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Resource for the Visualization of Biological Complexity (RVBC)

Model from tomogram of budding alphavirus

Model from tomogram
of budding alphavirus
(specimen from H. Cheng, UC Davis)

Recent Publications

Single-particle reconstruction
Techniques
Ribosome
Ryanodine receptor
Electron tomography
Techniques
Mitochondria
Tomography, other projects
General
Short Technical Reports

Single-particle reconstruction

Techniques

  • Lu Z , McMahon J, Mohammed H, Barnard D, Shaikh T R, Mannella C A, Wagenknecht T, T-M Lu T-M. (2009). Passive microfluidic devices for sub millisecond chaotic mixing. Sensors and Actuators B: Chemical (in press)
  • Lu Z, Shaikh T R, Barnard D, Meng X, Mohamed H, Yasin A, Mannella C A, Agrawal R K, T-M Lu T-M, Wagenknecht T. (2009). Monolithic microfluidic mixing-spraying devices for time-resolved cryo-electron microscopy. J. Struct Biol. Aug 14. (Epub ahead of print) Pub Med
  • Baxter, W.T., Grassucci, R.A., Gao, H. and Frank, J. (2009) Determination of signal-to-noise ratios and spectral SNRs in cryo-EM low-dose imaging of molecules. J. Struct. Biol. 166(2):126-132. Pub Med
  • Shaikh, T., Barnard, D., Meng, X. and Wagenknecht, T. (2009) Implementation of a flash-photolysis system for time-resolved cryo-electron microscopy. J. Struct Biol. 165: 184-189 Pub Med
  • Grassucci, R., Taylor, D., and Frank, J. (2008) Visualization of macromolecular complexes using cryo-electron microscopy with FEI Tecnai transmission electron microscopes. Nature Protocols 3(2) 330-339. Pub Med
  • Shaikh, T.R., Trujillo, R., LeBarron, J.S., Baxter, W.T. and Frank, J.(2008) Particle-verification for single-particle, reference-based reconstruction using multivariate data analysis and classification. J. Struct Biol. 164: 41-48. Pub Med
  • Trabuco, L., Villa, E., Mitra, K., Frank, J. and Schulten, K. (2008). Flexible fitting of atomic structure into electron microscopy maps using molecular dynamics. Structure 16: 673-683. Pub Med
  • Shaikh, T., Gao, H., Baxter, W., Asturias, F., Boisset, N., Leith, A., and Frank , J. (2008) SPIDER image processing for single-particle reconstruction of biological macromolecules from electron micrographs. Nature Protocols 3: 1941-1974. Pub Med
  • Fu J, Gao, H., Frank J (2007) Unsupervised classification of single particles by cluster tracking in multi-dimensional space. J. Struct Biol 157: 226-239. Pub Med
  • Grassucci, R., Taylor, D., and Frank, J. (2007) Preparation of macromolecular complexes for cryo-electron microscopy. Protocol 2(12)3239-3246. Pub Med
  • Scheres, S.H.W., Gao, H., Valle, M., Herman, G.T., Eggermont, P.B., Frank, J. and Carazo, J.M. (2006) Disentangling conformational states of macromolecules in 3D cryo-EM through likelihood optimization. Nature Meth. 4:27-29. Pub Med
  • Baxter, W.T., Leith, A., and Frank, J. (2006). SPIRE: The SPIDER Reconstruction Engine, J. Struct. Biol. 157, 56-63. Pub Med
  • Penczek PA, Frank, J. and Spahn, CMT. (2006) A method of focused classification, based on the bootstrap 3D variance analysis, and its application to EF-G-dependent translocation. J. Struct. Biol., 154:184-194. Pub Med
  • Sengupta, J. and Frank, J. (2006) Cryo-electron microscopy as a tool to study molecular machines. in: Protein Structures: Methods in Protein Structure and Stability Analysis, Nova Science Publishers, Inc., Hauppauge, NY.
  • Gao, H. and Frank, J. (2005) Molding atomic structures into intermediate-resolution cryo-EM density maps of ribosomal complexes using real-space refinement. Structure 13: 401-406. Pub Med
  • Rath, B.K. and Frank, J. (2004) Fast automatic particle picking from cryo-electron micrographs using a locally normalized cross-correlation function: a case study. J. Struct. Biol. 145(1-2): 84-90. Pub Med
  • Rath, B.K., Hegerl, R., Leith, A., Shaikh, T.R., Wagenknecht, T. and Frank, J. (2003) Fast 3D motif search of EM density maps using a locally normalized cross-correlation function. J. Struct. Biol. 144(1-2): 95-103. Pub Med
  • Frank, J. (2002). Single-particle imaging of macromolecules by cryo-electron microscopy. Ann. Rev. Biophys. Biomolec. Structure 31:303-19. Pub Med
  • Verschoor, A., Tivol, W.F., and Mannella, C.A. (2001). Single-particle approaches in the analysis of small 2D crystals of the mitochondrial channel, VDAC. J. Struct. Biol. 133:254-265. Pub Med
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Ribosome

  • Villa, E., Sengupta, J., Trabuco, L.G., LeBarron, J., Baxter, W.T., Shaikh, T.R., Grassucci, R.A., Nissen, P., Ehrenberg, M., Schulten, K. and Frank, J. (2009) Ribosome-induced changes in elongation factor Tu conformation control GTP hydrolysis. Proc. Natl. Acad. Sci. 106(4): 1063-1068. Pub Med
  • LeBarron, J., Grassucci, R., Shaikh, T., Baxter, W., Sengupta, J. and Frank, J. (2008) Exploration of parameters in cryo-EM leading to an improved density map of the E.coli ribosome. J. Struct. Biol. 164(1): 24-32. Pub Med
  • Frank, J., Gao, H., Sengupta, J., Gao, N., and Taylor, D. (2007) The process of mRNA-tRNA translocation. Proc. Natl. Acad. Sci. 104(50) 19671-19678. Pub Med
  • Frank, J., Profile of Joachim Frank (2007) Proc. Natl. Acad. Sci. 104(50) 19668-19670.
  • Frank, J., Sengupta, J., Gao, H., Li, W., Valle, M., Zavialov, A. and Ehrenberg, M. (2005) The role of tRNA as a molecular spring in decoding, accommodation, and peptidyl transfer. FEBS Let. 579:959-962. Pub Med
  • Gao, H., Ayub, M.J., Levin, M.J. and Frank, J. (2005) The structure of the 80S ribosome from Trypanosoma cruzi reveals unique rRNA components. Proc. Nat. Acad. Sci., USA 102 (29): 10206-10211 Pub Med
  • Gao, N., Zaviolov, A.V., Li, W., Sengupta, J., Valle, M., Gursky, R.P., Ehrenberg, M. and Frank, J. (2005) Mechanism for the disassembly of the posttermination complex inferred from cryo-EM studies. Mol. Cell 18:663-674. Pub Med
  • Halic, M. Becker, T., Pool, M.R., Spahn, C.M.T., Grassucci, R., Frank, J. and Beckmann, R. (2004) Structure of the signal recognition particle interacting with the elongation arrested ribosome. Nature 427: 808-814. Pub Med
  • Sengupta, J., Nilsson, J.,Gursky, R., Spahn, C.M.T., Nissen, P. and Frank, J. (2004) Identification of the versatile scaffold protein RACK1 on the eukaryotic ribosome by cryo-electron microscopy. Nat. Struct. & Mol. Biol. 11: 957-962. Pub Med
  • Spahn, C.M.T., Jan, E., Mulder, A., Grassucci, R.A., Sarnow, P. and Frank, J. (2004) Cryo-EM visualization of a viral internal ribosome entry site (IRES) bound to human 40S and 80S ribosomes: the IRES functions as an RNA-based translation factor. Cell 118: 465-475. Pub Med
  • Gao, H., Valle, M., Ehrenberg, M. and Frank, J. (2004) Dynamics of EF-G interaction with the ribosome explored by classification of a heterogeneous cryo-EM dataset. J. Struct. Biol. 147:283-290. Pub Med
  • Frank, J. (2004) The dynamics of the ribosome as inferred by cryo-EM: induced and self-organized motions. In: Conformational Proteomics of Macromolecular Architectures, World Scientific Publishing, Singapore.
  • Rawat, U.B.S., Zavialov, A., Sengupta, J., Valle, M., Grassucci, R., Linde, J., Vestergaard, B., Ehrenberg, M., and Frank, J. (2003). A cryo-electron microscopic study of ribosome-bound termination factor RF2. Nature 421:87-90
  • Valle, M., Zavialov, A., Li, W., Stagg, S.M., Sengupta, J., Nielsen, R.C., Nissen, P., Harvey, S.C., Ehrenberg, M. and Frank, J. (2003). Incorporation of aminoacyl-tRNA into the ribosome as seen by cryo-EM. Nature Struct. Biol. 10: 899-906. Pub Med
  • Frank, J. and Agrawal, R.K. (2002). Ratchet-like movements between the two ribosomal subunits: their mplications in elongation factor recognition and tRNA translocation. In Cold Spring Harbor Symposia on Quantitative Biology: The Ribosome 66:67-75.
  • Frank, J. (2002). Electron microscopy of functional ribosome complexes. Biopolymers, Nucleic Acid Sciences 68:223-233. Pub Med
  • Valle, M., Sengupta, J., Swami, N.K., Grassucci, R.A., Burkhardt, N., Nierhaus, K.H., Agrawal, R.K., and Frank, J. (2002). Cryo-EM reveals an active role for the aminoacyl-tRNA in the accommodation process. EMBO J. 21:3557-3567. Pub Med
  • Agrawal, R.K., Linde, J., Sengupta, J., Nierhaus, K.H., and Frank, J. (2001). Localization of L11 protein in the ribosome and elucidation of its involvement in EF-G-dependent translocation. J. Mol. Biol. 311:777-787. Pub Med
  • Frank, J. (2001). Ribosomal dynamics explored by cryo-electron microscopy. Methods 25:309-315. Pub Med
  • Gabashvilli, I.S., Gregory, S.T., Valle, M., Grassucci R., Worbs, M., Wahl, M.C., Dahlberg, A.E., and Frank, J. (2001). The polypeptide tunnel system in the ribosome and its gating in erythromycin resistance mutants of L4 and L22. Mol. Cell 8:181-188. Pub Med
  • Sengupta, J., Agrawal, R.K., and Frank, J. (2001). Visualization of protein S1 within the 30S ribosomal subunit, and its interaction with messenger RNA. Proc. Nat. Acad. Sci,. USA. 98:11991-11996. Pub Med
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Ryanodine receptor

  • Jones, P., Meng, X., Cai, S., Bolstad, J., Wagenknecht, T., Liu, Z., and Chen, S.R. (2008) Localization of PKA phosphorylation site, Ser 2030, in the three-dimensional structure of cardiac cyanodine receptor. Biochem Society 410, 261-270. Pub Med
  • Zhou, Q., Wang, Q., Meng, X., Shu, Y., Jiang, T., Wagenknecht, T., Yin, C., Sui, S., and Liu, Z. (2008) Structural and Functional Characterization of Ryanodine Receptor-Natrin Toxin Interaction. Biophys J. 95(9): 4289-99.
    Pub Med
  • Meng, X., Xiao, B.L., Cai, S.T., Huang, X.J., .Li, F., Bolstad, J., Trujillo, R., Airey, J., Chen, S.R.W., Wagenknecht, T., and Liu, Z. (2007) Three-dimensional localization of serine 2808, a phosphorylation site in cardiac ryanodine receptor. J. Biol. Chem. 282:25929-25939. Pub Med
  • Wang, R., Chen, W., Cai, S., Zhang, J., Bolstad, J., Wagenknecht, T., Liu, Z., and Chen, S.R. (2007) Localization of an NH(2)-terminal disease-causing mutation hot spot to the "clamp" region in the three-dimensional structure of the cardiac ryanodine receptor. J. Biol. Chem. 282:17785-17793. Pub Med
  • Sharma, M.R., Jeyackumar, L.H., Fleischer, S. and Wagenknecht, T. (2006) Three-dimensional visualization of FKBP12.6 binding to an open conformation of cardiac ryanodine receptor. Biophys. J. 90:164-172. Pub Med
  • Liu, J. and Wagenknecht, T. (2005) Three-dimensional reconstruction of ryanodine receptors. in: Ryanodine Receptors: Structure, Function and Dysfunction in Clinical Disease (ed. by H. T. Xander & A. R. Marks), pp. 25-34. Springer, New York.
  • Liu, Z., Wang, R., Zhang, J., Chen, S.R.W. and T.Wagenknecht. (2005) Localization of a disease associated mutation site in the three-dimensional structure of the cardiac muscle ryanodine receptor. J. Biol. Chem. 280:37941-37947. Pub Med
  • Samso, M., Wagenknecht, T. and Allen, P.D. (2005) Internal structure and visualization of transmembrane domains of the RyR1 calcium release channel by cryo-EM. Nature Struct. Mol. Biol. 12:539-544. Pub Med
  • Liu, Z., Zhang, J., Wang, R.W., Chen, S.R.W. and Wagenknecht, T. (2004) Location of divergent region 2 on the three-dimensional structure of cardiac muscle ryanodine receptor/calcium release channel. J. Mol. Biol. 338:533-545. Pub Med
  • Zhang,J., Liu, Z., Masumiya, H.,Wang, R., Jiang, D.W., Li, F., Wagenknecht, T. and Chen, S.R.W. (2003) Three-dimensional Localization of Divergent Region 3 of the Ryanodine Receptor to the Clamp-shaped Structures Adjacent to the FKBP Binding Sites. J. Biol. Chem. 278:14211. Pub Med
  • Rath, B.K., Hegerl, R., Leith, A., Shaikh, T.R., Wagenknecht, T., and Frank, J. (2003). Fast 3D motif search of EM density maps using a locally normalized cross-correlation function. J. Struct. Biol. 144:95-103. Pub Med
  • Wagenknecht, T. and Samso, M. (2002). Three-dimensional reconstruction of ryanodine receptors. Frontiers in Biosciences 7:D1464-D1474.
  • Liu,Z., Zhang,J., Li,P., Chen,S.R.W., and Wagenknecht,T. (2002). Three-dimensional reconstruction of the recombinant type 2 ryanodine receptor and localization of its divergent region 1. J. Biol. Chem. 277:46712-46719. Pub Med
  • Samso, M. and Wagenknecht, T. (2002). Apocalmodulin and CA2+ -calmodulin bind to neighboring locations of the ryanodine receptor. J. Biol. Chem. 277:1349-1353. Pub Med
  • Liu, Z., Zhang, J., Sharma, M.R., Li, P., Chen, S.R., and Wagenknecht, T. (2001). Three-dimensional reconstruction of the recombinant type 3 ryanodine receptor and localization of its amino terminus. Proc. Nat. Acad. Sci., USA. 98:6104-6109. Pub Med
  • Meng Z., Wang, G., Viero, C., Wang,Q., Mi,W., Su, XD, Wagenknecht, T., Williams, AJ, Liu, Z and Yin, CC. (2009) CLIC2-RyR1 interaction and structural characterization by cryo-electron microscopy. J Mol. Biol., 387:320-334. Pub Med
  • Samso, M. and Koonce, M. (2004) 25 A Resolution Structure of a Cytoplasmic Dynein Motor Reveals a Seven-member Planar Ring. J. Mol. Biol. 340:1059-1072. Pub Med
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Electron tomography

Electron tomography Techniques

  • Renken, C., Hsieh, C., Marko, M., Rath, B., Leith, A., Wagenknecht, T., Frank, T., and Mannella, C.A. (2009) Structure of Frozen-hydrated Triad Junctions: A Case Study in Motif Searching Inside Tomograms. J. Struct. Biol. 165: 53-63. Pub Med
  • McEwen, B.F., Renken, C., Marko. M.,and Mannella, C. (2008) Principles and practice in electron tomography. In: Eds. J. Correia and H.W. Dietrich, Methods in Cell Biology: Biophysical Tools for Biologists, Vol. 2: Methods In Vivo. Elsevier Academic Press (in press)
  • Marko, M., Hsieh, C., Schalek, R., Frank, J. and Mannella, C.A. (2007). Focused-ion-beam thinning of frozen-hydrated biological specimens for cryo-electron microscopy. Nature Methods: 4(3): 215-217. Pub Med
  • Marko, M. and Hsieh, C.-E. (2007) 3-D cryo-electron microscopy of cells and organelles, in Electron Microscopy Methods and Protocols, Second Edition. Ed. J. Kuo, Meth. Mol. Biol. (Humana Press) 396:407-429
  • McEwen BF, Dong, Y. and VandenBeldt, KJ. (2007) Using electron microscopy to understand functional mechanisms of chromosome alignment in the mitotic spindle. Meth. Cell Biol., 79:259-293. Pub Med
  • Hsieh, C.E., Leith, A., Mannella, C.A. and Frank, J., and Marko, M. (2006) Towards high-resolution three-dimensional imaging of native mammalian tissue: Electron tomography of frozen-hydrated rat liver sections. J. Struct. Biol. 153:1-13. Pub Med
  • Penczek, P.A. and Frank, J. (2006) Resolution in Electron Tomography. In: Electron tomography of cells and tissues, Ed. J. Frank, New York, Springer 307-330.
  • VandenBeldt, K., Barnard, R., Hergert, P. Meng, X., Maiato, H. and McEwen, B. (2006) Kinetochores use a novel mechanism for coordinating the dynamics of individual MTs within a kinetochore fiber. Curr Biol. 16(12): 1217-23. Pub Med
  • Jiang, M., Ji, Q., Wang, X., and McEwen, B.F. (2006) Segmentation of cell components using prior knowledge. In Electron Tomography of Cells and Tissue, 2nd Edition. J. Frank (ed.) (pp. 371-400). New York: Springer.
  • Frank, J. (2006) Three-Dimensional Electron of Cells and Tissues, 2nd Edition. Springer, New York.
  • Frangakis, A.S. and Rath, B.K. (2006) Motif search in electron tomography. In Electron Tomography of Cells and Tissue, 2nd edition, J. Frank (ed.) (pp. 401-416). New York: Springer.
  • Marko, M., Hsieh, C., Moberlychan, W., Mannella, C., and Frank, J. (2006) Focused ion beam milling of vitreous water: prospects for an alternative to cryo-ultramicrotomy. J. Microsc. 222(Pt 1):42-7. Pub Med
  • Marko, M., Hsieh, C.-E., and Mannella, C.A. (2005) Frozen-hydrated sections for electron tomography of cells and tissue, in Electron Tomography of Cells and Tissue, J. Frank (ed.)(pp. 49-82). New York: Springer.
  • Hsieh, C.-E., Marko, M., Frank, J., and Mannella, C.A. (2002). Electron tomographic analysis of frozen-hydrated tissue sections. J. Struct. Biol. 138:63-73. Pub Med
  • McEwen, B. F., Marko, M., Hsieh, C.-E., and Mannella, C. (2002). Use of frozen-hydrated axonemes to assess imaging parameters and resolution limits in cryo-electron tomography. J. Struct. Biol. 138:47-57. Pub Med
  • Penczek, P. (2002). Three-dimensional spectral signal-to-noise ratio for a class of reconstruction algorithms. J. Struct. Biol. 138:34-46. Pub Med
  • Frank, J., Wagenknecht, T., McEwen, B.F., Marko, M., Hsieh, C.-E., and Mannella, C.A. (2002). Three-dimensional imaging of biological complexity. J. Struct. Biol. 138:85-91. Pub Med
  • McEwen, B.F. and Frank, J. (2001). Electron tomographic (and other approaches) for imaging molecular machines. Curr. Opin. Neurobio. 11:594-600. Pub Med
  • McEwen, B. and Marko, M. (2001). The emergence ofelectron tomography as an important tool for investigatingcellular ultrastructure. J. Histochem. Cytochem. 49: 553-563. Pub Med
  • Marko, M. (1999) 3-D electron microscopy of cells and organelles by high-voltage EM, tomography, and stereopair analysis. In: Focus on Multidimensional Microscopy Ed. P. C. Cheng, et al., World Scientific, Singapore, pp 163-178.
  • McEwen, B. and Marko, M. (1999) Three-dimensional transmissionelectron microscopy and its application to mitosis research. In: Mitosis and Meiosis, Conly Rieder, Ed., (Methods in Cell Biology, Volume 61) Academic Press, San Francisco, pp. 81-111.
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Mitochondria

  • Kanazawa, T., Zappaterra, M.D., Hasegawa, A., Wright, A.P., Newman-Smith, E.D., Buttle, K.F., McDonald, K., Mannella, C.A. and van der Bliek, A.M. (2008) PLoS Genet 4(2): e1000022. doi:10.1371/journal.pgen.1000022. The C. elegans Opa1 Homologue EAT-3 Is Essential for Resistance to Free Radicals. Pub Med
  • Mannella, C.A. (2008) Structural diversity of mitochondria: Functional implications. Annals NY Acad Sci Dec; 1147: 171-9.
  • Prince, F. The Human Leydig Cell. (2007) The Leydig Cell in Health and Disease. Humana Press 5: 71-89
  • Tuma, R, (2006) Commentary: Spaced just right (Csordas, et al.) J. Cell Biol. 174(7): 907.
  • Mannella, C.A. (2006) Structure and dynamics of mitochondrial inner membrane cristae Biochim. Biophys. Acta 1763:542-548. Pub Med
  • Csordás, G., Renken, C., Várnai, P., Weaver, D., Buttle, K.F., Balla, T., Mannella, C.A., Hajnóczky, G, (2006) Structural and functional features and significance of the physical linkage between ER and mitochondria. Journal of Cell Biology 174(7) 915-921. Pub Med
  • Mannella, C.A. (2006) The relevance of mitochondrial membrane topology to mitochondrial function. Biochem. Biophys. Acta: 1762:140-147. Pub Med
  • Celotto, A.M., Frank, A.C., McGrath, S.W., Fergestad, T.J., Van Voorhies, W.A.., Buttle, K.F., Mannella, C.A. and Palladino, M.J. (2006). Mitochondrial encephalomyopathy in Drosophila. J. Neuroscience. 26:810-820. Pub Med
  • Keithly, J.S., Langreth, S.G., Buttle, K.F. and Mannella, C.A. (2005) Electron tomographic and ultrastructural analysis of the Cryptosporidium parvum relict mitochondrion, its associated membranes, and organelles. J. Eukaryotic Microbiology, 52:132-140. Pub Med
  • Khodjakov, A., Rieder, C., Mannella, C. and Kinnally, K. (2004) Lasermicro-irradiation of mitochondria: is there an amplified mitochondrial death signal in neural cells? Mitochondrion. 3(4): 217-27. Pub Med
  • Mannella, C. (2004) Mitochondrial Membranes, Structural Organization. Encyclopedia of Biological Chemistry Article Number BCHM 00046.
  • John, G.B., Li, L., Renken, C., Mannella, C.A., Bennett, J., and Zha, J. (2005). The Mitochondrial Inner Membrane Protein Mitofilin Controls Cristae Morphology. Mol. Miol. Cell. 16(3):1543-54 Pub Med
  • Prince, F.P. and Buttle, K.F. (2004). Mitochondrial structure in steroid producing cells: Three dimensional reconstruction of human Leydig cell mitochondria by electron microscopic tomography Anat. Rec. 278A:454-461. Pub Med
  • Scorrano, L., Ashiya, M., Buttle, K.F., Weiler, S., Oakes, S.A., Mannella, C.A., and Korsmeyer, S.J. (2002). A distinct pathway remodels mitochondrial cristae and mobilizes cytochrome c during apoptosis. Developmental Cell 2:55-67. Pub Med
  • Mannella, C.A., Pfeiffer, D.R., Bradshaw, P.C., Moraru, I.I., Slepchenko, B., Loew, L.M., Hsieh, C., Buttle, K.,and Marko, M. (2001). Topology of the mitochondrial inner membrane: dynamics and bioenergetic implications. IUBMB Life 52:93-100. Pub Med
  • Mootha, V.K., Wei, M.C., Buttle, K.F., Scorrano, L., Panoutsakopoulou, V., Mannella, C.A., and Korsmeyer, S.J. (2001). A reversable component of mitochondrial respiratory dysfunction in apoptosis can be rescued by exogenous cytochrome-c. EMBO J. 20:661-671. Pub Med
  • Mannella, C.A. (2001). Application of electrontomography to mitochondrial research. Meth. Cell Biology 65:245-256. Pub Med
  • Frey, T. and Mannella, C.A. (2000). The internal structure of mitochondria. Trends in Biochemical Sciences, 25: 319-324. Pub Med
  • Mannella, C.A. (2000). Our changing views of mitochondria. J. Bioenerg. Biomembr. 32:1-4. Pub Med
  • Deng, Y., Marko, M., Buttle, K., Leith, A., Mieczkowski, M., and Mannella, C.A. (1999). Cubic membrane structures in amoeba (Chaos carolinensis) mitochondria determined by electron microscopic tomography. J. Struct. Biol. 127: 231-239. Pub Med
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Tomography, Other Projects

  • Izard J, Renken C, Hsieh C E,Desrosiers D C, Dunham-Ems S, La Vake C, Gebhardt L L, Limberger R J, Marko M and Radolf J D (2009). Cryo-electron tomography elucidates the molecular architecture of Treponema pallidum, the syphilis spirochete. J. Bact. (in press/online doi:10.1128/JB.01031-09)
  • LaRocca, TJ, Holthausena, DJ, Hsieh, C., Renken, C, Mannella CA and Benach, JL. 2009. The bactericidal effect of a complement-independent antibody is osmolytic to specific borelia. Proc.Nat. Acad. Sci. USA 106(26): 10752-57. Pub Med
  • Charon, N.W., Goldstein, S.F., Marko, M., Hsieh, C., Gebhardt, L.L.,Motaleb, M.A., Wolgemuth, C.W., Limberger, R.J. and Rowe, N. (2009) The Flat-ribbon configuration of the periplasmic flagella of Borrelia burgdorferi and its relationship to motility and morphology. J. Bact. Jan:191(2) 600-7. Pub Med
  • Bernhard, J.M. and Bowser, S.S. (2008) Peroxisome proliferation in Foraminifera inhabiting the chemocline: an adaptation to reactive oxygen species exposure? J. Eukaryot Microbiol. 55(3): 135-44. Pub Med
  • Izard, J., Hsieh, C., Limberger, R., Mannella, C. and Marko, M. (2008) Cryo-electron tomography revealed Treponema denticola´s native cellular architecture and outer-membrane cell construction structure. Proc. Am Soc. Microbiol. June 1-5.
  • Mustardy, L., Buttle, K., Steinbach, G. and Garab, G. (2008). Three-dimensional architecture of the granum-stroma thylakoid membrane system revealed by electronic tomography. In: Allen, J.F., Gantt, E., Golbeck, J.H. and Osmond, B. (eds). Photosynthesis. Energy from the Sun: 14th International Congress on Photosynthesis, Springer, Heidelberg. 771-774.
  • Mustardy, L., Buttle, K., Steinbach, G., Garab, G. (2008) The three-dimensional network of the thylakoid membranes in plants: quasihelical model of the granum-stroma assembly. Plant Cell Oct; 20(10); 2552-7. Pub Med
  • Li, C., Wolgemuth, C., Marko, M., Morgan, D.G. and Charon, N. (2008) Genetic analysis of spirochete flagellin proteins and their involvement in motility, filament assembly, and flagellar morphology. J. Bact. 190(16) 5607-15. Pub Med
  • Izard, J., Hsieh, C.-E., Limberger, R.J., Mannella, C.A. and Marko, M. (2008) Native cellular architecture and outer-membrane cell constriction structures in Treponema denticola revealed by cryo-electron tomography. J. Struct. Biol. 163(1):10-17.
  • Ting, C.S., Hsieh, C., Sundararaman, S., Mannella, C., and Marko, M. (2007) Cryo-Electron Tomography Reveals the Comparative Three-Dimensional Architecture of Prochlorococcus, a Globally Important Marine Cyanobacterium. J. Bacteriol. 189, 4485-4493. Pub Med
  • Ash, C. (2007) MICROBIOLOGY: Form Follows Function: Science. June 2007 P B95 (Editor's Choice Highlights, re: Ting et al. 2007)
  • Baines, J.D., Hsieh, C.-E., Wills, E., Mannella, C. and Marko, M. (2007) Electron tomography of nascent herpes simplex virus virions. Journal of Virology. 81 (6) : 2726-2735. Pub Med
  • Dong, Y., K.J. VandenBeldt, X. Meng, A Khodjakov, and B.F. McEwen (2007) The Outer Plate in Vertebrate Kinetochores is a Flexible Network with Multiple Microtubule Interactions. Nature Cell Biology 9: 516-522. Pub Med
  • Jiang, M., Q. Ji., and B. McEwen (2006) Model-Based Automated Extraction of Microtubules from Electron Tomography Volume. IEEE Transactions on Information Technology in Biomedicine 10: 608-617. Pub Med
  • Lossinsky, A.S., Jong, A., Fiala, M., Mukhtar, M., , Buttle, K.F. and Ingram, M. (2006) The histopathology of Candida albicans invasion in neonatal rat tissues and in the human blood-brain barrier in culture revealed by light, scanning, transmission and immunoelectron microscopy. Histol Histopathol. 21: 1029-1041. Pub Med
  • Jiang, M., Ji, Q., and McEwen, B. (2006) Automated extraction of fine-features of kinetochore microtubules and plus ends from electron tomography. IEEE Transactions on Image Processing 15: 2035-2048. Pub Med
  • Takvorian, PM, Buttle, KF, Mannella, CA, Weiss, LM and Cali, A., (2006) High Voltage Electron Microscopy and Computerized Tomography: New Approaches to Study Microsporidian Spore Internal Organization. J. Eukaryot Microbiol. 53 Supp. 1: S55-7. Pub Med
  • Lossinsky, A.S. (2005) When Endothelial Cells Become Phagocytes. A Fine Structural Perspective. Histol & Histopathol.
  • Izard J., McEwen, B.F., Barnard, R.M., Portuese, T., Samsonoff, W.A., and Limberger, R.J. (2004). Tomographic reconstruction of treponemal cytoplasmic filaments reveals novel bridging and anchoring components. Mol. Microbiol. 51:609-618. Pub Med
  • Jensen, C.G., Poole, C.A., McGlashan, S.R., Marko, M., Issa, Z.I., Vujcich, K.V., and Bowser, S.S. (2004). Ultrastructural, tomographic and confocal imaging of the chondrocyte primary cilium in situ. Cell Biol. 28:101-110. Pub Med
  • Lossinsky, AS., Shivers RR. (2003) Studies of cerebral endothelium by scanning and high-voltage electron microscopy. Methods in Molecular Medicine. 89:67-82. Pub Med
  • Wagenknecht, T., Hsieh, C.-E., Rath, B. K., Fleischer, S., and Marko, M. (2002). Electron tomography of frozen-hydrated isolated triad junction. Biophys. J. 83:2491-2501. Pub Med
  • Marsh, B.J., Mastronarde, D.N., Buttle, K.F., Howell, K.E., and McIntosh, J.R. (2001). Organellar relationships in the Golgi region of the pancreatic beta cell line, HIT-T15, visualized by high resolution electron tomography. Proc. Nat. Acad. Sci., USA 98:2399-2406. Pub Med
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General RVBC-related publications

  • LaRocca T J, Holthausen D J, Hsieh C, Renken C, Mannella C A, and Benach J L. (2009). The bactericidal effect of a complement-independent anti-body is osmolytic and specific to Borrelia.Proc.Nat.Acad.Sci USA 106(26):10752-7 PMCID2705580.
  • Bernhard JM, A Habura and SS Bowser. 2006. An endobiont-bearing allogromiid from the Santa Barbara Basin: Implications for the early diversification of foraminifera. J. Geophys. Res., 111:G03002, doi: 10.1029/2005JG000158.
  • Izard, J. and Limberger, R.J. (2006) Structural and genomic aspects contributing to Treponema architecture in Molecular and Cellular Biology of Treponemes and Pathogenesis of Treponemal Infection. S.A. Lukehart and J. Radolf (ed.) Horizon Scientific Press, Chapter 3:39-60.
  • Frank, J. (ed.) (2006) Three-Dimensional Electron Microscopy of Macromolecular Assemblies - Visualization of Biological Molecules in Their Native State. Oxford University Press, New York.
  • Faruki, S., Cole, R.W., and Rieder, C.L. (2002). Separating centrosomes interact in the absence of associated chromosomes during mitosis in cultured vertebrate cells. Cell Motil. Cytoskel. 52:107-121. Pub Med
  • Bowser, S.S., Bernhard, J.M., Habura, A., and Gooday, A.J. (2002). Structure, taxonomy and ecology of Astrammina triangularis (Earland), an allogromid-like agglutinated foraminifer from Explorers Cove, Antarctica. J. Foraminiferal Research 32:364-374.
  • Khodjakov, A., Rieder, C.L., Sluder, G., Cassels, G., Sibon, O., and Wang, C-L. (2002). De novo formation of centrosomes in vertebrate cells arrested during S phase. J. Cell Biol. 158:1171-1181. Pub Med
  • Cimini, D., Howell, B., Maddox, P., Khodjakov, A., Degrassi, F., and Salmon, E.D. (2001). Merotelic kinetochore orientation is a major mechanism of aneuploidy in mitotic mammalian tissue cells. J. Cell Biol. 153:517-527. Pub Med
  • Erlandsen, S.L., Bitterman, A.G., White, J., Leith, A., and Marko, M. (2001). High resolution cryoFESEM of individual cell adhesion molecules (CAM) in the glycocalyx of human platelets; detection of P-selectin (CD62P), GPI-IX complex (CD42a/CD42ba,bB), and integrin GPIIbIIIa (CD41/CD61) by immunogold labeling and stereo imaging. J. Histochem. Cytochem. 49:809-819. Pub Med
  • McEwen, B.F., Chan, G.K.T., Zubrowski, B., Savoian, M.S., Sauer, M.T., and Yen, T.J. (2001). CENP-E is essential for reliable bioriented spindle attachment, but chromosome alignment can be achieved via redundant mechanisms in mammalian cells. Mol. Biol Cell . 12:2776-89. Pub Med
  • Sedzik, J., Hammar, L., Haag, L., Skoging-Nyberg, U., Tars, K., Marko, M. and Cheng, R.H. (2001). Structural proteomics of enveloped viruses: Crystallization, crystallography, mutagenesis, and cryo-electron microscopy. Rec. Res. Dev. Virol. 3:41-60.
  • Sharp, A.H., Black, III, J.L.., Dubel, S.J., Sundarraj, S., Shen, J.-P., Yunker, A.M.R., Copeland T.D. and McEnery. M.W. (2001). Biochemical and anatomical evidence for specialized voltage-dependent calcium channel gamma isoform expression in the epileptic and ataxtic mouse, Stargazer. Neuroscience, 105:599-617. Pub Med
  • Gooday, A.J., Bowser, S.S., Bett, B.J., and Smith, C.R. (2000). A large, testate protest, Gromia sphaerica sp. nov. (Order Filosea), from the bathyal Arabian Sea. Deep Sea Research II 47:55-73.
  • Kriete, A., T. Schwebel, H.-R. Duncker, and Marko, M. (1999). Multiscale imaging, analysis and modeling of the pulmonary bronchial tree. In: Focus on Multidimensional Microscopy Ed. P. C. Cheng, et al., World Scientific. 122-145.
  • Sluder, G., E. H. Hinchcliffe and Rieder, C.L. (1999). Mitosis: The culmination of the cell cycle. Molecular Basis of Cell Cycle and Growth Control. Ed. G.S. Stein, R. Baserga, A. Giordano, and D. T. Denhardt. Wiley-Liss, Inc.
  • Rieder, C. L., and Cole, R.W. (1999). Chromatid cohesion during mitosis: lessons from meiosis. J.Cell Sci. 112:2607-2613. Pub Med
  • Lossinsky, A.S., K.F. Buttle, R. Pluta, M.J. Mossakowski and Wisniewski, H.M. (1999). Immuno-ultrastructural expression of intercellular adhesion molecule-1 (ICAM-1/CD54) in endothelial cell vesiculo-tubular structures (VTS) and vesiculo-vacuolar organelles (VVO) in blood-brain barrier development and injury. Cell and Tissue Research 295:77-88. Pub Med
  • Landis, W.J. (1999). An overview of vertebrate mineralization with emphasis on collagen-mineral interaction. Amer. Soc. Gravitational and Space Biology Bulletin 12:15-26. Pub Med
  • Landis, W.J., C.H. Owen, K.J. Hodgens, D. Block, A.R. Hand, G. Gronowicz, K. Buttle and Marko, M. (1999). Studies of adhesion and signal transduction through localization of bone proteins by 3D immunocytochemistry. In: Chemistry and Biology of MineralizedTissues, M. Goldberg, A. Boskey, and C. Robinson (Eds.),: Proceedings of the Sixth International Conference. American Academy of Orthopaedic Surgeons. 243-247.
  • Tivol, W.F. (1999). Introduction to electron crystallography. Microscopy Res. Tech. 46:69-74. Pub Med
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Short Technical Reports

  • Lu, Z., McMahon, J., Mohamed, H., Barnard. D.Shaikh, T.R., Wagenknecht, T., Lu, T-M. (2008) Microfluidic mixing system for time resolved cryo-electron microscopy. Microsc. Microanal. 14 (Suppl. 2): 1598 CD.
  • Barnard D., Lu Z., Shaikh T.R., Yassin A., Mohamed H., Agrawal R., Lu T.-M., and Wagenknecht T. (2009) Time Resolved Cryo-Electron Microscopy Of Ribosome Assembly using Microfluidic Mixing. Microscopy and Microanalysis 15: 942-943 Cambridge University Press doi:10.1017/S1431927609096925
  • Dong, Y., Vagnarelli, P., Meng, X., Ribeiro, S., Earnshaw, W.C., McEwen, B.F. (2008) Localizing kinetochores in condensin deficient DT40 cells using same cell correlative confocal light microscopy/electron tomography. Microsc. Microanal. 14 (Suppl. 2): 1070 CD.
  • Marko, M., Hsieh, C. Salmon, N., Rodriguez, M., Frank, J. Mannella, C. (2008) FIB milling of frozen-hydrated cells and tissue for TEM cryo-tomography. Microsc. Microanal. 13 (Suppl 2): 968 CD.
  • Barnard, D., Lu, Z., Mohamed, H., Shaikh, T., McMahon, J., Aguirrezabala, X., Meng, X., Buttle, K., Lu, T.M. and Wagenknecht, T. (2007) Development of Microfluidic Mixers for Time Resolved Electron Microscopy Applied to Single Particle Reconstruction. Microsc. Microanal. 13 (Suppl 2: Proceedings) 424-425.
  • Mannella C.A., Buttle K.F., Walker D.W., Benzer S. (2007) Electron Tomographic Studies of Mitochondrial Cristae Topology: "Swirl" Mitochondria of Drosophila Flight Muscle. Microsc. Microanal. 13 (Suppl 2: Proceedings), 4-5.
  • Taylor D. J. , Nilsson J., Merrill A. R. , Andersen G. R., Nissen P., and Frank J. (2007). Critical movements of a single diphthamide residue of eukaryotic elongation factor 2 monitored by cryo-EM. Microsc. Microanal. 13 Suppl 2: Proceedings), 388 CD
  • Sengupta1, J., Fabiola, F., Gao, H., Valle, M., Zavialov, A., Chapman, M., Ehrenberg, M., and Frank, J. (2007) Visualization of ribosomal conformational changes during the initial selection process of decoding using cryo-EM. Microsc. Microanal. 13 (Suppl 2: Proceedings), 390CD.
  • Ting , C. S., Hsieh, C., Sundararaman, S., Mannella, C., Marko, M. (2007) Comparative Three-Dimensional Architecture of Prochlorococcus: Towards an Integrative Understanding of Cell Function. Microsc. Microanal. 13 (Suppl 2: Proceedings), 230CD.
  • Marko, M., Sheeff, M., Hsieh, C., Rodriguez, M., Salmon, N., Frank, J. and Mannella, C. (2007) Use of Focused Ion Beam Milling for Preparation of Frozen-Hydrated Specimens for TEM Tomography Microsc. Microanal. 13 (Suppl 2: Proceedings) 1460CD.
  • Marko, M. (2007). "Universal" Phase-Plate Imaging for Cryo-Electron Tomography. Microsc. Microanal. 13 (Suppl 2: Proceedings) 1212CD.
  • Cole, R.W., Mannella, C.A., Renken, C. and Turner, J.N. (2006) Intermediate magnification imaging system for whole organs/organisms. Microsc. Today 14:48-51.
  • Soonsawad, P., Ma, S., Morgan, D.G., Hultenby, K., Haag, L., Wu, S.-R., Forsell, K., Garoff, H., Hsieh, C.-E., Marko, M., Cheng, R.H. (2006) Comparative analysis of viral particles using different electron microscopy methodologies. Microsc. Microanal. 12 (Suppl 2): 1586CD.
  • Ting, C.S., Hsieh, C., Sundararaman, S., Frost, A., Mannella, C., Marko, M. (2006) Visualizing molecular responses to environmental stress in marine cyanobacteria. Microsc. Microanal. 12 (Suppl 2): 40-41.
  • Marko, M., Hsieh, C.-E., Shalek, R., Ting, C.S., Mannella, C.A., Frank, J. (2006) Focused ion beam (FIB) preparation methods for 3-D biological cryo-TEM. Microsc. Microanal. 12 (Suppl 2): 98-99.
  • Izard, J., Hsieh, C.-E., Mannella, C.A., Limberger, R.J., and Marko, M. (2005) Periplasm organization in Treponema denticola as studied by cryo-electron tomography. Microsc. Microanal. 11 (Suppl 2): 340CD.
  • Ting, C.S., Hsieh, C., Sundararaman, S., Mannella, C. and Marko, M. (2005) Comparative three-dimensional imaging of environmentally critical cyanobacteria through cryo-electron tomography. Microsc. Microanal. 11 (Suppl 2): 332CD.
  • Marko, M. (2005) Basics of biological cryo-TEM. Microsc. Microanal.11 (Suppl 2): 1090CD.
  • Marko, M. (2005) A survey of electron microscopic methods for 3-D imaging. Microsc. Microanal. 11 (Suppl 2): 624CD.
  • Marko, M., Hsieh, MoberlyChan, W.J., Mannella, C.A. and Frank, J. (2005) Feasibility of focused ion beam milling for preparation of TEM specimens ofbiological material embedded in vitreous ice. Microsc. Microanl. 11 (Suppl 2): 802CD.
  • Marko, M., Hsieh, C.-E., Dunn, K.A., Typke, D., Mannella, C.A. and Frank, J. (2005) Use of the Zernike phase plate for electron tomography of frozen-hydrated specimens. Microsc. Microanal. 11 (Suppl 2): 310CD.
  • MoberlyChan, W.J., Marko. M., and Hsieh, C.E. (2005) Cryo-FIB for thinning cryo-TEM samples and evading ice during cryo-transfer. Microsc. Microanal. 11 (Suppl 2): 854CD.
  • Dong, Y., Meng, X., Vandenbeldt, K., Hergert, P. and McEwen, B.F. (2005) Ultrastructure of nocodazole-treated PtK1 kinetochore after high-pressure freezing and freeze-substitution. Microsc. Microanal. 11 (Suppl 2): 338CD
  • Renken, C., Buttle, K., Marko, M., Hsieh, C.-E., Mannella, C. (2004) Electron tomographic study of the microdomain between mitochondria and the endoplasmic reticulum. Microsc. Microanal. 10 (Suppl. 2) 1206CD.
  • VandenBeldt, K.J., Meng, X., Barnard, R.M., Hergert, P.J., and McEwen, B.F. (2004). Statistical Profiles of PTK1 Kinetochore Microtubule Plus-End Conformations Using High-Throughput Electron Tomography. Microsc. Microanal. 10 (Suppl. 2): 1194CD.
  • Hsieh, C., He, W., Marko, M., Stokes, D.L. (2004) 3D Tomographic Map of Desmosome from Frozen-hydrated Skin Sections. Microsc. Microanal. 10 (Suppl 2): 1188CD.
  • Marko, M. Techniques for Electron Tomography in Biological and Materials Science. (2004) Microsc. Microanal. 10 (Suppl 2): 154-155 .
  • Marko, M. Quantitative Techniques in Biological TEM. (2004) Microsc. Microanal. 10 (Suppl 2):1202CD
  • Marko, M., Wagenknecht, T. and Mannella, C. (2003) Correlative electron tomography and elemental microanalysis in biology: a preview. Micros. Today 11(6):14-20.
  • Hsieh, C.-E., Marko, M., Leith, A., Frank, J., and Mannella, C.A. (2003). Electron Tomographic Comparison of Frozen-Hydrated and Freeze-Substituted Sections of High-Pressure Frozen Rat-Liver Tissue. Microsc. Microanal. 9 (Suppl 2): 1178CD.
  • Marko, M, Wagenknecht, T.W., Ichas, F., Bernardi, P., and Mannella, C.A. (2003). Correlative Electron Tomography and Elemental Microanalysis in Biology. Microsc. Microanal. 9 (Suppl 2): 1180CD.
  • Renken, C. and McEwen, B. (2003). Markerless alignment: Bridging the gap between theory and practice. Microsc. Microanal. 9 (Suppl 2): 1170CD.
  • McEwen, B.F., VandenBeldt, K.J., Barnard, R.M., Portuese, T.J., and Smith, D. (2003). Employing high-throughput electron tomography to asses the dynamic state of kinetochore microtubules. Microsc. Microanal. 9 (Suppl 2: Proceedings), 1160CD.
  • Baxter, W.T., Leith, A., and Frank, J. (2002). A scripting language approach to control software for cryo-electron microscopy. IEEE International Symposium on Biomedical Imaging, Washington DC, July 7-10, 2002.
  • McEwen, B.F., Barnard, R.M., Portuese, T. and Hsieh, C.-E. (2002). Using electron tomography to determine the interaction between mammalian kinetochores and mictotubules. Proc. 15th International Congress on Electron Microscopy, R. Cross, Ed., Microscopy Soc. of Southern Africa, Onderspoort, SA. 2:179-180.
  • Samso, M., Marko, M., Tikhonenko, I., and Koonce, M.P. (2002). Subunit structure of the dynein motor domain. Proc. 15th International Congress on Electron Microscopy, R. Cross, Ed., Microscopy Soc. of Southern Africa, Onderspoort, SA. 2:183-184.
  • Hsieh, C.-E., Marko, M., Frank, J., and Mannella, C.A. (2002). Electron tomography of frozen-hydrated sections. Microsc. Microanal. 8(2):878CD.
  • Turner, J.N., Szarowski, D.H., Shain, W., Buttle, K., Tivol, W.F., Bagle, H., Spence, A.J., Retterer, S., Lapek, L., Richards, T., Issacson, M., and Spencer, M.(2002). Lab-on-chip nanofabricated collagen membranes observed by high-voltage electron microscopy. Microsc. Microanal. 8 (2):1118CD.
  • Marko, M., Hsieh, C.-E., Mannella, C.A., and Frank, J. (2002) Electron tomography of frozen-hydrated specimens: application to tissue sections. Proc. 15th International Congress on Electron Microscopy, R. Cross, Ed., Microscopy Soc. of Southern Africa, Onderspoort, SA. 2:205-206.
  • McEwen, B.F., Barnard, R.M., Hsieh, C.-E. and Frank, J. (2001). Using electron tomography to determine binding and conformation states of kinetochore microtubules. Microsc. Microanal. 7(2):86-87.
  • Hsieh, C.-E., Marko, M., Rath, B.K., Fleischer, S. and Wagenknecht, T. (2001). Cryo-electron tomography of isolated triad junctions from skeletal muscle. Microsc. Microanal. 7(2):94-95.
  • Cheng, R.H., Hultenby, K., Haag, L., Forsell, K., Garoff, H., Hsieh, C.-E. and Marko, M. (2001). Bringing together high- and low-resolution data: electron tomography of budding enveloped alphavirus. Microsc. Microanal. 7 (2):104-105.
  • Marko, M., Hsieh, C.-E., Rath, B.K., Mannella, C.A. and McEwen, B.F. (2000). Electron tomography of frozen-hydrated samples. Microsc. Microanal. 6 (2):310-311.
  • McEwen, B.F., Hsieh, C.E., Barnard, R.M., and Rieder, C.L. (1999). Using high pressure freezing and freeze substitution to investigate kinetochore ultrastructure in vertebrate somatic cells. Microscopy and Microanalysis 5:436-437.
  • Marko, M., Hsieh, C.-E., Mannella, C.A., and McEwen, B. (1999). Imaging considerations for cryo-tomography of organelles and whole cells at high accelerating voltage. Microscopy and Microanalysis 5:414-415.
  • McEwen, B.F., Marko, M., Hsieh, C.-E., and Frank, J. (1999). The potential of cryo-electron tomography as assessed by reconstructions of sea urchin axonemes. Microscopy and Microanalysis 5:410-411.
  • Mannella, C.A., Hsieh, C.-E., and Marko, M. (1999). Electron microscopic tomography of whole, frozen-hydrated rat-liver mitochondria at 400kV. Microscopy and Microanalysis 5:416-417.
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