1
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Buxboim A, Kronenberg-Tenga R, Salajkova S, Avidan N, Shahak H, Thurston A, Medalia O. Scaffold, mechanics and functions of nuclear lamins. FEBS Lett 2023; 597:2791-2805. [PMID: 37813648 DOI: 10.1002/1873-3468.14750] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2023] [Revised: 09/05/2023] [Accepted: 09/26/2023] [Indexed: 10/11/2023]
Abstract
Nuclear lamins are type-V intermediate filaments that are involved in many nuclear processes. In mammals, A- and B-type lamins assemble into separate physical meshwork underneath the inner nuclear membrane, the nuclear lamina, with some residual fraction localized within the nucleoplasm. Lamins are the major part of the nucleoskeleton, providing mechanical strength and flexibility to protect the genome and allow nuclear deformability, while also contributing to gene regulation via interactions with chromatin. While lamins are the evolutionary ancestors of all intermediate filament family proteins, their ultimate filamentous assembly is markedly different from their cytoplasmic counterparts. Interestingly, hundreds of genetic mutations in the lamina proteins have been causally linked with a broad range of human pathologies, termed laminopathies. These include muscular, neurological and metabolic disorders, as well as premature aging diseases. Recent technological advances have contributed to resolving the filamentous structure of lamins and the corresponding lamina organization. In this review, we revisit the multiscale lamin organization and discuss its implications on nuclear mechanics and chromatin organization within lamina-associated domains.
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Affiliation(s)
- Amnon Buxboim
- The Rachel and Selim Benin School of Computer Science and Engineering and The Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Israel
| | | | - Sarka Salajkova
- Department of Biochemistry, University of Zurich, Switzerland
| | - Nili Avidan
- The Rachel and Selim Benin School of Computer Science and Engineering and The Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Israel
| | - Hen Shahak
- The Rachel and Selim Benin School of Computer Science and Engineering and The Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Israel
| | - Alice Thurston
- Department of Biochemistry, University of Zurich, Switzerland
| | - Ohad Medalia
- Department of Biochemistry, University of Zurich, Switzerland
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2
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Mishra YG, Manavathi B. Focal adhesion dynamics in cellular function and disease. Cell Signal 2021; 85:110046. [PMID: 34004332 DOI: 10.1016/j.cellsig.2021.110046] [Citation(s) in RCA: 65] [Impact Index Per Article: 21.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Accepted: 05/13/2021] [Indexed: 02/06/2023]
Abstract
Acting as a bridge between the cytoskeleton of the cell and the extra cellular matrix (ECM), the cell-ECM adhesions with integrins at their core, play a major role in cell signalling to direct mechanotransduction, cell migration, cell cycle progression, proliferation, differentiation, growth and repair. Biochemically, these adhesions are composed of diverse, yet an organised group of structural proteins, receptors, adaptors, various enzymes including protein kinases, phosphatases, GTPases, proteases, etc. as well as scaffolding molecules. The major integrin adhesion complexes (IACs) characterised are focal adhesions (FAs), invadosomes (podosomes and invadopodia), hemidesmosomes (HDs) and reticular adhesions (RAs). The varied composition and regulation of the IACs and their signalling, apart from being an integral part of normal cell survival, has been shown to be of paramount importance in various developmental and pathological processes. This review per-illustrates the recent advancements in the research of IACs, their crucial roles in normal as well as diseased states. We have also touched on few of the various methods that have been developed over the years to visualise IACs, measure the forces they exert and study their signalling and molecular composition. Having such pertinent roles in the context of various pathologies, these IACs need to be understood and studied to develop therapeutical targets. We have given an update to the studies done in recent years and described various techniques which have been applied to study these structures, thereby, providing context in furthering research with respect to IAC targeted therapeutics.
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Affiliation(s)
- Yasaswi Gayatri Mishra
- Department of Biochemistry, School of Life Sciences, University of Hyderabad, Hyderabad 500046, India
| | - Bramanandam Manavathi
- Department of Biochemistry, School of Life Sciences, University of Hyderabad, Hyderabad 500046, India.
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3
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Zilman A. Aggregation, Phase Separation and Spatial Morphologies of the Assemblies of FG Nucleoporins. J Mol Biol 2018; 430:4730-4740. [DOI: 10.1016/j.jmb.2018.07.011] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2018] [Revised: 07/03/2018] [Accepted: 07/09/2018] [Indexed: 11/17/2022]
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4
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Dahan I, Sorrentino S, Boujemaa-Paterski R, Medalia O. Tiopronin-Protected Gold Nanoparticles as a Potential Marker for Cryo-EM and Tomography. Structure 2018; 26:1408-1413.e3. [PMID: 30078643 DOI: 10.1016/j.str.2018.06.009] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2018] [Revised: 06/03/2018] [Accepted: 06/27/2018] [Indexed: 10/28/2022]
Abstract
Gold nanoparticles (AuNPs) and their conjugation to biological samples have numerous potential applications. When combined with cryo-electron microscopy and tomography analysis, AuNPs may provide a versatile and powerful tool to identify and precisely localize proteins even when attached to cellular components. Here, we describe a general and facile approach for the synthesis of homogeneous and stable AuNPs, which can readily be conjugated to a molecule of interest and imaged by cryo-electron tomography (cryo-ET). We demonstrate the synthesis of 2.2 ± 0.45-nm tiopronin-protected AuNPs, followed by their conjugation with recombinant proteins and peptides. Visualization of the ∼2.2-nm gold-tagged peptides by cryo-ET reveals the potential use of this strategy to label and localize accessible proteins in a cellular environment with nanometric resolution.
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Affiliation(s)
- Idit Dahan
- Department of Life Sciences and the National Institute for Biotechnology in the Negev, Ben-Gurion University, 84105 Beer-Sheva, Israel
| | - Simona Sorrentino
- Department of Biochemistry, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland
| | - Rajaa Boujemaa-Paterski
- Department of Biochemistry, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland; Université Grenoble Alpes, 38400 Grenoble, France
| | - Ohad Medalia
- Department of Life Sciences and the National Institute for Biotechnology in the Negev, Ben-Gurion University, 84105 Beer-Sheva, Israel; Department of Biochemistry, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland.
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5
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Insight into the functional organization of nuclear lamins in health and disease. Curr Opin Cell Biol 2018; 54:72-79. [PMID: 29800922 DOI: 10.1016/j.ceb.2018.05.001] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2018] [Revised: 04/24/2018] [Accepted: 05/08/2018] [Indexed: 11/20/2022]
Abstract
Lamins are the main component of the nuclear lamina, a protein meshwork at the inner nuclear membrane which primarily provide mechanical stability to the nucleus. Lamins, type V intermediate filament proteins, are also involved in many nuclear activities. Structural analysis of nuclei revealed that lamins form 3.5nm thick filaments often interact with nuclear pore complexes. Mutations in the LMNA gene, encoding A-type lamins, have been associated with at least 15 distinct diseases collectively termed laminopathies, including muscle, metabolic and neurological disorders, and premature aging syndrome. It is unclear how laminopathic mutations lead to such a wide array of diseases, essentially affecting almost all tissues.
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Wang Z, Chen Y, Zhang J, Li L, Wan X, Liu Z, Sun F, Zhang F. ICON-MIC: Implementing a CPU/MIC Collaboration Parallel Framework for ICON on Tianhe-2 Supercomputer. J Comput Biol 2017; 25:270-281. [PMID: 29185807 DOI: 10.1089/cmb.2017.0151] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Electron tomography (ET) is an important technique for studying the three-dimensional structures of the biological ultrastructure. Recently, ET has reached sub-nanometer resolution for investigating the native and conformational dynamics of macromolecular complexes by combining with the sub-tomogram averaging approach. Due to the limited sampling angles, ET reconstruction typically suffers from the "missing wedge" problem. Using a validation procedure, iterative compressed-sensing optimized nonuniform fast Fourier transform (NUFFT) reconstruction (ICON) demonstrates its power in restoring validated missing information for a low-signal-to-noise ratio biological ET dataset. However, the huge computational demand has become a bottleneck for the application of ICON. In this work, we implemented a parallel acceleration technology ICON-many integrated core (MIC) on Xeon Phi cards to address the huge computational demand of ICON. During this step, we parallelize the element-wise matrix operations and use the efficient summation of a matrix to reduce the cost of matrix computation. We also developed parallel versions of NUFFT on MIC to achieve a high acceleration of ICON by using more efficient fast Fourier transform (FFT) calculation. We then proposed a hybrid task allocation strategy (two-level load balancing) to improve the overall performance of ICON-MIC by making full use of the idle resources on Tianhe-2 supercomputer. Experimental results using two different datasets show that ICON-MIC has high accuracy in biological specimens under different noise levels and a significant acceleration, up to 13.3 × , compared with the CPU version. Further, ICON-MIC has good scalability efficiency and overall performance on Tianhe-2 supercomputer.
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Affiliation(s)
- Zihao Wang
- 1 High Performance Computer Research Center, Institute of Computing Technology , Chinese Academy of Sciences, Beijing, China .,2 University of Chinese Academy of Sciences , Beijing, China .,6 These authors contributed equally to this work
| | - Yu Chen
- 1 High Performance Computer Research Center, Institute of Computing Technology , Chinese Academy of Sciences, Beijing, China .,2 University of Chinese Academy of Sciences , Beijing, China .,6 These authors contributed equally to this work
| | - Jingrong Zhang
- 1 High Performance Computer Research Center, Institute of Computing Technology , Chinese Academy of Sciences, Beijing, China .,2 University of Chinese Academy of Sciences , Beijing, China
| | - Lun Li
- 1 High Performance Computer Research Center, Institute of Computing Technology , Chinese Academy of Sciences, Beijing, China .,3 School of Mathematical Sciences, University of Chinese Academy of Sciences , Beijing, China
| | - Xiaohua Wan
- 1 High Performance Computer Research Center, Institute of Computing Technology , Chinese Academy of Sciences, Beijing, China
| | - Zhiyong Liu
- 1 High Performance Computer Research Center, Institute of Computing Technology , Chinese Academy of Sciences, Beijing, China
| | - Fei Sun
- 2 University of Chinese Academy of Sciences , Beijing, China .,4 National Key Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics , Chinese Academy of Sciences, Beijing, China .,5 Center for Biological Imaging, Institute of Biophysics , Chinese Academy of Sciences, Beijing, China
| | - Fa Zhang
- 1 High Performance Computer Research Center, Institute of Computing Technology , Chinese Academy of Sciences, Beijing, China
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7
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Chen Y, Wang Z, Zhang J, Li L, Wan X, Sun F, Zhang F. Accelerating electron tomography reconstruction algorithm ICON with GPU. BIOPHYSICS REPORTS 2017; 3:36-42. [PMID: 28781999 PMCID: PMC5516007 DOI: 10.1007/s41048-017-0041-z] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2017] [Accepted: 04/07/2017] [Indexed: 10/30/2022] Open
Abstract
Electron tomography (ET) plays an important role in studying in situ cell ultrastructure in three-dimensional space. Due to limited tilt angles, ET reconstruction always suffers from the "missing wedge" problem. With a validation procedure, iterative compressed-sensing optimized NUFFT reconstruction (ICON) demonstrates its power in the restoration of validated missing information for low SNR biological ET dataset. However, the huge computational demand has become a major problem for the application of ICON. In this work, we analyzed the framework of ICON and classified the operations of major steps of ICON reconstruction into three types. Accordingly, we designed parallel strategies and implemented them on graphics processing units (GPU) to generate a parallel program ICON-GPU. With high accuracy, ICON-GPU has a great acceleration compared to its CPU version, up to 83.7×, greatly relieving ICON's dependence on computing resource.
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Affiliation(s)
- Yu Chen
- Key Laboratory of Intelligent Information Processing, Institute of Computing Technology, Chinese Academy of Sciences, Beijing, 100190 China.,University of Chinese Academy of Sciences, Beijing, 100049 China
| | - Zihao Wang
- Key Laboratory of Intelligent Information Processing, Institute of Computing Technology, Chinese Academy of Sciences, Beijing, 100190 China.,University of Chinese Academy of Sciences, Beijing, 100049 China
| | - Jingrong Zhang
- Key Laboratory of Intelligent Information Processing, Institute of Computing Technology, Chinese Academy of Sciences, Beijing, 100190 China.,University of Chinese Academy of Sciences, Beijing, 100049 China
| | - Lun Li
- Key Laboratory of Intelligent Information Processing, Institute of Computing Technology, Chinese Academy of Sciences, Beijing, 100190 China.,School of Mathematical Sciences, University of Chinese Academy of Sciences, Beijing, 100049 China
| | - Xiaohua Wan
- Key Laboratory of Intelligent Information Processing, Institute of Computing Technology, Chinese Academy of Sciences, Beijing, 100190 China
| | - Fei Sun
- University of Chinese Academy of Sciences, Beijing, 100049 China.,National Key Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101 China.,Center for Biological Imaging, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101 China
| | - Fa Zhang
- Key Laboratory of Intelligent Information Processing, Institute of Computing Technology, Chinese Academy of Sciences, Beijing, 100190 China
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8
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Chen Y, Zhang Y, Zhang K, Deng Y, Wang S, Zhang F, Sun F. FIRT: Filtered iterative reconstruction technique with information restoration. J Struct Biol 2016; 195:49-61. [DOI: 10.1016/j.jsb.2016.04.015] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2015] [Revised: 04/27/2016] [Accepted: 04/28/2016] [Indexed: 12/31/2022]
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9
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Zhang J, Ji G, Huang X, Xu W, Sun F. An improved cryo-FIB method for fabrication of frozen hydrated lamella. J Struct Biol 2016; 194:218-23. [DOI: 10.1016/j.jsb.2016.02.013] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2015] [Revised: 01/02/2016] [Accepted: 02/11/2016] [Indexed: 10/22/2022]
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10
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Sorrentino S, Studt JD, Horev MB, Medalia O, Sapra KT. Toward correlating structure and mechanics of platelets. Cell Adh Migr 2016; 10:568-575. [PMID: 27104281 DOI: 10.1080/19336918.2016.1173803] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022] Open
Abstract
The primary physiological function of blood platelets is to seal vascular lesions after injury and form hemostatic thrombi in order to prevent blood loss. This task relies on the formation of strong cellular-extracellular matrix interactions in the subendothelial lesions. The cytoskeleton of a platelet is key to all of its functions: its ability to spread, adhere and contract. Despite the medical significance of platelets, there is still no high-resolution structural information of their cytoskeleton. Here, we discuss and present 3-dimensional (3D) structural analysis of intact platelets by using cryo-electron tomography (cryo-ET) and atomic force microscopy (AFM). Cryo-ET provides in situ structural analysis and AFM gives stiffness maps of the platelets. In the future, combining high-resolution structural and mechanical techniques will bring new understanding of how structural changes modulate platelet stiffness during activation and adhesion.
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Affiliation(s)
- Simona Sorrentino
- a Department of Biochemistry , University of Zurich , Zurich , Switzerland
| | - Jan-Dirk Studt
- b Division of Hematology , University Hospital Zurich , Zurich , Switzerland
| | - Melanie Bokstad Horev
- c The National Institute for Biotechnology in the Negev and Department of Life Sciences , Ben-Gurion University , Beer-Sheva , Israel
| | - Ohad Medalia
- a Department of Biochemistry , University of Zurich , Zurich , Switzerland.,c The National Institute for Biotechnology in the Negev and Department of Life Sciences , Ben-Gurion University , Beer-Sheva , Israel
| | - K Tanuj Sapra
- a Department of Biochemistry , University of Zurich , Zurich , Switzerland
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11
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Oikonomou CM, Chang YW, Jensen GJ. A new view into prokaryotic cell biology from electron cryotomography. Nat Rev Microbiol 2016; 14:205-20. [PMID: 26923112 PMCID: PMC5551487 DOI: 10.1038/nrmicro.2016.7] [Citation(s) in RCA: 60] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Electron cryotomography (ECT) enables intact cells to be visualized in 3D in an essentially native state to 'macromolecular' (∼4 nm) resolution, revealing the basic architectures of complete nanomachines and their arrangements in situ. Since its inception, ECT has advanced our understanding of many aspects of prokaryotic cell biology, from morphogenesis to subcellular compartmentalization and from metabolism to complex interspecies interactions. In this Review, we highlight how ECT has provided structural and mechanistic insights into the physiology of bacteria and archaea and discuss prospects for the future.
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Affiliation(s)
- Catherine M Oikonomou
- Howard Hughes Medical Institute; Division of Biology and Biological Engineering, California Institute of Technology, 1200 E. California Blvd., Pasadena, California 91125, USA
| | - Yi-Wei Chang
- Howard Hughes Medical Institute; Division of Biology and Biological Engineering, California Institute of Technology, 1200 E. California Blvd., Pasadena, California 91125, USA
| | - Grant J Jensen
- Howard Hughes Medical Institute; Division of Biology and Biological Engineering, California Institute of Technology, 1200 E. California Blvd., Pasadena, California 91125, USA
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12
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Abstract
Cryo-electron tomography (cryo-ET) has emerged as a leading technique for three-dimensional visualization of large macromolecular complexes and their conformational changes in their native cellular environment. However, the resolution and potential applications of cryo-ET are fundamentally limited by specimen thickness, preventing high-resolution in situ visualization of macromolecular structures in many bacteria (such as Escherichia coli and Salmonella enterica). Minicells, which were discovered nearly 50 years ago, have recently been exploited as model systems to visualize molecular machines in situ, due to their smaller size and other unique properties. In this review, we discuss strategies for producing minicells and highlight their use in the study of chemotactic signaling, protein secretion, and DNA translocation. In combination with powerful genetic tools and advanced imaging techniques, minicells provide a springboard for in-depth structural studies of bacterial macromolecular complexes in situ and therefore offer a unique approach for gaining novel structural insights into many important processes in microbiology.
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13
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Irobalieva RN, Martins B, Medalia O. Cellular structural biology as revealed by cryo-electron tomography. J Cell Sci 2016; 129:469-76. [DOI: 10.1242/jcs.171967] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
ABSTRACT
Understanding the function of cellular machines requires a thorough analysis of the structural elements that underline their function. Electron microscopy (EM) has been pivotal in providing information about cellular ultrastructure, as well as macromolecular organization. Biological materials can be physically fixed by vitrification and imaged with cryo-electron tomography (cryo-ET) in a close-to-native condition. Using this technique, one can acquire three-dimensional (3D) information about the macromolecular architecture of cells, depict unique cellular states and reconstruct molecular networks. Technical advances over the last few years, such as improved sample preparation and electron detection methods, have been instrumental in obtaining data with unprecedented structural details. This presents an exciting opportunity to explore the molecular architecture of both individual cells and multicellular organisms at nanometer to subnanometer resolution. In this Commentary, we focus on the recent developments and in situ applications of cryo-ET to cell and structural biology.
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Affiliation(s)
- Rossitza N. Irobalieva
- Department of Biochemistry, University of Zurich, Winterthurerstrasse 190, Zurich 8057, Switzerland
| | - Bruno Martins
- Department of Biochemistry, University of Zurich, Winterthurerstrasse 190, Zurich 8057, Switzerland
| | - Ohad Medalia
- Department of Biochemistry, University of Zurich, Winterthurerstrasse 190, Zurich 8057, Switzerland
- Department of Life Sciences and the National Institute for Biotechnology in the Negev, Ben-Gurion University, Beer-Sheva 84105, Israel
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14
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Cryo-planing of frozen-hydrated samples using cryo triple ion gun milling (CryoTIGM™). J Struct Biol 2015; 192:569-579. [PMID: 26549007 DOI: 10.1016/j.jsb.2015.11.002] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2015] [Revised: 11/04/2015] [Accepted: 11/05/2015] [Indexed: 11/23/2022]
Abstract
Cryo-SEM is a high throughput technique for imaging biological ultrastructure in its most pristine state, i.e. without chemical fixation, embedding, or drying. Freeze fracture is routinely used to prepare internal surfaces for cryo-SEM imaging. However, the propagation of the fracture plane is highly dependent on sample properties, and the resulting surface frequently shows substantial topography, which can complicate image analysis and interpretation. We have developed a broad ion beam milling technique, called cryogenic triple ion gun milling (CryoTIGM™ ['krī-ə-,tīm]), for cryo-planing frozen-hydrated biological specimens. Comparing sample preparation by CryoTIGM™ and freeze fracture in three model systems, Baker's yeast, mouse liver tissue, and whole sea urchin embryos, we find that CryoTIGM™ yields very large (∼700,000 μm(2)) and smooth sections that present ultrastructural details at similar or better quality than freeze-fractured samples. A particular strength of CryoTIGM™ is the ability to section samples with hard-soft contrast such as brittle calcite (CaCO3) spicules in the sea urchin embryo.
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15
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Tafti AP, Kirkpatrick AB, Alavi Z, Owen HA, Yu Z. Recent advances in 3D SEM surface reconstruction. Micron 2015; 78:54-66. [DOI: 10.1016/j.micron.2015.07.005] [Citation(s) in RCA: 67] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2015] [Revised: 07/08/2015] [Accepted: 07/18/2015] [Indexed: 11/27/2022]
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16
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Ercius P, Alaidi O, Rames MJ, Ren G. Electron Tomography: A Three-Dimensional Analytic Tool for Hard and Soft Materials Research. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2015; 27:5638-63. [PMID: 26087941 PMCID: PMC4710474 DOI: 10.1002/adma.201501015] [Citation(s) in RCA: 88] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/28/2015] [Revised: 04/22/2015] [Indexed: 05/23/2023]
Abstract
Three-dimensional (3D) structural analysis is essential to understand the relationship between the structure and function of an object. Many analytical techniques, such as X-ray diffraction, neutron spectroscopy, and electron microscopy imaging, are used to provide structural information. Transmission electron microscopy (TEM), one of the most popular analytic tools, has been widely used for structural analysis in both physical and biological sciences for many decades, in which 3D objects are projected into two-dimensional (2D) images. In many cases, 2D-projection images are insufficient to understand the relationship between the 3D structure and the function of nanoscale objects. Electron tomography (ET) is a technique that retrieves 3D structural information from a tilt series of 2D projections, and is gradually becoming a mature technology with sub-nanometer resolution. Distinct methods to overcome sample-based limitations have been separately developed in both physical and biological science, although they share some basic concepts of ET. This review discusses the common basis for 3D characterization, and specifies difficulties and solutions regarding both hard and soft materials research. It is hoped that novel solutions based on current state-of-the-art techniques for advanced applications in hybrid matter systems can be motivated.
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Affiliation(s)
- Peter Ercius
- Lawrence Berkeley National Laboratory, 1 Cyclotron Rd., Berkeley, CA 94720, USA
| | - Osama Alaidi
- Lawrence Berkeley National Laboratory, 1 Cyclotron Rd., Berkeley, CA 94720, USA
| | - Matthew J. Rames
- Lawrence Berkeley National Laboratory, 1 Cyclotron Rd., Berkeley, CA 94720, USA
| | - Gang Ren
- Lawrence Berkeley National Laboratory, 1 Cyclotron Rd., Berkeley, CA 94720, USA
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17
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Park J, Park H, Ercius P, Pegoraro AF, Xu C, Kim JW, Han SH, Weitz DA. Direct Observation of Wet Biological Samples by Graphene Liquid Cell Transmission Electron Microscopy. NANO LETTERS 2015; 15:4737-4744. [PMID: 26065925 DOI: 10.1021/acs.nanolett.5b01636] [Citation(s) in RCA: 87] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Recent development of liquid phase transmission electron microscopy (TEM) enables the study of specimens in wet ambient conditions within a liquid cell; however, direct structural observation of biological samples in their native solution using TEM is challenging since low-mass biomaterials embedded in a thick liquid layer of the host cell demonstrate low contrast. Furthermore, the integrity of delicate wet samples is easily compromised during typical sample preparation and TEM imaging. To overcome these limitations, we introduce a graphene liquid cell (GLC) using multilayer graphene sheets to reliably encapsulate and preserve biological samples in a liquid for TEM observation. We achieve nanometer scale spatial resolution with high contrast using low-dose TEM at room temperature, and we use the GLC to directly observe the structure of influenza viruses in their native buffer solution at room temperature. The GLC is further extended to investigate whole cells in wet conditions using TEM. We also demonstrate the potential of the GLC for correlative studies by TEM and fluorescence light microscopy imaging.
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Affiliation(s)
- Jungwon Park
- †Department of Applied Physics, Harvard University, Cambridge, Massachusetts 02138, United States
- ‡School of Engineering and Applied Sciences, Harvard University, Cambridge, Massachusetts 02138, United States
| | - Hyesung Park
- §School of Energy and Chemical Engineering, Ulsan National Institute of Science and Technology, Ulsan 689-798, South Korea
| | - Peter Ercius
- ∥The Molecular Foundry, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
| | - Adrian F Pegoraro
- †Department of Applied Physics, Harvard University, Cambridge, Massachusetts 02138, United States
- ‡School of Engineering and Applied Sciences, Harvard University, Cambridge, Massachusetts 02138, United States
| | - Chen Xu
- ⊥Rosenstiel Basic Medical Sciences Research Center, Brandeis University, Waltham, Massachusetts 02454, United States
| | - Jin Woong Kim
- #Department of Applied Chemistry, Hanyang University, Ansan 426-791, South Korea
- ∇Department of Bionano Technology, Hanyang University, Ansan 426-791, South Korea
| | | | - David A Weitz
- †Department of Applied Physics, Harvard University, Cambridge, Massachusetts 02138, United States
- ‡School of Engineering and Applied Sciences, Harvard University, Cambridge, Massachusetts 02138, United States
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18
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Alvare G, Gordon R. CT brush and CancerZap!: two video games for computed tomography dose minimization. Theor Biol Med Model 2015; 12:7. [PMID: 25962597 PMCID: PMC4469010 DOI: 10.1186/s12976-015-0003-4] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2014] [Accepted: 04/20/2015] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND X-ray dose from computed tomography (CT) scanners has become a significant public health concern. All CT scanners spray x-ray photons across a patient, including those using compressive sensing algorithms. New technologies make it possible to aim x-ray beams where they are most needed to form a diagnostic or screening image. We have designed a computer game, CT Brush, that takes advantage of this new flexibility. It uses a standard MART algorithm (Multiplicative Algebraic Reconstruction Technique), but with a user defined dynamically selected subset of the rays. The image appears as the player moves the CT brush over an initially blank scene, with dose accumulating with every "mouse down" move. The goal is to find the "tumor" with as few moves (least dose) as possible. RESULTS We have successfully implemented CT Brush in Java and made it available publicly, requesting crowdsourced feedback on improving the open source code. With this experience, we also outline a "shoot 'em up game" CancerZap! for photon limited CT. CONCLUSIONS We anticipate that human computing games like these, analyzed by methods similar to those used to understand eye tracking, will lead to new object dependent CT algorithms that will require significantly less dose than object independent nonlinear and compressive sensing algorithms that depend on sprayed photons. Preliminary results suggest substantial dose reduction is achievable.
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Affiliation(s)
- Graham Alvare
- BioInformation Technology Laboratory, Department of Plant Science, University of Manitoba, E2-532 EITC, Winnipeg, R3T 2N2, MB, Canada. .,Current address: Faculty of Medicine, University of Manitoba, Box 107, Winnipeg, Canada.
| | - Richard Gordon
- Embryogenesis Center, Gulf Specimen Aquarium and Marine Laboratory, 222Clark Drive, Panacea, FL, 32346, USA. .,C.S. Mott Center for Human Growth and Development, Department of Obstetrics and Gynecology, Wayne State University, 275 E. Hancock, Detroit, MI, 48201, USA. .,Stellarray, 9210 Cameron Road Suite #300, Austin, TX, 78754, USA.
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19
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Structural analysis of multicellular organisms with cryo-electron tomography. Nat Methods 2015; 12:634-6. [PMID: 25961413 DOI: 10.1038/nmeth.3401] [Citation(s) in RCA: 68] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2014] [Accepted: 03/16/2015] [Indexed: 01/22/2023]
Abstract
We developed a method for visualizing tissues from multicellular organisms using cryo-electron tomography. Our protocol involves vitrifying samples with high-pressure freezing, thinning them with cryo-FIB-SEM (focused-ion-beam scanning electron microscopy) and applying fiducial gold markers under cryogenic conditions to the lamellae post-milling. We applied this protocol to acquire tomograms of vitrified Caenorhabditis elegans embryos and worms, which showed the intracellular organization of selected tissues at particular developmental stages in otherwise intact specimens.
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20
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Galetti E, Curtis A, Meles GA, Baptie B. Uncertainty loops in travel-time tomography from nonlinear wave physics. PHYSICAL REVIEW LETTERS 2015; 114:148501. [PMID: 25910166 DOI: 10.1103/physrevlett.114.148501] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/07/2014] [Indexed: 06/04/2023]
Abstract
Estimating image uncertainty is fundamental to guiding the interpretation of geoscientific tomographic maps. We reveal novel uncertainty topologies (loops) which indicate that while the speeds of both low- and high-velocity anomalies may be well constrained, their locations tend to remain uncertain. The effect is widespread: loops dominate around a third of United Kingdom Love wave tomographic uncertainties, changing the nature of interpretation of the observed anomalies. Loops exist due to 2nd and higher order aspects of wave physics; hence, although such structures must exist in many tomographic studies in the physical sciences and medicine, they are unobservable using standard linearized methods. Higher order methods might fruitfully be adopted.
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Affiliation(s)
- Erica Galetti
- School of GeoSciences, The University of Edinburgh, Grant Institute, The King's Buildings, James Hutton Road, Edinburgh EH9 3FE, United Kingdom
| | - Andrew Curtis
- School of GeoSciences, The University of Edinburgh, Grant Institute, The King's Buildings, James Hutton Road, Edinburgh EH9 3FE, United Kingdom
| | - Giovanni Angelo Meles
- School of GeoSciences, The University of Edinburgh, Grant Institute, The King's Buildings, James Hutton Road, Edinburgh EH9 3FE, United Kingdom
| | - Brian Baptie
- British Geological Survey, Murchison House, West Mains Road, Edinburgh EH9 3LA, United Kingdom
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21
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Hu GB. Whole cell cryo-electron tomography suggests mitochondria divide by budding. MICROSCOPY AND MICROANALYSIS : THE OFFICIAL JOURNAL OF MICROSCOPY SOCIETY OF AMERICA, MICROBEAM ANALYSIS SOCIETY, MICROSCOPICAL SOCIETY OF CANADA 2014; 20:1180-1187. [PMID: 24870811 DOI: 10.1017/s1431927614001317] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
Eukaryotes rely on mitochondrial division to guarantee that each new generation of cells acquires an adequate number of mitochondria. Mitochondrial division has long been thought to occur by binary fission and, more recently, evidence has supported the idea that binary fission is mediated by dynamin-related protein (Drp1) and the endoplasmic reticulum. However, studies to date have depended on fluorescence microscopy and conventional electron microscopy. Here, we utilize whole cell cryo-electron tomography to visualize mitochondrial division in frozen hydrated intact HeLa cells. We observe a large number of relatively small mitochondria protruding from and connected to large mitochondria or mitochondrial networks. Therefore, this study provides evidence that mitochondria divide by budding.
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Affiliation(s)
- Guo-Bin Hu
- Department of Biological Chemistry and Molecular Pharmacology,Harvard Medical School,240 Longwood Avenue,Boston,MA 02115,USA
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22
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Durrant JD, Amaro RE. LipidWrapper: an algorithm for generating large-scale membrane models of arbitrary geometry. PLoS Comput Biol 2014; 10:e1003720. [PMID: 25032790 PMCID: PMC4102414 DOI: 10.1371/journal.pcbi.1003720] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2014] [Accepted: 05/21/2014] [Indexed: 11/19/2022] Open
Abstract
As ever larger and more complex biological systems are modeled in silico, approximating physiological lipid bilayers with simple planar models becomes increasingly unrealistic. In order to build accurate large-scale models of subcellular environments, models of lipid membranes with carefully considered, biologically relevant curvature will be essential. In the current work, we present a multi-scale utility called LipidWrapper capable of creating curved membrane models with geometries derived from various sources, both experimental and theoretical. To demonstrate its utility, we use LipidWrapper to examine an important mechanism of influenza virulence. A copy of the program can be downloaded free of charge under the terms of the open-source FreeBSD License from http://nbcr.ucsd.edu/lipidwrapper. LipidWrapper has been tested on all major computer operating systems.
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Affiliation(s)
- Jacob D. Durrant
- Department of Chemistry & Biochemistry, University of California San Diego, La Jolla, California, United States of America
| | - Rommie E. Amaro
- Department of Chemistry & Biochemistry, University of California San Diego, La Jolla, California, United States of America
- * E-mail:
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23
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Law SM, Frank AT, Brooks CL. PCASSO: a fast and efficient Cα-based method for accurately assigning protein secondary structure elements. J Comput Chem 2014; 35:1757-61. [PMID: 24995959 DOI: 10.1002/jcc.23683] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2014] [Revised: 06/05/2014] [Accepted: 06/24/2014] [Indexed: 11/10/2022]
Abstract
Proteins are often characterized in terms of their primary, secondary, tertiary, and quaternary structure. Algorithms such as define secondary structure of proteins (DSSP) can automatically assign protein secondary structure based on the backbone hydrogen-bonding pattern. However, the assignment of secondary structure elements (SSEs) becomes a challenge when only the Cα coordinates are available. In this work, we present protein C-alpha secondary structure output (PCASSO), a fast and accurate program for assigning protein SSEs using only the Cα positions. PCASSO achieves ∼95% accuracy with respect to DSSP and takes ∼0.1 s using a single processor to analyze a 1000 residue system with multiple chains. Our approach was compared with current state-of-the-art Cα-based methods and was found to outperform all of them in both speed and accuracy. A practical application is also presented and discussed.
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Affiliation(s)
- Sean M Law
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan, 48109; Department of Biophysics, University of Michigan, Ann Arbor, Michigan, 48109, Fax: +1 (734) 647 1604
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24
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Harapin J, Eibauer M, Medalia O. Structural analysis of supramolecular assemblies by cryo-electron tomography. Structure 2014; 21:1522-30. [PMID: 24010711 DOI: 10.1016/j.str.2013.08.003] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2013] [Revised: 08/05/2013] [Accepted: 08/07/2013] [Indexed: 11/29/2022]
Abstract
Structural analysis of macromolecular assemblies in their physiological environment is a challenging task that is instrumental in answering fundamental questions in cellular and molecular structural biology. The continuous development of computational and analytical tools for cryo-electron tomography (cryo-ET) enables the study of these assemblies at a resolution of a few nanometers. Through the implementation of thinning procedures, cryo-ET can now be applied to the reconstruction of macromolecular structures located inside thick regions of vitrified cells and tissues, thus becoming a central tool for structural determinations in various biological disciplines. Here, we focus on the successful in situ applications of cryo-ET to reveal structures of macromolecular complexes within eukaryotic cells.
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Affiliation(s)
- Jan Harapin
- Department of Biochemistry, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland
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25
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Elia N, Ott C, Lippincott-Schwartz J. Incisive imaging and computation for cellular mysteries: lessons from abscission. Cell 2014; 155:1220-31. [PMID: 24315094 DOI: 10.1016/j.cell.2013.11.011] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2013] [Indexed: 02/06/2023]
Abstract
The final cleavage event that terminates cell division, abscission of the small, dense intercellular bridge, has been particularly challenging to resolve. Here, we describe imaging innovations that helped answer long-standing questions about the mechanism of abscission. We further explain how computational modeling of high-resolution data was employed to test hypotheses and generate additional insights. We present the model that emerges from application of these complimentary approaches. Similar experimental strategies will undoubtedly reveal exciting details about other underresolved cellular structures.
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Affiliation(s)
- Natalie Elia
- Department of Life Sciences and the NIBN, Ben Gurion University of the Negev, Beer Sheva 84105, Israel.
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26
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Davidson PM, Lammerding J. Broken nuclei--lamins, nuclear mechanics, and disease. Trends Cell Biol 2013; 24:247-56. [PMID: 24309562 DOI: 10.1016/j.tcb.2013.11.004] [Citation(s) in RCA: 187] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2013] [Revised: 11/04/2013] [Accepted: 11/06/2013] [Indexed: 11/19/2022]
Abstract
Mutations in lamins, which are ubiquitous nuclear intermediate filaments, lead to a variety of disorders including muscular dystrophy and dilated cardiomyopathy. Lamins provide nuclear stability, help connect the nucleus to the cytoskeleton, and can modulate chromatin organization and gene expression. Nonetheless, the diverse functions of lamins remain incompletely understood. We focus here on the role of lamins on nuclear mechanics and their involvement in human diseases. Recent findings suggest that lamin mutations can decrease nuclear stability, increase nuclear fragility, and disturb mechanotransduction signaling, possibly explaining the muscle-specific defects in many laminopathies. At the same time, altered lamin expression has been reported in many cancers, where the resulting increased nuclear deformability could enhance the ability of cells to transit tight interstitial spaces, thereby promoting metastasis.
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Affiliation(s)
- Patricia M Davidson
- Weill Institute for Cell and Molecular Biology, Cornell University, 526 Campus Road, Ithaca, NY 14853, USA
| | - Jan Lammerding
- Department of Biomedical Engineering/Weill Institute for Cell and Molecular Biology, Cornell University, 526 Campus Road, Ithaca, NY 14853, USA.
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27
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Delgado L, Carrión O, Martínez G, López-Iglesias C, Mercadé E. The stack: a new bacterial structure analyzed in the Antarctic bacterium Pseudomonas deceptionensis M1(T) by transmission electron microscopy and tomography. PLoS One 2013; 8:e73297. [PMID: 24039905 PMCID: PMC3767748 DOI: 10.1371/journal.pone.0073297] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2013] [Accepted: 07/18/2013] [Indexed: 01/06/2023] Open
Abstract
In recent years, improvements in transmission electron microscopy (TEM) techniques and the use of tomography have provided a more accurate view of the complexity of the ultrastructure of prokaryotic cells. Cryoimmobilization of specimens by rapid cooling followed by freeze substitution (FS) and sectioning, freeze fracture (FF) and observation of replica, or cryoelectron microscopy of vitreous sections (CEMOVIS) now allow visualization of biological samples close to their native state, enabling us to refine our knowledge of already known bacterial structures and to discover new ones. Application of these techniques to the new Antarctic cold-adapted bacterium Pseudomonasdeceptionensis M1T has demonstrated the existence of a previously undescribed cytoplasmic structure that does not correspond to known bacterial inclusion bodies or membranous formations. This structure, which we term a “stack”, was mainly visualized in slow growing cultures of P. deceptionensis M1T and can be described as a set of stacked membranous discs usually arranged perpendicularly to the cell membrane, but not continuous with it, and found in variable number in different locations within the cell. Regardless of their position, stacks were mostly observed very close to DNA fibers. Stacks are not exclusive to P. deceptionensis M1T and were also visualized in slow-growing cultures of other bacteria. This new structure deserves further study using cryoelectron tomography to refine its configuration and to establish whether its function could be related to chromosome dynamics.
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Affiliation(s)
- Lidia Delgado
- Crio-Microscòpia Electrònica. Centres Científics i Tecnològics, Universitat de Barcelona, Barcelona, Spain
- Laboratori de Microbiologia, Facultat de Farmàcia, Universitat de Barcelona, Barcelona, Spain
| | - Ornella Carrión
- Laboratori de Microbiologia, Facultat de Farmàcia, Universitat de Barcelona, Barcelona, Spain
| | - Gema Martínez
- Crio-Microscòpia Electrònica. Centres Científics i Tecnològics, Universitat de Barcelona, Barcelona, Spain
| | - Carmen López-Iglesias
- Crio-Microscòpia Electrònica. Centres Científics i Tecnològics, Universitat de Barcelona, Barcelona, Spain
- * E-mail: ; (CLL)
| | - Elena Mercadé
- Laboratori de Microbiologia, Facultat de Farmàcia, Universitat de Barcelona, Barcelona, Spain
- * E-mail: ; (CLL)
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28
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Elad N, Volberg T, Patla I, Hirschfeld-Warneken V, Grashoff C, Spatz JP, Fässler R, Geiger B, Medalia O. The role of integrin-linked kinase in the molecular architecture of focal adhesions. J Cell Sci 2013; 126:4099-107. [PMID: 23843624 DOI: 10.1242/jcs.120295] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
Integrin-mediated focal adhesions (FAs) are large, multi-protein complexes that link the actin cytoskeleton to the extracellular matrix and take part in adhesion-mediated signaling. These adhesions are highly complex and diverse at the molecular level; thus, assigning particular structural or signaling functions to specific components is highly challenging. Here, we combined functional, structural and biophysical approaches to assess the role of a major FA component, namely, integrin-linked kinase (ILK), in adhesion formation. We show here that ILK plays a key role in the formation of focal complexes, early forms of integrin adhesions, and confirm its involvement in the assembly of fibronectin-bound fibrillar adhesions. Examination of ILK-null fibroblasts by cryo-electron tomography pointed to major structural changes in their FAs, manifested as disarray of the associated actin filaments and an increase in the packing density of FA-related particles. Interestingly, adhesion of the mutant cells to the substrate required a higher ligand density than in control cells. These data indicate that ILK has a key role in integrin adhesion assembly and sub-structure, and in the regulation of the FA-associated cytoskeleton.
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Affiliation(s)
- Nadav Elad
- Department of Life Sciences and the National Institute for Biotechnology in the Negev, Ben Gurion University of the Negev, Beer-Sheva 84120, Israel
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29
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Abstract
Lamin proteins are the major constituents of the nuclear lamina, a proteinaceous network that lines the inner nuclear membrane. Primarily, the nuclear lamina provides structural support for the nucleus and the nuclear envelope; however, lamins and their associated proteins are also involved in most of the nuclear processes, including DNA replication and repair, regulation of gene expression, and signaling. Mutations in human lamin A and associated proteins were found to cause a large number of diseases, termed 'laminopathies.' These diseases include muscular dystrophies, lipodystrophies, neuropathies, and premature aging syndromes. Despite the growing number of studies on lamins and their associated proteins, the molecular organization of lamins in health and disease is still elusive. Likewise, there is no comprehensive view how mutations in lamins result in a plethora of diseases, selectively affecting different tissues. Here, we discuss some of the structural aspects of lamins and the nuclear lamina organization, in light of recent results.
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30
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Parmryd I, Onfelt B. Consequences of membrane topography. FEBS J 2013; 280:2775-84. [PMID: 23438106 DOI: 10.1111/febs.12209] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2012] [Revised: 01/11/2013] [Accepted: 02/18/2013] [Indexed: 12/28/2022]
Abstract
The surface of mammalian cells is neither smooth nor flat and cells have several times more plasma membrane than the minimum area required to accommodate their shape. We discuss the biological function of this apparent excess membrane that allows the cells to migrate and undergo shape changes and probably plays a role in signal transduction. Methods for studying membrane folding and topography--atomic force microscopy, scanning ion conductance microscopy, fluorescence polarization microscopy and linear dichroism--are described and evaluated. Membrane folding and topography is frequently ignored when interpreting microscopy data. This has resulted in several misconceptions regarding for instance colocalization, membrane organization and molecular clustering. We suggest simple ways to avoid these pitfalls and invoke Occam's razor--that simple explanations are preferable to complex ones. Topography, i.e. deviations from a smooth surface, should always be ruled out as the cause of anomalous data before other explanations are presented.
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Affiliation(s)
- Ingela Parmryd
- Department of Medical Cell Biology, Uppsala University, Sweden.
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31
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Linnik O, Liesche J, Tilsner J, Oparka KJ. Unraveling the structure of viral replication complexes at super-resolution. FRONTIERS IN PLANT SCIENCE 2013; 4:6. [PMID: 23386855 PMCID: PMC3560349 DOI: 10.3389/fpls.2013.00006] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/15/2012] [Accepted: 01/09/2013] [Indexed: 05/20/2023]
Abstract
During infection, many RNA viruses produce characteristic inclusion bodies that contain both viral and host components. These structures were first described over a century ago and originally termed "X-bodies," as their function was not immediately appreciated. Whilst some inclusion bodies may represent cytopathic by-products of viral protein over-accumulation, X-bodies have emerged as virus "factories," quasi-organelles that coordinate diverse viral infection processes such as replication, protein expression, evasion of host defenses, virion assembly, and intercellular transport. Accordingly, they are now generally referred to as viral replication complexes (VRCs). We previously used confocal fluorescence microscopy to unravel the complex structure of X-bodies produced by Potato virus X (PVX). Here we used 3D-structured illumination (3D-SIM) super-resolution microscopy to map the PVX X-body at a finer scale. We identify a previously unrecognized membrane structure induced by the PVX "triple gene block" (TGB) proteins, providing new insights into the complex interplay between virus and host within the X-body.
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Affiliation(s)
- Olga Linnik
- Institute of Molecular Plant Sciences, University of EdinburghEdinburgh, UK
| | - Johannes Liesche
- Faculty of Life Sciences, University of CopenhagenFrederiksberg C, Denmark
| | - Jens Tilsner
- Biomedical Sciences Research Complex, University of St AndrewsFife, UK
- Cell and Molecular Sciences, The James Hutton InstituteDundee, UK
| | - Karl J. Oparka
- Institute of Molecular Plant Sciences, University of EdinburghEdinburgh, UK
- *Correspondence: Karl J. Oparka, Institute of Molecular Plant Sciences, University of Edinburgh, King’s Buildings, Mayfield Road, Edinburgh EH9 3JR, UK. e-mail:
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32
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Viewing Golgi structure and function from a different perspective--insights from electron tomography. Methods Cell Biol 2013; 118:259-79. [PMID: 24295312 DOI: 10.1016/b978-0-12-417164-0.00016-1] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/09/2022]
Abstract
Historically, ultrastructural investigations, which have focused on elucidating the biological idiosyncrasies of the Golgi apparatus, have tended towards oversimplified or fallacious hypotheses when postulating how the Golgi apparatus reorganizes itself both structurally and functionally to fulfill the plethora of cellular processes underpinned by this complex organelle. Key questions are still unanswered with regard to how changes in Golgi architecture correlate so reproducibly to changes in its functional priorities under different physiological conditions or experimental perturbations. This fact alone serves to highlight how the technical limitations associated with conventional two-dimensional imaging approaches employed in the past failed to adequately capture the extraordinary complexity of the Golgi's three-dimensional (3D) structure-now a hallmark of this challenging organelle. Consequently, this has hampered progress towards developing a clear understanding of how changes in its structure and function typically occur in parallel. In this chapter, we highlight but a few of the significant new insights regarding variations in the Golgi's structure-function relationships that have been afforded over recent years through advanced electron microscopic techniques for 3D image reconstruction, commonly referred to as electron tomography.
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