Biology subjects

Leapman, R. D.

Publications and source records attributed to Leapman, R. D..

4 recordsLinked to original sources

bioRxiv2020

Dense cellular segmentation using 2D-3D neural network ensembles for electron microscopy

Cell biologists can now build 3D models from segmentations of electron microscopy (EM) images, but accurate manual segmentation of densely-packed organelles across gigavoxel image volumes is infeasible. Here, we introduce 2D-3D neural network ensembles that produce dense cellular segmentations at scale, with accuracy levels that outperform baseline methods and approach those of human annotators.

microbiology↗

bioRxiv2019

Quantitative method for estimating stain density in electron microscopy of conventionally prepared biological specimens

Stain density is an important parameter for optimizing the quality of ultrastructural data obtained from several types of 3D electron microscopy techniques, including serial block-face electron microscopy (SBEM), and focused ion beam scanning electron microscopy (FIB-SEM). Here, we show how some straightforward measurements in the TEM can be used to determine the stain density based on a simple expression that we derive. Numbers of stain atoms per unit volume are determined from the measured ratio of the bright-field intensities from regions of the specimen that contain both pure embedding material and the embedded biological structures of interest. The determination only requires knowledge of the section thickness, which can either be estimated from the microtome setting, or from low-dose electron tomography, and the elastic scattering cross section for the heavy atoms used to stain the specimen. The method is tested on specimens of embedded blood platelets, brain tissue, and liver tissue.

biophysics↗

bioRxiv2019

Use of dual electron probes reveals role of ferritin in erythropoiesis

Much is known about the finely regulated process of mammalian erythropoiesis that occurs in the bone marrow, whereby erythropoietic stem cells undergo terminal differentiation accompanied by enormous morphological changes to generate highly functional specialized red blood cells. However, a crucial step in erythropoiesis, the labile iron pool and its transport to mitochondria for heme production, is not well understood1. We apply a dual 3D imaging and spectroscopic technique, based on scanned electron probes, to measure distributions of ferritin iron-storage protein in ex vivo human erythropoietic stem cells, and to determine how those distributions change during terminal differentiation. After seven days of differentiation, the cells display a highly specialized architecture of organelles with anchored clustering of mitochondria and massive accumulation of Fe3+ in loaded ferritin cores localized to lysosomal storage depots, providing an iron source for heme production. Macrophages are not present in our ex vivo cultures, so they cannot be the source of the ferritin2. We suggest that lysosomal iron depots are required by developing reticulocytes while terminally differentiating and continuing to produce heme and globin, which assemble and concentrate to fill the cytoplasm after much of the cellular machinery is expelled.

cell biology↗

bioRxiv2019

Determination of secretory granule maturation times in pancreatic islet beta-cells by serial block face scanning electron microscopy

It is shown how serial block-face electron microscopy (SBEM) of insulin-secreting beta cells in wild-type mouse pancreatic islets of Langerhans can be used to determine maturation times of secretory granules. Although SBEM captures the beta cell structure at a snapshot in time, the observed ultrastructure can be considered representative of a dynamic equilibrium state of the cells since the pancreatic islets are maintained in culture in approximate homeostasis. It is found that 7.2{+/-}1.2% ({+/-}st. dev.) of the beta cell volume is composed of secretory granule dense-cores exhibiting angular shapes surrounded by wide (typically {gtrsim}100 nm) electron-lucent halos. These organelles are identified as mature granules that store insulin for regulated release through the plasma membrane, with a release time of 96{+/-}12 hours, as previously obtained from pulsed 35S-radiolabeling of cysteine and methionine. Analysis of beta cell 3D volumes reveals a subpopulation of secretory organelles without electron-lucent halos, identified as immature secretory granules. Another subpopulation of secretory granules is found with thin (typically [lsim]30 nm) electron-lucent halos, which are attributed to immature granules that are transforming from proinsulin to insulin by action of prohormone convertases. From the volume ratio of proinsulin in the immature granules to insulin in the mature granules, we estimate that the newly formed immature granules remain in morphologically-defined immature states for an average time of 135{+/-}14 minutes, and the immature transforming granules for an average time of 130{+/-}17 minutes.

biophysics↗