Computational biology promises to offer advanced simulations cellular environment so that more personalized care and diagnosis may be provided in real time. Heart failure is still a leading cause of death in the US and around the world. Scientists at UCSD have collaborated in a new study just published in the Journal of Cell Science that yielded detailed information on the subcellular anatomy in a mouse model of heart failure. Subcellular anatomy is considered to be important in calcium regulation, and its variation over time may hold clues to the progression of heart diseases. Hoshijima and colleagues (1) at the Neurosciences department, UCSD, used a combination of light microscopy and electron microscopy to provide a high definition image of the subcellular organelles such as junctional sarcoplasmic reticulum (jSR), T-tubules and mitochondria, and how they form an intricate membrane system inside the cell. This study could change how scientists think about these organelles, and the regulatory molecules such as ryanodine receptors (RyR), L-type calcium channels, are distributed in the cell. Such detailed geometric studies are important to the development of realistic models for computational studies that may help researchers, and eventually physicians, to better understand the progression of heart diseases.
The challenge in getting accurate subcellular structures and mathematical models, known as meshes, to represent them, is huge. A major obstacle is that many of the subcellular structures have dimensions at or below the diffraction limit of the light microscopy (LM) or beyond the general view field of conventional electron microscopy (EM). Through the use of image pre-processing and tracking capabilities of software packages including GAMer (Geometry-preserving Adaptive MeshER) (2), IMOD (3), and TxBR (Transform Based Back-Projection and Bundle Adjustment) (4), the availability of these high definition images allow the reconstruction of these organelles in 3D through a process called tomographic reconstruction (Figure 1).
These highly detailed 3D measurements indicated that the dyadic clefts, small intermembrance space between the T-tubules and jSR are polymorphic and occupy a much smaller volume than previously reported, almost an order of magnitude smaller. The estimated distance between nearest dyadic clefts is also an order of magnitude smaller. A possible connection between mitochondria and Ca2+ signaling is suggested with the observation of “tethers” or “bridges” between mitochondria and jSR. At the molecular level, the quantity of RyR tetramers is estimated to be about 8 for an average dyadic cleft observed in mice. The heterogeneity in RyR clusters or single units could offer explanations for the quantal nature of calcium sparks, the measurable changes of calcium concentration during cellular events.
With these advanced 3D imaging data, more accurate mesoscale simulations possible to better understand the local control of calcium dynamics in cardiac myocytes. Tools from NBCR such as SMOL (5) and new software under development (6) will be able to take advantage of these advanced geometric studies.
GAMer, TxBR, SMOL are all supported by funding from the National Center for Research Resources (NCRR) to the National Biomedical Computation Resource (NBCR), and are available for download from http://tools.nbcr.net.
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Figure 1. The 3-D mesh models of polymorphicT-tubules (green), jSR (yellow), and mitochondria (magenta) are shown within the 2-D image of a middle slice of the tomographic volume of mouse myocardium through electron microscopy. The bar in the lower left indicates the length scale of 1μm.
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References:
1. Hayashi, T., Martone, M. E., Yu, Z., Thor, A., Doi, M., Holst, M., Ellisman, M. H. & Hoshijima, M. (2009). Three-dimensional electron microscopy reveals new details of membrane systems for calcium signaling in the heart. J. Cell. Sci.
2. Yu, Z. Y., Holst, M. J. & McCammon, J. A. (2008). High-fidelity geometric modeling for biomedical applications. Finite Elements in Analysis and Design 44, 715-723.
3. Kremer, J. R., Mastronarde, D. N. & McIntosh, J. R. (1996). Computer visualization of three-dimensional image data using IMOD. J Struct Biol 116, 71-6.
4. Lawrence, A., Bouwer, J. C., Perkins, G. & Ellisman, M. H. (2006). Transform-based backprojection for volume reconstruction of large format electron microscope tilt series. J Struct Biol 154, 144-67.
5. Cheng, Y., Suen, J. K., Zhang, D., Bond, S. D., Zhang, Y., Song, Y., Baker, N. A., Bajaj, C. L., Holst, M. J. & McCammon, J. A. (2007). Finite element analysis of the time-dependent Smoluchowski equation for acetylcholinesterase reaction rate calculations. Biophys J 92, 3397-406.
6. Lu, S., Michailova, A., Cheng, Y., Yu, Z., Kaiser, T. H., Li, W. W., Banks, R. E., Holst, M., McCammon, J. A., Hoshijima, M. & McCulloch, A. D. (2008). Multi-Scale Modeling of Ventricular Myocytes: Contributions of structural and functional heterogeneities to excitation-contraction coupling in the normal and failing rodent heart. IEEE Engineering in Medicine and Biology, 1-13.
Links:
NCMIR: http://ncmir.ucsd.edu
NBCR: http://www.nbcr.net
NBCR Tools: http://tools.nbcr.net
FETK: http://www.fetk.org
NCRR: http://www.ncrr.nih.gov
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