Browsing by Subject "3D imaging"

Now showing 1 - 4 of 4
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    3D Mapping Reveals a Complex and Transient Interstitial Matrix During Murine Kidney Development
    (Wolters Kluwer, 2021) Lipp, Sarah N.; Jacobson, Kathryn R.; Hains, David S.; Schwarderer, Andrew L.; Calve, Sarah; Pediatrics, School of Medicine
    ESKD is increasing in incidence and a limited number of organs are available for transplantation. Therefore, researchers have focused on understanding how cellular signaling influences kidney development to expand strategies to rebuild a kidney. However, the extracellular matrix (ECM), another critical component that biomechanically regulates nephrogenesis, has been largely neglected. Proteomics and 3D imaging of the murine kidney resolved previously undescribed dynamics of the interstitial matrix in the cortex and corticomedullary junction during development. Combined with cells and growth factors, scaffolds modeled after the composition and organization of the developmental ECM have the potential to improve engineered models of the kidney.
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    Sensory innervation in the prostate and a role for calcitonin gene-related peptide in prostatic epithelial proliferation
    (Frontiers Media, 2024-12-18) Xia, Hanyu; Jerde, Travis J.; Fehrenbacher, Jill C.; Pharmacology and Toxicology, School of Medicine
    Introduction: The prostate is densely innervated like many visceral organs and glands. However, studies to date have focused on sympathetic and parasympathetic nerves and little attention has been given to the presence or function of sensory nerves in the prostate. Recent studies have highlighted a role for sensory nerves beyond perception of noxious stimuli, as anterograde release of neuropeptides from sensory nerves can affect vascular tone and local immune responses. Methods: To identify the degree of sensory innervation in the prostate, we utilized state-of-the-art tissue clearing and microscopy to visualize sensory innervation in the different lobes of the mouse prostate. To determine whether sensory nerves have a role in regulating proliferation within the prostate, we used an intersectional genetic and toxin approach to ablate peptidergic sensory nerves systemically. Results: We found that sensory neurons are abundant in the prostate both in nerve bundles along the vasculature and as independent nerve fibers wrapped around prostatic acini in a net-like fashion. In addition to the dense innervation of the prostate, we found that Calca haploinsufficiency, the genotype control for our intersectional ablation model, results in a diminished level of Ki67 staining in the stromal compartment of the dorsal lobe and a diminishing Ki67 trend in other lobes. Discussion: These findings suggest that sensory neurons might have developmental or homeostatic effects within the prostate. Further studies are warranted to assess the role of sensory neurons and the sensory neuropeptides on prostatic development and on proliferation in the presence of pro-inflammatory stimuli such as bacterial infection or tumor cells.
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    Simultaneous visualisation of calcified bone microstructure and intracortical vasculature using synchrotron X-ray phase contrast-enhanced tomography
    (Nature Publishing group, 2017-10-16) Núñez, Juan A.; Goring, Alice; Hesse, Eric; Thurner, Philipp J.; Schneider, Philipp; Clarkin, Claire E.; Anatomy and Cell Biology, School of Medicine
    3D imaging of the bone vasculature is of key importance in the understanding of skeletal disease. As blood vessels in bone are deeply encased in the calcified matrix, imaging techniques that are applicable to soft tissues are generally difficult or impossible to apply to the skeleton. While canals in cortical bone can readily be identified and characterised in X-ray computed tomographic data in 3D, the soft tissue comprising blood vessels that are putatively contained within the canal structures does not provide sufficient image contrast necessary for image segmentation. Here, we report an approach that allows for rapid, simultaneous visualisation of calcified bone tissue and the vasculature within the calcified bone matrix. Using synchrotron X-ray phase contrast-enhanced tomography we show exemplar data with intracortical capillaries uncovered at sub-micrometre level without the need for any staining or contrast agent. Using the tibiofibular junction of 15 week-old C57BL/6 mice post mortem, we show the bone cortical porosity simultaneously along with the soft tissue comprising the vasculature. Validation with histology confirms that we can resolve individual capillaries. This imaging approach could be easily applied to other skeletal sites and transgenic models, and could improve our understanding of the role the vasculature plays in bone disease.
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    Tissue Cytometry With Machine Learning in Kidney: From Small Specimens to Big Data
    (Frontiers, 2022) El-Achkar, Tarek M.; Winfree, Seth; Talukder, Niloy; Barwinska, Daria; Ferkowicz, Michael J.; Al Hasan, Mohammad; Computer and Information Science, School of Science
    Advances in cellular and molecular interrogation of kidney tissue have ushered a new era of understanding the pathogenesis of kidney disease and potentially identifying molecular targets for therapeutic intervention. Classifying cells and identifying subtypes and states induced by injury is a foundational task in this context. High resolution Imaging-based approaches such as large-scale fluorescence 3D imaging offer significant advantages because they allow preservation of tissue architecture and provide a definition of the spatial context of each cell. We recently described the Volumetric Tissue Exploration and Analysis cytometry tool which enables an interactive analysis, quantitation and semiautomated classification of labeled cells in 3D image volumes. We also established and demonstrated an imaging-based classification using deep learning of cells in intact tissue using 3D nuclear staining with 4',6-diamidino-2-phenylindole (DAPI). In this mini-review, we will discuss recent advancements in analyzing 3D imaging of kidney tissue, and how combining machine learning with cytometry is a powerful approach to leverage the depth of content provided by high resolution imaging into a highly informative analytical output. Therefore, imaging a small tissue specimen will yield big scale data that will enable cell classification in a spatial context and provide novel insights on pathological changes induced by kidney disease.