Open Access Highly Accessed Research article

Resolution of the three dimensional structure of components of the glomerular filtration barrier

Kenton P Arkill14*, Klaus Qvortrup2, Tobias Starborg3, Judith M Mantell4, Carlo Knupp5, C Charles Michel6, Steve J Harper7, Andy HJ Salmon7, John M Squire7, Dave O Bates8 and Chris R Neal7

Author Affiliations

1 Nanoscale Physics Research Laboratories, School of Physics and Astronomy, University of Birmingham, Birmingham, UK

2 CFIM, Pannum Institute, Copenhagen, Denmark

3 Wellcome Trust Centre for Cell Matrix Research, Faculty of Life Sciences, University of Manchester, Manchester, UK

4 Wolfson Bioimaging Facility and School of Biochemistry, University of Bristol, Bristol, BS8 1TD, UK

5 Optometry and Vision Sciences, Cardiff University, Cardiff, UK

6 Bioengineering, Imperial College, London, UK

7 School of Physiology and Pharmacology, University of Bristol, Bristol, UK

8 Cancer Biology, Division of Oncology, School of Medicine, University of Nottingham, Queen’s Medical Centre, Nottingham NG2 7UH, UK

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BMC Nephrology 2014, 15:24  doi:10.1186/1471-2369-15-24

Published: 1 February 2014



The human glomerulus is the primary filtration unit of the kidney, and contains the Glomerular Filtration Barrier (GFB). The GFB had been thought to comprise 3 layers – the endothelium, the basement membrane and the podocyte foot processes. However, recent studies have suggested that at least two additional layers contribute to the function of the GFB, the endothelial glycocalyx on the vascular side, and the sub-podocyte space on the urinary side. To investigate the structure of these additional layers is difficult as it requires three-dimensional reconstruction of delicate sub-microscopic (<1 μm) cellular and extracellular elements.


Here we have combined three different advanced electron microscopic techniques that cover multiple orders of magnitude of volume sampled, with a novel staining methodology (Lanthanum Dysprosium Glycosaminoglycan adhesion, or LaDy GAGa), to determine the structural basis of these two additional layers. Serial Block Face Scanning Electron Microscopy (SBF-SEM) was used to generate a 3-D image stack with a volume of a 5.3 x 105 μm3 volume of a whole kidney glomerulus (13% of glomerular volume). Secondly, Focused Ion Beam milling Scanning Electron Microscopy (FIB-SEM) was used to image a filtration region (48 μm3 volume). Lastly Transmission Electron Tomography (Tom-TEM) was performed on a 0.3 μm3 volume to identify the fine structure of the glycocalyx.


Tom-TEM clearly showed 20 nm fibre spacing in the glycocalyx, within a limited field of view. FIB-SEM demonstrated, in a far greater field of view, how the glycocalyx structure related to fenestrations and the filtration slits, though without the resolution of TomTEM. SBF-SEM was able to determine the extent of the sub-podocyte space and glycocalyx coverage, without additional heavy metal staining. Neither SBF- nor FIB-SEM suffered the anisotropic shrinkage under the electron beam that is seen with Tom-TEM.


These images demonstrate that the three dimensional structure of the GFB can be imaged, and investigated from the whole glomerulus to the fine structure of the glycocalyx using three dimensional electron microscopy techniques. This should allow the identification of structural features regulating physiology, and their disruption in pathological states, aiding the understanding of kidney disease.

Urinary space; Podocyte; Glycocalyx; GFB; Tomography; Serial block face (SBF); Focused ion beam (FIB); Electron microscopy; Glomerulus; 3D reconstruction