A cell-centered database for electron tomographic data

Martone, Maryann E.; Gupta, Amarnath; Wong, Mona; Qian, Xufei; Sosinsky, Gina E.; Ludäscher, Bertram; Ellisman, Mark H.

doi:10.1016/s1047-8477(02)00006-0

Cited by 106 publications

(65 citation statements)

References 46 publications

(56 reference statements)

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“…As the necessarily limited size of figure 1B makes it difficult for the reader to evaluate immunostaining in detail, high resolution images of several parasagittal sections stained for PMCA1a were created using an automatic mosaic acquisition and processing system (Chow et al, 2006). These large-scale mosaics can be browsed through the CellCentered Database (Martone et al, 2002;Martone et al, 2008) at http://ccdb.ucsd.edu by selecting project ID:P2061 (record ID: MP7266, MP7351).…”

Section: Resultsmentioning

confidence: 99%

Cellular and subcellular localization of the neuron‐specific plasma membrane calcium ATPase PMCA1a in the rat brain

Kenyon

Bushong

Mauer

et al. 2010

J of Comparative Neurology

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Regulation of intracellular calcium is crucial both for proper neuronal function and survival. By coupling ATP hydrolysis with Ca 2+ extrusion from the cell, the plasma membrane calciumdependent ATPases (PMCAs) play an essential role in controlling intracellular calcium levels in neurons. In contrast to PMCA2 and PMCA3, which are expressed in significant levels only in the brain and a few other tissues, PMCA1 is ubiquitously distributed, and is thus widely believed to play a "housekeeping" function in mammalian cells. Whereas the PMCA1b splice variant is predominant in most tissues, an alternative variant, PMCA1a, is the major form of PMCA1 in the adult brain. Here, we use immunohistochemistry to analyze the cellular and subcellular distribution of PMCA1a in the brain. We show that PMCA1a is not ubiquitously expressed, but rather is confined to neurons, where it concentrates in the plasma membrane of somata, dendrites and spines. Thus, rather than serving a general "housekeeping" function, our data suggest that PMCA1a is a calcium pump specialized for neurons, where it may contribute to the modulation of somatic and dendritic Ca 2+ transients.Keywords calcium extrusion; calcium pump; immunohistochemistry; Cell Centered Database Transient changes in the intracellular concentration of free calcium ([Ca 2+ ] i ) act to regulate or control numerous neuronal processes ranging from electrical excitability and neurotransmitter release (Neher and Sakaba, 2008, Spitzer et al., 2002), to dendritic integration and gene expression (Cohen and Greenberg, 2008, Larkum andNevian, 2008). This versatility requires an elaborate "toolkit" of proteins to control the influx, efflux, and buffering of Ca 2+ within and between cellular compartments, creating signals with widely different spatial and temporal profiles (Berridge et al., 2000;Friel and Chiel, 2008 (Berliocchi et al., 2005). Perturbation of Ca 2+ homeostasis is implicated in a variety of neuropathologies including stroke and Alzheimer's disease (Bezprozvanny and Mattson, 2008;Mattson, 2007). Not surprisingly, neurons use multiple strategies to deal with Ca 2+ loads, including buffers (Schwaller et al., 2002), intracellular sinks (Verkhratsky, 2002), and membrane extrusion systems (Lytton, 2007;Strehler, 1990). As the sole high-affinity Ca 2+ extrusion mechanism in the plasma membrane, the plasma membrane Ca 2+ ATPases (PMCAs) play a key role in regulating [Ca 2+ ] i (Di Leva et al., 2008).Mammals express four isoforms of PMCA, encoded by four different genes (ATP2B1-4 in humans). The transcripts of these genes are subject to developmental and tissue-specific alternative splicing, resulting altogether in over 20 PMCA variants (Strehler and Zacharias, 2001). In vitro studies show that each isoform differs in its kinetics and affinity for Ca 2+ and calmodulin. However, availability of calmodulin is but one of the factors that regulate PMCA activity in vivo. The isoforms also are differentially regulated by phosphorylation (e.g., via protein kinases A and C), by prote...

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Section: Resultsmentioning

confidence: 99%

Cellular and subcellular localization of the neuron‐specific plasma membrane calcium ATPase PMCA1a in the rat brain

Kenyon

Bushong

Mauer

et al. 2010

J of Comparative Neurology

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“…It was one of the first web databases devoted to the then emerging technique of electron tomography [18,19]. The data are released together with application-specific validation performed for each antibody, including immunohistochemisty, Western blot analysis and, for a large fraction, a protein array assay and immunofluorescent based confocal microscopy.…”

Section: Cell Centered Database Tmmentioning

confidence: 99%

Public Health and Epidemiological Databases for the Enhancement of Medical Education

Jamal

Siddiqui

Alzohairy

et al. 2015

OJPHI

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The collaboration of public health education and information technology has made patient care safer and more reliable than before. Nurses and doctors use handheld computers to record a patient's medical history and check that they are administering the correct treatment. Fortunately Public Health Informatics (PHI) is the intersecting point of technology and public health. Therefore, the inclusion of online medical and epidemiology databases in the course curriculum of budding medical professionals and postgraduate students would be beneficial in enhancing the quality of health care, extensive epidemiological research, health education, health policies, health planning and consumer satisfaction as well. The purpose of this article is to discuss and provide introduction of various databases which have huge information and it could be used to enhance the public health education.

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“…The volumes used for the experiments were provided by the National Center for Microscopy and Imaging Research (NCMIR) from their Cell-Centered Database (Martone et al, 2002(Martone et al, , 2003(Martone et al, , 2008 and are part of a collection of 3D reconstructions. Four images, which demonstrate typical challenging features of EMT, were utilized for both algorithmic parameter optimization and testing.…”

Section: Data Setmentioning

confidence: 99%

Computerized detection and segmentation of mitochondria on electron microscope images

Mumcuoglu

Hassanpour

Tasel

et al. 2012

Journal of Microscopy

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SummaryMitochondrial function plays an important role in the regulation of cellular life and death, including disease states. Disturbance in mitochondrial function and distribution can be accompanied by significant morphological alterations. Electron microscopy tomography (EMT) is a powerful technique to study the 3D structure of mitochondria, but the automatic detection and segmentation of mitochondria in EMT volumes has been challenging due to the presence of subcellular structures and imaging artifacts. Therefore, the interpretation, measurement and analysis of mitochondrial distribution and features have been time consuming, and development of specialized software tools is very important for high-throughput analyses needed to expedite the myriad studies on cellular events. Typically, mitochondrial EMT volumes are segmented manually using special software tools. Automatic contour extraction on large images with multiple mitochondria and many other subcellular structures is still an unaddressed problem. The purpose of this work is to develop computer algorithms to detect and segment both fully and partially seen mitochondria on electron microscopy images. The detection method relies on mitochondria's approximately elliptical shape and double membrane boundary. Initial detection results are first refined using active contours. Then, our seed point selection method automatically selects reliable seed points along the contour, and segmentation is finalized by automatically incorporating a live-wire graph search algorithm between these seed points. In our evaluations on four images containing multiple mitochondria, 52 ellipses are detected among which 42

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A cell-centered database for electron tomographic data

Cited by 106 publications

References 46 publications

Cellular and subcellular localization of the neuron‐specific plasma membrane calcium ATPase PMCA1a in the rat brain

Cellular and subcellular localization of the neuron‐specific plasma membrane calcium ATPase PMCA1a in the rat brain

Public Health and Epidemiological Databases for the Enhancement of Medical Education

Computerized detection and segmentation of mitochondria on electron microscope images

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