambridge, Cambridge, UK
| | - Omid Siddiqui
- Sensor CDT 2015-2016 student cohort, University of Cambridge, Cambridge, UK
| | - Farah Alimagham
- Sensor CDT 2015-2016 student cohort, University of Cambridge, Cambridge, UK
| | - Miranda Robbins
- Laser Analytics Group, Department of Chemical Engineering and Biotechnology, University of Cambridge, Cambridge, UK
- Sensor CDT 2015-2016 student cohort, University of Cambridge, Cambridge, UK
| | - Andrew Stretton
- Sensor CDT 2015-2016 student cohort, University of Cambridge, Cambridge, UK
| | - Dimitrios Simatos
- Sensor CDT 2015-2016 student cohort, University of Cambridge, Cambridge, UK
| | - Oliver Hadeler
- Laser Analytics Group, Department of Chemical Engineering and Biotechnology, University of Cambridge, Cambridge, UK
| | - Eric J Rees
- Laser Analytics Group, Department of Chemical Engineering and Biotechnology, University of Cambridge, Cambridge, UK
| | - Florian Ströhl
- Laser Analytics Group, Department of Chemical Engineering and Biotechnology, University of Cambridge, Cambridge, UK
- Department of Physics and Technology, UiT The Arctic University of Norway, NO-9037, Tromsø, Norway
| | - Romain F Laine
- Laser Analytics Group, Department of Chemical Engineering and Biotechnology, University of Cambridge, Cambridge, UK
- Medical Research Council Laboratory for Molecular Cell Biology (LMCB), University College London, Gower Street, London, WC1E 6BT, UK
| | - Clemens F Kaminski
- Laser Analytics Group, Department of Chemical Engineering and Biotechnology, University of Cambridge, Cambridge, UK.
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37
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Tesařová M, Heude E, Comai G, Zikmund T, Kaucká M, Adameyko I, Tajbakhsh S, Kaiser J. An interactive and intuitive visualisation method for X-ray computed tomography data of biological samples in 3D Portable Document Format. Sci Rep 2019; 9:14896. [PMID: 31624273 PMCID: PMC6797759 DOI: 10.1038/s41598-019-51180-2] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2019] [Accepted: 09/25/2019] [Indexed: 12/14/2022] Open
Abstract
3D imaging approaches based on X-ray microcomputed tomography (microCT) have become increasingly accessible with advancements in methods, instruments and expertise. The synergy of material and life sciences has impacted biomedical research by proposing new tools for investigation. However, data sharing remains challenging as microCT files are usually in the range of gigabytes and require specific and expensive software for rendering and interpretation. Here, we provide an advanced method for visualisation and interpretation of microCT data with small file formats, readable on all operating systems, using freely available Portable Document Format (PDF) software. Our method is based on the conversion of volumetric data into interactive 3D PDF, allowing rotation, movement, magnification and setting modifications of objects, thus providing an intuitive approach to analyse structures in a 3D context. We describe the complete pipeline from data acquisition, data processing and compression, to 3D PDF formatting on an example of craniofacial anatomical morphology in the mouse embryo. Our procedure is widely applicable in biological research and can be used as a framework to analyse volumetric data from any research field relying on 3D rendering and CT-biomedical imaging.
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Affiliation(s)
- Markéta Tesařová
- Central European Institute of Technology, Brno University of Technology, Brno, Czech Republic
| | - Eglantine Heude
- Department Adaptation du Vivant, Museum national d'Histoire naturelle, CNRS UMR 7221, Paris, France.,Department of Developmental and Stem Cell Biology, Stem Cells and Development Unit, Institut Pasteur, Paris, France.,CNRS UMR, 3738, Paris, France
| | - Glenda Comai
- Department of Developmental and Stem Cell Biology, Stem Cells and Development Unit, Institut Pasteur, Paris, France.,CNRS UMR, 3738, Paris, France
| | - Tomáš Zikmund
- Central European Institute of Technology, Brno University of Technology, Brno, Czech Republic
| | - Markéta Kaucká
- Department of Physiology and Pharmacology, Karolinska Institutet, Solna, Sweden.,Department of Molecular Neurosciences, Medical University of Vienna, Vienna, Austria
| | - Igor Adameyko
- Department of Physiology and Pharmacology, Karolinska Institutet, Solna, Sweden.,Department of Molecular Neurosciences, Medical University of Vienna, Vienna, Austria
| | - Shahragim Tajbakhsh
- Department of Developmental and Stem Cell Biology, Stem Cells and Development Unit, Institut Pasteur, Paris, France.,CNRS UMR, 3738, Paris, France
| | - Jozef Kaiser
- Central European Institute of Technology, Brno University of Technology, Brno, Czech Republic.
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38
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Huang Y, Li M, Huang D, Qiu Q, Lin W, Liu J, Yang W, Yao Y, Yan G, Qu N, Tuchin VV, Fan S, Liu G, Zhao Q, Chen X. Depth-Resolved Enhanced Spectral-Domain OCT Imaging of Live Mammalian Embryos Using Gold Nanoparticles as Contrast Agent. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2019; 15:e1902346. [PMID: 31304667 DOI: 10.1002/smll.201902346] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/09/2019] [Revised: 06/21/2019] [Indexed: 05/12/2023]
Abstract
High-resolution and real-time visualization of the morphological changes during embryonic development are critical for studying congenital anomalies. Optical coherence tomography (OCT) has been used to investigate the process of embryogenesis. However, the structural visibility of the embryo is decreased with the depth due to signal roll-off and high light scattering. To overcome these obstacles, in this study, combined is a spectral-domain OCT (SD-OCT) with gold nanorods (GNRs) for 2D/3D imaging of live mouse embryos. Inductively coupled plasma mass spectrometry is used to confirm that GNRs can be effectively delivered to the embryos during ex vivo culture. OCT signal, image contrast, and penetration depth are all enhanced on the embryos with GNRs. These results show that after GNR treatment, more accurate spatial localization and better contrasting of the borders among organs can be observed on E9.5 and E10.5 mouse embryos. Furthermore, the strong optical absorbance of GNRs results in much clearer 3D images of the embryos, which can be used for calculating the heart areas and volumes of E9.5 and E10.5 embryos. These findings provide a promising strategy for monitoring organ development and detecting congenital structural abnormalities in mice.
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Affiliation(s)
- Yali Huang
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, Organ Transplantation Institute, Center for Molecular Imaging and Translational Medicine, School of Medicine, School of Public Health, Xiamen University, Xiamen, 361102, China
| | - Minghui Li
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, Organ Transplantation Institute, Center for Molecular Imaging and Translational Medicine, School of Medicine, School of Public Health, Xiamen University, Xiamen, 361102, China
| | - Doudou Huang
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, Organ Transplantation Institute, Center for Molecular Imaging and Translational Medicine, School of Medicine, School of Public Health, Xiamen University, Xiamen, 361102, China
| | - Qi Qiu
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, Organ Transplantation Institute, Center for Molecular Imaging and Translational Medicine, School of Medicine, School of Public Health, Xiamen University, Xiamen, 361102, China
| | - Wenzhen Lin
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, Organ Transplantation Institute, Center for Molecular Imaging and Translational Medicine, School of Medicine, School of Public Health, Xiamen University, Xiamen, 361102, China
| | - Jiyan Liu
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, Organ Transplantation Institute, Center for Molecular Imaging and Translational Medicine, School of Medicine, School of Public Health, Xiamen University, Xiamen, 361102, China
| | - Wensheng Yang
- Department of Pathology, Affiliated Chenggong Hospital, Xiamen University, Xiamen, 361000, China
| | - Youliang Yao
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, Organ Transplantation Institute, Center for Molecular Imaging and Translational Medicine, School of Medicine, School of Public Health, Xiamen University, Xiamen, 361102, China
| | - Guoliang Yan
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, Organ Transplantation Institute, Center for Molecular Imaging and Translational Medicine, School of Medicine, School of Public Health, Xiamen University, Xiamen, 361102, China
| | - Ning Qu
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, Organ Transplantation Institute, Center for Molecular Imaging and Translational Medicine, School of Medicine, School of Public Health, Xiamen University, Xiamen, 361102, China
| | - Valery V Tuchin
- Research-Educational Institute of Optics and Biophotonics, Saratov State University, Saratov, 410012, Russia
- Laboratory of Laser Diagnostics of Technical and Living Systems, Institute of Precision Mechanics and Control of the Russian Academy of Science, Saratov, 410028, Russia
- Laboratory of Molecular Imaging, Bach Institute of Biochemistry, Research Center of Biotechnology of the Russian Academy of Sciences, Moscow, 119071, Russia
- Interdisciplinary Laboratory of Biophotonics, Tomsk State University, Tomsk, 634050, Russia
| | - Shanhui Fan
- College of Life Information Science and Instrument Engineering, Hangzhou Dianzi University, Hangzhou, 310018, China
| | - Gang Liu
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, Organ Transplantation Institute, Center for Molecular Imaging and Translational Medicine, School of Medicine, School of Public Health, Xiamen University, Xiamen, 361102, China
| | - Qingliang Zhao
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, Organ Transplantation Institute, Center for Molecular Imaging and Translational Medicine, School of Medicine, School of Public Health, Xiamen University, Xiamen, 361102, China
| | - Xiaoyuan Chen
- Laboratory of Molecular Imaging and Nanomedicine, National Institute of Biomedical Imaging and Bioengineering (NIBIB), National Institutes of Health (NIH), Bethesda, MD, 20892, USA
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39
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Vasung L, Charvet CJ, Shiohama T, Gagoski B, Levman J, Takahashi E. Ex vivo fetal brain MRI: Recent advances, challenges, and future directions. Neuroimage 2019; 195:23-37. [PMID: 30905833 PMCID: PMC6617515 DOI: 10.1016/j.neuroimage.2019.03.034] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2017] [Revised: 03/12/2019] [Accepted: 03/16/2019] [Indexed: 12/21/2022] Open
Abstract
During early development, the fetal brain undergoes dynamic morphological changes. These changes result from neurogenic events, such as neuronal proliferation, migration, axonal elongation, retraction, and myelination. The duration and intensity of these events vary across species. Comparative assessments of these neurogenic events give us insight into evolutionary changes and the complexity of human brain development. Recent advances in magnetic resonance imaging (MRI), especially ex vivo MRI, permit characterizing and comparing fetal brain development across species. Comparative ex vivo MRI studies support the detection of species-specific differences that occur during early brain development. In this review, we provide a comprehensive overview of ex vivo MRI studies that characterize early brain development in humans, monkeys, cats, as well as rats/mice. Finally, we discuss the current advantages and limitations of ex vivo fetal brain MRI.
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Affiliation(s)
- Lana Vasung
- Division of Newborn Medicine, Department of Medicine, Boston Children's Hospital, Harvard Medical School, 401 Park Dr., Boston, MA, 02215, USA
| | - Christine J Charvet
- Department of Molecular Biology and Genetics, Cornell University, 526 Campus Rd, Ithaca, NY, 14850, USA; Department of Psychology, Delaware State University, Dover, DE, 19901, USA
| | - Tadashi Shiohama
- Division of Newborn Medicine, Department of Medicine, Boston Children's Hospital, Harvard Medical School, 401 Park Dr., Boston, MA, 02215, USA; Department of Pediatrics, Chiba University Hospital, Inohana 1-8-1, Chiba-shi, Chiba, 2608670, Japan
| | - Borjan Gagoski
- Department of Radiology, Boston Children's Hospital, Harvard Medical School, 401 Park Dr., Boston, MA, 02215, USA
| | - Jacob Levman
- Division of Newborn Medicine, Department of Medicine, Boston Children's Hospital, Harvard Medical School, 401 Park Dr., Boston, MA, 02215, USA; Department of Mathematics, Statistics and Computer Science, St. Francis Xavier University, Antigonish, NS, B2G 2W5, Canada
| | - Emi Takahashi
- Division of Newborn Medicine, Department of Medicine, Boston Children's Hospital, Harvard Medical School, 401 Park Dr., Boston, MA, 02215, USA.
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40
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Griffing AH, Sanger TJ, Daza JD, Nielsen SV, Pinto BJ, Stanley EL, Gamble T. Embryonic development of a parthenogenetic vertebrate, the mourning gecko (
Lepidodactylus lugubris
). Dev Dyn 2019; 248:1070-1090. [DOI: 10.1002/dvdy.72] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2019] [Revised: 06/10/2019] [Accepted: 06/11/2019] [Indexed: 12/11/2022] Open
Affiliation(s)
- Aaron H. Griffing
- Department of Biological SciencesMarquette University Milwaukee Wisconsin
| | - Thomas J. Sanger
- Department of BiologyLoyola University in Chicago Chicago Illinois
| | - Juan D. Daza
- Department of Biological SciencesSam Houston State University Huntsville Texas
| | - Stuart V. Nielsen
- Department of HerpetologyFlorida Museum of Natural History Gainesville Florida
| | - Brendan J. Pinto
- Department of Biological SciencesMarquette University Milwaukee Wisconsin
| | - Edward L. Stanley
- Department of HerpetologyFlorida Museum of Natural History Gainesville Florida
| | - Tony Gamble
- Department of Biological SciencesMarquette University Milwaukee Wisconsin
- Milwaukee Public Museum Milwaukee Wisconsin
- Bell Museum of Natural HistoryUniversity of Minnesota Saint Paul Minnesota
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41
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Ban S, Cho NH, Min E, Bae JK, Ahn Y, Shin S, Park SA, Lee Y, Jung W. Label-free optical projection tomography for quantitative three-dimensional anatomy of mouse embryo. JOURNAL OF BIOPHOTONICS 2019; 12:e201800481. [PMID: 30729697 DOI: 10.1002/jbio.201800481] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/22/2018] [Revised: 02/04/2019] [Accepted: 02/05/2019] [Indexed: 05/19/2023]
Abstract
Recent progress in three-dimensional optical imaging techniques allows visualization of many comprehensive biological specimens. Optical clearing methods provide volumetric and quantitative information by overcoming the limited depth of light due to scattering. However, current imaging technologies mostly rely on the synthetic or genetic fluorescent labels, thus limits its application to whole-body visualization of generic mouse models. Here, we report a label-free optical projection tomography (LF-OPT) technique for quantitative whole mouse embryo imaging. LF-OPT is based on the attenuation contrast of light rather than fluorescence, and it utilizes projection imaging technique similar to computed tomography for visualizing the volumetric structure. We demonstrate this with a collection of mouse embryo morphologies in different stages using LF-OPT. Additionally, we extract quantitative organ information applicable toward high-throughput phenotype screening. Our results indicate that LF-OPT can provide multi-scale morphological information in various tissues including bone, which can be difficult in conventional optical imaging technique.
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Affiliation(s)
- Sungbea Ban
- Samsung Electro-Mechanics, Global Technology Center (GTC), Suwon, Republic of Korea
| | - Nam Hyun Cho
- Department of Otorhinolaryngology, Harvard Medical School, Boston, Massachusetts
- Massachusetts Eye and Ear Infirmary, Boston, Massachusetts
| | - Eunjung Min
- Rowland Institute at Harvard, Cambridge, Massachusetts
| | - Jung Kweon Bae
- Department of Biomedical Engineering, Ulsan National Institute of Science and Technology (UNIST), Ulsan, Republic of Korea
| | - Yujin Ahn
- Department of Biomedical Engineering, Ulsan National Institute of Science and Technology (UNIST), Ulsan, Republic of Korea
| | - Sungwon Shin
- Department of Mechanical Engineering, Sogang University, Seoul, Republic of Korea
| | - Soo-Ah Park
- In Vivo Research Center, UNIST Central Research Facilities, Ulsan, Republic of Korea
| | - Yoonsung Lee
- Center for Genomic Integrity Institute for Basic Science, UNIST, Ulsan, Republic of Korea
| | - Woonggyu Jung
- Department of Biomedical Engineering, Ulsan National Institute of Science and Technology (UNIST), Ulsan, Republic of Korea
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42
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Hsu CW, Kalaga S, Akoma U, Rasmussen TL, Christiansen AE, Dickinson ME. High Resolution Imaging of Mouse Embryos and Neonates with X-Ray Micro-Computed Tomography. ACTA ACUST UNITED AC 2019; 9:e63. [PMID: 31195428 DOI: 10.1002/cpmo.63] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
Iodine-contrast micro-computed tomography (microCT) 3D imaging provides a non-destructive and high-throughput platform for studying mouse embryo and neonate development. Here we provide protocols on preparing mouse embryos and neonates between embryonic day 8.5 (E8.5) to postnatal day 4 (P4) for iodine-contrast microCT imaging. With the implementation of the STABILITY method to create a polymer-tissue hybrid structure, we have demonstrated that not only is soft tissue shrinkage minimized but also the minimum required time for soft tissue staining with iodine is decreased, especially for E18.5 to P4 samples. In addition, we also provide a protocol on using commercially available X-CLARITYTM hydrogel solution to create the similar polymer-tissue hybrid structure on delicate early post-implantation stage (E8.5 to E14.5) embryos. With its simple sample staining and mounting processes, this protocol is easy to adopt and implement for most of the commercially available, stand-alone microCT systems in order to study mouse development between early post-implantation to early postnatal stages. © 2019 by John Wiley & Sons, Inc.
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Affiliation(s)
- Chih-Wei Hsu
- Department of Molecular Physiology and Biophysics, Baylor College of Medicine, Houston, Texas.,Optical Imaging and Vital Microscopy Core, Baylor College of Medicine, Houston, Texas
| | - Sowmya Kalaga
- Department of Molecular Physiology and Biophysics, Baylor College of Medicine, Houston, Texas.,Optical Imaging and Vital Microscopy Core, Baylor College of Medicine, Houston, Texas
| | - Uchechukwu Akoma
- Department of Molecular Physiology and Biophysics, Baylor College of Medicine, Houston, Texas
| | - Tara L Rasmussen
- Department of Molecular Physiology and Biophysics, Baylor College of Medicine, Houston, Texas
| | - Audrey E Christiansen
- Department of Molecular Physiology and Biophysics, Baylor College of Medicine, Houston, Texas
| | - Mary E Dickinson
- Department of Molecular Physiology and Biophysics, Baylor College of Medicine, Houston, Texas.,Optical Imaging and Vital Microscopy Core, Baylor College of Medicine, Houston, Texas.,Cardiovascular Research Institute, Baylor College of Medicine, Houston, Texas
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43
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Percival CJ, Devine J, Darwin BC, Liu W, van Eede M, Henkelman RM, Hallgrimsson B. The effect of automated landmark identification on morphometric analyses. J Anat 2019; 234:917-935. [PMID: 30901082 DOI: 10.1111/joa.12973] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/07/2019] [Indexed: 01/20/2023] Open
Abstract
Morphometric analysis of anatomical landmarks allows researchers to identify specific morphological differences between natural populations or experimental groups, but manually identifying landmarks is time-consuming. We compare manually and automatically generated adult mouse skull landmarks and subsequent morphometric analyses to elucidate how switching from manual to automated landmarking will impact morphometric analysis results for large mouse (Mus musculus) samples (n = 1205) that represent a wide range of 'normal' phenotypic variation (62 genotypes). Other studies have suggested that the use of automated landmarking methods is feasible, but this study is the first to compare the utility of current automated approaches to manual landmarking for a large dataset that allows the quantification of intra- and inter-strain variation. With this unique sample, we investigated how switching to a non-linear image registration-based automated landmarking method impacts estimated differences in genotype mean shape and shape variance-covariance structure. In addition, we tested whether an initial registration of specimen images to genotype-specific averages improves automatic landmark identification accuracy. Our results indicated that automated landmark placement was significantly different than manual landmark placement but that estimated skull shape covariation was correlated across methods. The addition of a preliminary genotype-specific registration step as part of a two-level procedure did not substantially improve on the accuracy of one-level automatic landmark placement. The landmarks with the lowest automatic landmark accuracy are found in locations with poor image registration alignment. The most serious outliers within morphometric analysis of automated landmarks displayed instances of stochastic image registration error that are likely representative of errors common when applying image registration methods to micro-computed tomography datasets that were initially collected with manual landmarking in mind. Additional efforts during specimen preparation and image acquisition can help reduce the number of registration errors and improve registration results. A reduction in skull shape variance estimates were noted for automated landmarking methods compared with manual landmarking. This partially reflects an underestimation of more extreme genotype shapes and loss of biological signal, but largely represents the fact that automated methods do not suffer from intra-observer landmarking error. For appropriate samples and research questions, our image registration-based automated landmarking method can eliminate the time required for manual landmarking and have a similar power to identify shape differences between inbred mouse genotypes.
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Affiliation(s)
| | - Jay Devine
- Department of Cell Biology and Anatomy, University of Calgary, Calgary, AB, Canada
| | - Benjamin C Darwin
- Mouse Imaging Centre, The Hospital for Sick Children, Toronto, ON, Canada
| | - Wei Liu
- Department of Cell Biology and Anatomy, University of Calgary, Calgary, AB, Canada
| | - Matthijs van Eede
- Mouse Imaging Centre, The Hospital for Sick Children, Toronto, ON, Canada
| | - R Mark Henkelman
- Mouse Imaging Centre, The Hospital for Sick Children, Toronto, ON, Canada.,Department of Medical Biophysics, University of Toronto, Toronto, ON, Canada
| | - Benedikt Hallgrimsson
- Department of Cell Biology and Anatomy, University of Calgary, Calgary, AB, Canada.,Alberta Children's Hospital Research Institute for Child and Maternal Health, University of Calgary, Calgary, AB, Canada.,The McCaig Institute for Bone and Joint Health, University of Calgary, Calgary, AB, Canada
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44
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Contrast-Enhanced MicroCT for Virtual 3D Anatomical Pathology of Biological Tissues: A Literature Review. CONTRAST MEDIA & MOLECULAR IMAGING 2019; 2019:8617406. [PMID: 30944550 PMCID: PMC6421764 DOI: 10.1155/2019/8617406] [Citation(s) in RCA: 44] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/02/2018] [Accepted: 02/07/2019] [Indexed: 11/17/2022]
Abstract
To date, the combination of histological sectioning, staining, and microscopic assessment of the 2D sections is still the golden standard for structural and compositional analysis of biological tissues. X-ray microfocus computed tomography (microCT) is an emerging 3D imaging technique with high potential for 3D structural analysis of biological tissues with a complex and heterogeneous 3D structure, such as the trabecular bone. However, its use has been mostly limited to mineralized tissues because of the inherently low X-ray absorption of soft tissues. To achieve sufficient X-ray attenuation, chemical compounds containing high atomic number elements that bind to soft tissues have been recently adopted as contrast agents (CAs) for contrast-enhanced microCT (CE-CT); this novel technique is very promising for quantitative "virtual" 3D anatomical pathology of both mineralized and soft biological tissues. In this paper, we provided a review of the advances in CE-CT since the very first reports on the technology to date. Perfusion CAs for in vivo imaging have not been discussed, as the focus of this review was on CAs that bind to the tissue of interest and that are, thus, used for ex vivo imaging of biological tissues. As CE-CT has mostly been applied for the characterization of musculoskeletal tissues, we have put specific emphasis on these tissues. Advantages and limitations of multiple CAs for different musculoskeletal tissues have been highlighted, and their reproducibility has been discussed. Additionally, the advantages of the "full" 3D CE-CT information have been pinpointed, and its importance for more detailed structural, spatial, and functional characterization of the tissues of interest has been shown. Finally, the remaining challenges that are still hampering a broader adoption of CE-CT have been highlighted, and suggestions have been made to move the field of CE-CT imaging one step further towards a standard accepted tool for quantitative virtual 3D anatomical pathology.
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45
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Behavioral and neuroanatomical approaches in models of neurodevelopmental disorders: opportunities for translation. Curr Opin Neurol 2019; 31:126-133. [PMID: 29493556 DOI: 10.1097/wco.0000000000000537] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
PURPOSE OF REVIEW This review highlights the invaluable contribution of in-vivo rodent models in dissecting the underlying neurobiology for numerous neurodevelopmental disorders. Currently, models are routinely generated with precision genomics and characterized for research on neurodevelopmental disorders. In order to impact translation, outcome measures that are translationally relevant are essential. This review emphasizes the importance of accurate neurobehavioral and anatomical analyses. RECENT FINDINGS Numerous well validated assays for testing alterations across behavioral domains with sensitivity and throughput have become important tools for studying the effects of genetic mutations on neurodevelopment. Recent work has highlighted relationships and links between behavioral outcomes and various anatomical metrics from neuroimaging via magnetic resonance. These readouts are biological markers and outcome measures for translational research and will be have important roles for genetic or pharmacologic intervention strategies. SUMMARY Combinatorial approaches that leverage translationally relevant behavior and neuroanatomy can be used to develop a platform for assessment of cutting edge preclinical models. Reliable, robust behavioral phenotypes in preclinical model systems, with clustering of brain disease will lead to well informed, precise biochemical mechanistic hypotheses. Ultimately, these steadfast workhorse techniques will accelerate the progress of developing and testing targeted treatments for multiple neurodevelopmental disorders.
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46
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Visualising the Cardiovascular System of Embryos of Biomedical Model Organisms with High Resolution Episcopic Microscopy (HREM). J Cardiovasc Dev Dis 2018; 5:jcdd5040058. [PMID: 30558275 PMCID: PMC6306920 DOI: 10.3390/jcdd5040058] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2018] [Revised: 12/09/2018] [Accepted: 12/11/2018] [Indexed: 12/17/2022] Open
Abstract
The article will briefly introduce the high-resolution episcopic microscopy (HREM) technique and will focus on its potential for researching cardiovascular development and remodelling in embryos of biomedical model organisms. It will demonstrate the capacity of HREM for analysing the cardiovascular system of normally developed and genetically or experimentally malformed zebrafish, frog, chick and mouse embryos in the context of the whole specimen and will exemplarily show the possibilities HREM offers for comprehensive visualisation of the vasculature of adult human skin. Finally, it will provide examples of the successful application of HREM for identifying cardiovascular malformations in genetically altered mouse embryos produced in the deciphering the mechanisms of developmental disorders (DMDD) program.
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47
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Brown JM, Horner NR, Lawson TN, Fiegel T, Greenaway S, Morgan H, Ring N, Santos L, Sneddon D, Teboul L, Vibert J, Yaikhom G, Westerberg H, Mallon AM. A bioimage informatics platform for high-throughput embryo phenotyping. Brief Bioinform 2018; 19:41-51. [PMID: 27742664 PMCID: PMC5862285 DOI: 10.1093/bib/bbw101] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2016] [Indexed: 11/13/2022] Open
Abstract
High-throughput phenotyping is a cornerstone of numerous functional genomics projects. In recent years, imaging screens have become increasingly important in understanding gene-phenotype relationships in studies of cells, tissues and whole organisms. Three-dimensional (3D) imaging has risen to prominence in the field of developmental biology for its ability to capture whole embryo morphology and gene expression, as exemplified by the International Mouse Phenotyping Consortium (IMPC). Large volumes of image data are being acquired by multiple institutions around the world that encompass a range of modalities, proprietary software and metadata. To facilitate robust downstream analysis, images and metadata must be standardized to account for these differences. As an open scientific enterprise, making the data readily accessible is essential so that members of biomedical and clinical research communities can study the images for themselves without the need for highly specialized software or technical expertise. In this article, we present a platform of software tools that facilitate the upload, analysis and dissemination of 3D images for the IMPC. Over 750 reconstructions from 80 embryonic lethal and subviable lines have been captured to date, all of which are openly accessible at mousephenotype.org. Although designed for the IMPC, all software is available under an open-source licence for others to use and develop further. Ongoing developments aim to increase throughput and improve the analysis and dissemination of image data. Furthermore, we aim to ensure that images are searchable so that users can locate relevant images associated with genes, phenotypes or human diseases of interest.
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Affiliation(s)
- James M Brown
- MRC Harwell Institute, Harwell Campus, Oxfordshire
- Corresponding author: James Brown, MRC Harwell Institute, Harwell Campus, Oxfordshire, OX11 0RD. Tel. +44-0-1235-841237; Fax: +44-0-1235-841172; E-mail:
| | | | | | - Tanja Fiegel
- MRC Harwell Institute, Harwell Campus, Oxfordshire
| | | | - Hugh Morgan
- MRC Harwell Institute, Harwell Campus, Oxfordshire
| | - Natalie Ring
- MRC Harwell Institute, Harwell Campus, Oxfordshire
| | - Luis Santos
- MRC Harwell Institute, Harwell Campus, Oxfordshire
| | | | - Lydia Teboul
- MRC Harwell Institute, Harwell Campus, Oxfordshire
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48
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Voronina VA, Harris FM, Schmahl J, Galligan C, Oristian D, Zamfirova R, Gong G, Bai Y, Fury W, Rajamani S, Walls JR, Poueymirou WT, Esau L, Gale NW, Auerbach W, Murphy AJ, Macdonald LE. Deletion of Adam6 in Mus musculus leads to male subfertility and deficits in sperm ascent into the oviduct. Biol Reprod 2018; 100:686-696. [DOI: 10.1093/biolre/ioy210] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2018] [Revised: 08/08/2018] [Accepted: 10/03/2018] [Indexed: 02/06/2023] Open
Affiliation(s)
| | - Faith M Harris
- Regeneron Pharmaceuticals, Inc., Tarrytown, New York, USA
| | | | - Caryn Galligan
- Regeneron Pharmaceuticals, Inc., Tarrytown, New York, USA
| | | | | | - Guochun Gong
- Regeneron Pharmaceuticals, Inc., Tarrytown, New York, USA
| | - Yu Bai
- Regeneron Pharmaceuticals, Inc., Tarrytown, New York, USA
| | - Wen Fury
- Regeneron Pharmaceuticals, Inc., Tarrytown, New York, USA
| | | | | | | | - Lakeisha Esau
- Regeneron Pharmaceuticals, Inc., Tarrytown, New York, USA
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49
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Brown SDM, Holmes CC, Mallon AM, Meehan TF, Smedley D, Wells S. High-throughput mouse phenomics for characterizing mammalian gene function. Nat Rev Genet 2018; 19:357-370. [PMID: 29626206 PMCID: PMC6582361 DOI: 10.1038/s41576-018-0005-2] [Citation(s) in RCA: 63] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
We are entering a new era of mouse phenomics, driven by large-scale and economical generation of mouse mutants coupled with increasingly sophisticated and comprehensive phenotyping. These studies are generating large, multidimensional gene-phenotype data sets, which are shedding new light on the mammalian genome landscape and revealing many hitherto unknown features of mammalian gene function. Moreover, these phenome resources provide a wealth of disease models and can be integrated with human genomics data as a powerful approach for the interpretation of human genetic variation and its relationship to disease. In the future, the development of novel phenotyping platforms allied to improved computational approaches, including machine learning, for the analysis of phenotype data will continue to enhance our ability to develop a comprehensive and powerful model of mammalian gene-phenotype space.
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Affiliation(s)
| | - Chris C Holmes
- Nuffield Department of Medicine and Department of Statistics, University of Oxford, Oxford, UK.
| | | | - Terrence F Meehan
- European Molecular Biology Laboratory - European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK.
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50
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Boughner JC, van Eede MC, Spring S, Yu LX, Rostampour N, Henkelman RM. P63 expression plays a role in developmental rate, embryo size, and local morphogenesis. Dev Dyn 2018; 247:779-787. [DOI: 10.1002/dvdy.24622] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2017] [Revised: 01/23/2018] [Accepted: 01/30/2018] [Indexed: 12/16/2022] Open
Affiliation(s)
- Julia C. Boughner
- Department of Anatomy & Cell Biology, College of Medicine; University of Saskatchewan; Saskatoon Saskatchewan Canada
| | | | - Shoshana Spring
- Mouse Imaging Centre; Hospital for Sick Children; Toronto Ontario Canada
| | - Lisa X. Yu
- Mouse Imaging Centre; Hospital for Sick Children; Toronto Ontario Canada
| | - Nasim Rostampour
- Department of Anatomy & Cell Biology, College of Medicine; University of Saskatchewan; Saskatoon Saskatchewan Canada
| | - R. Mark Henkelman
- Mouse Imaging Centre; Hospital for Sick Children; Toronto Ontario Canada
- Department of Medical Biophysics; University of Toronto; Toronto Ontario Canada
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