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Nicolas N, Dinet V, Roux E. 3D imaging and morphometric descriptors of vascular networks on optically cleared organs. iScience 2023; 26:108007. [PMID: 37810224 PMCID: PMC10551892 DOI: 10.1016/j.isci.2023.108007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/10/2023] Open
Abstract
The vascular system is a multi-scale network whose functionality depends on its structure, and for which structural alterations can be linked to pathological shifts. Though biologists use multiple 3D imaging techniques to visualize vascular networks, the 3D image processing methodologies remain sources of biases, and the extraction of quantitative morphometric descriptors remains flawed. The article, first, reviews the current 3D image processing methodologies, and morphometric descriptors of vascular network images mainly obtained by light-sheet microscopy on optically cleared organs, found in the literature. Second, it proposes operator-independent segmentation and skeletonization methodologies using the freeware ImageJ. Third, it gives more extractable network-level (density, connectivity, fractal dimension) and segment-level (length, diameter, tortuosity) 3D morphometric descriptors and how to statistically analyze them. Thus, it can serve as a guideline for biologists using 3D imaging techniques of vascular networks, allowing the production of more comparable studies in the future.
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Affiliation(s)
- Nabil Nicolas
- University Bordeaux, INSERM, Biologie des maladies cardiovasculaires, U1034, F-33600 Pessac, France
| | - Virginie Dinet
- University Bordeaux, INSERM, Biologie des maladies cardiovasculaires, U1034, F-33600 Pessac, France
| | - Etienne Roux
- University Bordeaux, INSERM, Biologie des maladies cardiovasculaires, U1034, F-33600 Pessac, France
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Nicolas N, Roux E. 3D Imaging and Quantitative Characterization of Mouse Capillary Coronary Network Architecture. BIOLOGY 2021; 10:biology10040306. [PMID: 33917130 PMCID: PMC8067837 DOI: 10.3390/biology10040306] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/01/2021] [Revised: 04/01/2021] [Accepted: 04/04/2021] [Indexed: 11/23/2022]
Abstract
Simple Summary The cardiovascular system is composed of two physically and functionally linked parts, the heart and the vascular network, composed of the arteries, capillaries, and veins. In this system, the heart maintains the blood flow, including its own through the coronary vascular network, bringing oxygen and nutrients required for its activity. Microvascularization constitutes the distal part of this network and is composed of small vessels, i.e., arterioles and capillaries. Coronary microvascular diseases are associated with the development of cardiac dysfunction. Identification of the coronary microvascular network structure is hence of critical importance for the understanding of heart diseases. The aim of our study was to establish an accessible methodology for 3D imaging and 3D processing to quantitatively characterize the capillary coronary network architecture in mice, a species largely used as an animal model of cardiac failure. This study proposes a standardized methodology for 3D image processing that allows the quantification of the 3D capillary architecture. Based on an open source software, the whole process is easily accessible for biologists. It is hence useful for the study of cardiovascular diseases and the development of future therapies. Abstract Characterization of the cardiac capillary network structure is of critical importance to understand the normal coronary functional properties and coronary microvascular diseases. The aim of our study was to establish an accessible methodology for 3D imaging and 3D processing to quantitatively characterize the capillary coronary network architecture in mice. Experiments were done on C57BL/6J mice. 3D imaging was performed by light sheet microscopy and confocal microscopy on iDISCO+ optical cleared hearts after labelling of the capillary endothelium by lectin injection. 3D images were processed with the open source software ImageJ. Non-visual image segmentation was based of the frequency distribution of the voxel greyscale values, followed by skeletonization and distance mapping. Capillary networks in left and right ventricles and septum were characterized by the volume network density, the fractal dimension, the number of segments and nodes and their ratio, the total network length, and the average length, diameter, and tortuosity of the segments. Scale-dependent parameter values can be impacted by the resolution limit of the 3D imaging technique. The proposed standardized methodology for 3D image processing is easily accessible for a biologist in terms of investment and difficulty level, and allows the quantification of the 3D capillary architecture and its statistical comparison in different conditions.
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Šaherl LK, Gosak M, Rakuša M. Identification and quantitative analysis of branching networks of the posterior intercostal arteries. Anat Sci Int 2020; 95:508-515. [PMID: 32435892 DOI: 10.1007/s12565-020-00548-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2019] [Accepted: 04/30/2020] [Indexed: 02/03/2023]
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Ellestad LE, Cogburn LA, Simon J, Le Bihan-Duval E, Aggrey SE, Byerly MS, Duclos MJ, Porter TE. Transcriptional profiling and pathway analysis reveal differences in pituitary gland function, morphology, and vascularization in chickens genetically selected for high or low body weight. BMC Genomics 2019; 20:316. [PMID: 31023219 PMCID: PMC6482517 DOI: 10.1186/s12864-019-5670-9] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2018] [Accepted: 04/08/2019] [Indexed: 12/15/2022] Open
Abstract
Background Though intensive genetic selection has led to extraordinary advances in growth rate and feed efficiency in production of meat-type chickens, endocrine processes controlling these traits are still poorly understood. The anterior pituitary gland is a central component of the neuroendocrine system and plays a key role in regulating important physiological processes that directly impact broiler production efficiency, though how differences in pituitary gland function contribute to various growth and body composition phenotypes is not fully understood. Results Global anterior pituitary gene expression was evaluated on post-hatch weeks 1, 3, 5, and 7 in male broiler chickens selected for high (HG) or low (LG) growth. Differentially expressed genes (DEGs) were analyzed with gene ontology categorization, self-organizing maps, gene interaction network determination, and upstream regulator identification to uncover novel pituitary genes and pathways contributing to differences in growth and body composition. A total of 263 genes were differentially expressed between HG and LG anterior pituitary glands (P ≤ 0.05 for genetic line-by-age interaction or main effect of line; ≥1.6-fold difference between lines), including genes encoding four anterior pituitary hormones. Genes involved in signal transduction, transcriptional regulation, and vesicle-mediated transport were differentially expressed and are predicted to influence expression and secretion of pituitary hormones. DEGs involved in immune regulation provide evidence that inflammation and response to cellular stressors may compromise pituitary function in LG birds, affecting their ability to adequately produce pituitary hormones. Many DEGs were also predicted to function in processes that regulate organ morphology and angiogenesis, suggesting pituitary gland structure differs between the divergently selected lines. Conclusions The large number of DEGs within the anterior pituitary gland of birds selected for high or low body weight highlights the importance of this gland in regulating economically important traits such as growth and body composition in broiler chickens. Intracellular signaling, transcriptional regulation, and membrane trafficking are important cellular processes contributing to proper hormone production and secretion. The data also suggest that pituitary function is intimately tied to structure, and organization of the gland could influence hypothalamic and systemic metabolic inputs and delivery of hormones regulating growth and metabolism into peripheral circulation. Electronic supplementary material The online version of this article (10.1186/s12864-019-5670-9) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Laura E Ellestad
- Department of Poultry Science, University of Georgia, Athens, GA, 30602, USA.,Department of Animal and Avian Sciences, University of Maryland, College Park, MD, 20742, USA
| | - Larry A Cogburn
- Department of Animal and Food Sciences, University of Delaware, Newark, DE, 19716, USA
| | - Jean Simon
- Biologie des Oiseaux et Aviculture, Institut National de la Recherche Agronomique (INRA), Université de Tours, UR83 Recherches Avicoles, 37380, Nouzilly, France
| | - Elisabeth Le Bihan-Duval
- Biologie des Oiseaux et Aviculture, Institut National de la Recherche Agronomique (INRA), Université de Tours, UR83 Recherches Avicoles, 37380, Nouzilly, France
| | - Samuel E Aggrey
- Department of Poultry Science, University of Georgia, Athens, GA, 30602, USA
| | - Mardi S Byerly
- Department of Animal and Avian Sciences, University of Maryland, College Park, MD, 20742, USA
| | - Michel J Duclos
- Biologie des Oiseaux et Aviculture, Institut National de la Recherche Agronomique (INRA), Université de Tours, UR83 Recherches Avicoles, 37380, Nouzilly, France
| | - Tom E Porter
- Department of Animal and Avian Sciences, University of Maryland, College Park, MD, 20742, USA.
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Gosak M, Markovič R, Dolenšek J, Slak Rupnik M, Marhl M, Stožer A, Perc M. Network science of biological systems at different scales: A review. Phys Life Rev 2018; 24:118-135. [DOI: 10.1016/j.plrev.2017.11.003] [Citation(s) in RCA: 174] [Impact Index Per Article: 24.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2017] [Revised: 10/13/2017] [Accepted: 10/15/2017] [Indexed: 12/20/2022]
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Bragdon B, Lam S, Aly S, Femia A, Clark A, Hussein A, Morgan EF, Gerstenfeld LC. Earliest phases of chondrogenesis are dependent upon angiogenesis during ectopic bone formation in mice. Bone 2017; 101:49-61. [PMID: 28412469 PMCID: PMC5500242 DOI: 10.1016/j.bone.2017.04.002] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/13/2017] [Revised: 04/09/2017] [Accepted: 04/11/2017] [Indexed: 01/12/2023]
Abstract
Endochondral ossification is the process where cartilage forms prior to ossification and in which new bone forms during both fracture healing and ectopic bone formation. Transitioning to ossification is a highly coordinated process between hypertrophic chondrocytes, vascular endothelial cells, osteoblasts and osteoclasts. A critical biological process that is central to the interactions of these various cell types is angiogenesis. Although it is well established that angiogenesis is crucial for fracture repair, less is known pertaining to the role of angiogenesis in ectopic bone formation. Furthermore, fracture repair models are complicated by extensive trauma, subsequent inflammatory responses and concurrent repair processes in multiple tissues. In order to more definitively characterize the relationship between angiogenesis and postnatal endochondral ossification, a model of ectopic bone formation was used. Human demineralized bone matrix (DBM) was implanted in immune-deficient mice (rag null (B6.129S7-Rag1tm1/MOM/J)) to induce ectopic bone. Inhibition of angiogenesis with either a small molecule (TNP-470) or a targeted biological (Vascular Endothelial Growth Factor Receptor type 2 [VEGFR2] blocking antibody) prevented ectopic bone formation by 83% and 77%, respectively. Most striking was that the progression of chondrogenesis was halted during very early phases of chondrocyte differentiation between condensation and prehypertrophy (TNP-470) or the proliferative phase (VEGFR2 blockade) prior to hypertrophy, while osteoclast recruitment and resorption were almost completely inhibited. Our results demonstrate angiogenesis plays a developmental role in endochondral bone formation at a much earlier phase of chondrogenesis than suggested by prior findings.
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Affiliation(s)
- Beth Bragdon
- Department of Orthopaedic Surgery, Boston University School of Medicine, Boston, MA 02118, USA.
| | - Stephanie Lam
- Department of Orthopaedic Surgery, Boston University School of Medicine, Boston, MA 02118, USA
| | - Sherif Aly
- Department of Orthopaedic Surgery, Boston University School of Medicine, Boston, MA 02118, USA
| | - Alexandra Femia
- Department of Orthopaedic Surgery, Boston University School of Medicine, Boston, MA 02118, USA
| | - Abigail Clark
- Department of Orthopaedic Surgery, Boston University School of Medicine, Boston, MA 02118, USA
| | - Amira Hussein
- Department of Orthopaedic Surgery, Boston University School of Medicine, Boston, MA 02118, USA
| | - Elise F Morgan
- Department of Mechanical Engineering, Boston University College of Engineering, Boston, MA 02215, USA
| | - Louis C Gerstenfeld
- Department of Orthopaedic Surgery, Boston University School of Medicine, Boston, MA 02118, USA
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