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Sazzed S, Scheible P, He J, Wriggers W. Untangling Irregular Actin Cytoskeleton Architectures in Tomograms of the Cell with Struwwel Tracer. Int J Mol Sci 2023; 24:17183. [PMID: 38139012 PMCID: PMC10743648 DOI: 10.3390/ijms242417183] [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: 10/09/2023] [Revised: 11/09/2023] [Accepted: 11/15/2023] [Indexed: 12/24/2023] Open
Abstract
In this work, we established, validated, and optimized a novel computational framework for tracing arbitrarily oriented actin filaments in cryo-electron tomography maps. Our approach was designed for highly complex intracellular architectures in which a long-range cytoskeleton network extends throughout the cell bodies and protrusions. The irregular organization of the actin network, as well as cryo-electron-tomography-specific noise, missing wedge artifacts, and map dimensions call for a specialized implementation that is both robust and efficient. Our proposed solution, Struwwel Tracer, accumulates densities along paths of a specific length in various directions, starting from locally determined seed points. The highest-density paths originating from the seed points form short linear candidate filament segments, which are further scrutinized and classified by users via inspection of a novel pruning map, which visualizes the likelihood of being a part of longer filaments. The pruned linear candidate filament segments are then iteratively fused into continuous, longer, and curved filaments based on their relative orientations, gap spacings, and extendibility. When applied to the simulated phantom tomograms of a Dictyostelium discoideum filopodium under experimental conditions, Struwwel Tracer demonstrated high efficacy, with F1-scores ranging from 0.85 to 0.90, depending on the noise level. Furthermore, when applied to a previously untraced experimental tomogram of mouse fibroblast lamellipodia, the filaments predicted by Struwwel Tracer exhibited a good visual agreement with the experimental map. The Struwwel Tracer framework is highly time efficient and can complete the tracing process in just a few minutes. The source code is publicly available with version 3.2 of the free and open-source Situs software package.
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Affiliation(s)
- Salim Sazzed
- Department of Computer Science, Old Dominion University, Norfolk, VA 23529, USA; (S.S.)
| | - Peter Scheible
- Department of Computer Science, Old Dominion University, Norfolk, VA 23529, USA; (S.S.)
| | - Jing He
- Department of Computer Science, Old Dominion University, Norfolk, VA 23529, USA; (S.S.)
| | - Willy Wriggers
- Department of Mechanical and Aerospace Engineering, Old Dominion University, Norfolk, VA 23529, USA
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Sazzed S, Scheible P, He J, Wriggers W. Tracing Randomly Oriented Filaments in Cryo-Electron Tomography Maps. MICROSCOPY AND MICROANALYSIS : THE OFFICIAL JOURNAL OF MICROSCOPY SOCIETY OF AMERICA, MICROBEAM ANALYSIS SOCIETY, MICROSCOPICAL SOCIETY OF CANADA 2023; 29:915-916. [PMID: 37613398 DOI: 10.1093/micmic/ozad067.453] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/25/2023]
Affiliation(s)
- Salim Sazzed
- Dept. of Computer Science, Old Dominion University, Norfolk, VA, United States
| | - Peter Scheible
- Dept. of Computer Science, Old Dominion University, Norfolk, VA, United States
| | - Jing He
- Dept. of Computer Science, Old Dominion University, Norfolk, VA, United States
| | - Willy Wriggers
- Dept. of Mechanical & Aerospace Engineering, Old Dominion University, Norfolk, VA, United States
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Sazzed S, Scheible P, He J, Wriggers W. Spaghetti Tracer: A Framework for Tracing Semiregular Filamentous Densities in 3D Tomograms. Biomolecules 2022; 12:biom12081022. [PMID: 35892332 PMCID: PMC9394354 DOI: 10.3390/biom12081022] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2022] [Revised: 07/13/2022] [Accepted: 07/17/2022] [Indexed: 11/30/2022] Open
Abstract
Within cells, cytoskeletal filaments are often arranged into loosely aligned bundles. These fibrous bundles are dense enough to exhibit a certain regularity and mean direction, however, their packing is not sufficient to impose a symmetry between—or specific shape on—individual filaments. This intermediate regularity is computationally difficult to handle because individual filaments have a certain directional freedom, however, the filament densities are not well segmented from each other (especially in the presence of noise, such as in cryo-electron tomography). In this paper, we develop a dynamic programming-based framework, Spaghetti Tracer, to characterizing the structural arrangement of filaments in the challenging 3D maps of subcellular components. Assuming that the tomogram can be rotated such that the filaments are oriented in a mean direction, the proposed framework first identifies local seed points for candidate filament segments, which are then grown from the seeds using a dynamic programming algorithm. We validate various algorithmic variations of our framework on simulated tomograms that closely mimic the noise and appearance of experimental maps. As we know the ground truth in the simulated tomograms, the statistical analysis consisting of precision, recall, and F1 scores allows us to optimize the performance of this new approach. We find that a bipyramidal accumulation scheme for path density is superior to straight-line accumulation. In addition, the multiplication of forward and backward path densities provides for an efficient filter that lifts the filament density above the noise level. Resulting from our tests is a robust method that can be expected to perform well (F1 scores 0.86–0.95) under experimental noise conditions.
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Affiliation(s)
- Salim Sazzed
- Department of Computer Science, Old Dominion University, Norfolk, VA 23529, USA; (S.S.); (P.S.)
| | - Peter Scheible
- Department of Computer Science, Old Dominion University, Norfolk, VA 23529, USA; (S.S.); (P.S.)
| | - Jing He
- Department of Computer Science, Old Dominion University, Norfolk, VA 23529, USA; (S.S.); (P.S.)
- Correspondence: (J.H.); (W.W.)
| | - Willy Wriggers
- Department of Mechanical and Aerospace Engineering, Old Dominion University, Norfolk, VA 23529, USA
- Correspondence: (J.H.); (W.W.)
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Scheible P, Sazzed S, He J, Wriggers W. TomoSim: Simulation of Filamentous Cryo-Electron Tomograms. PROCEEDINGS. IEEE INTERNATIONAL CONFERENCE ON BIOINFORMATICS AND BIOMEDICINE 2021; 2021:2560-2565. [PMID: 37448648 PMCID: PMC10338425 DOI: 10.1109/bibm52615.2021.9669370] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/15/2023]
Abstract
As automated filament tracing algorithms in cryo-electron tomography (cryo-ET) continue to improve, the validation of these approaches has become more incumbent. Having a known ground truth on which to base predictions is crucial to reliably test predicted cytoskeletal filaments because the detailed structure of the filaments in experimental tomograms is obscured by a low resolution, as well as by noise and missing Fourier space wedge artifacts. We present a software tool for the realistic simulation of tomographic maps (TomoSim) based on a known filament trace. The parameters of the simulated map are automatically matched to those of a corresponding experimental map. We describe the computational details of the first prototype of our approach, which includes wedge masking in Fourier space, noise color, and signal-to-noise matching. We also discuss current and potential future applications of the approach in the validation of concurrent filament tracing methods in cryo-ET.
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Affiliation(s)
- Peter Scheible
- Department of Computer Science, Old Dominion University, Norfolk, VA 23529
| | - Salim Sazzed
- Department of Computer Science, Old Dominion University, Norfolk, VA 23529
| | - Jing He
- Department of Computer Science, Old Dominion University, Norfolk, VA 23529
| | - Willy Wriggers
- Department of Mechanical and Aerospace Engineering, Old Dominion University, Norfolk, VA 23529
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Sazzed S, Scheible P, He J, Wriggers W. Tracing Filaments in Simulated 3D Cryo-Electron Tomography Maps Using a Fast Dynamic Programming Algorithm. PROCEEDINGS. IEEE INTERNATIONAL CONFERENCE ON BIOINFORMATICS AND BIOMEDICINE 2021; 2021:2553-2559. [PMID: 37465415 PMCID: PMC10353374 DOI: 10.1109/bibm52615.2021.9669318] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/20/2023]
Abstract
We propose a fast, dynamic programming-based framework for tracing actin filaments in 3D maps of subcellular components in cryo-electron tomography. The approach can identify high-density filament segments in various orientations, but it takes advantage of the arrangement of actin filaments within cells into more or less tightly aligned bundles. Assuming that the tomogram can be rotated such that the filaments can be oriented to be directed in a dominant direction (i.e., the X, Y, or Z axis), the proposed framework first identifies local seed points that form the origin of candidate filament segments (CFSs), which are then grown from the seeds using a fast dynamic programming algorithm. The CFS length l can be tuned to the nominal resolution of the tomogram or the separation of desired features, or it can be used to restrict the curvature of filaments that deviate from the overall bundle direction. In subsequent steps, the CFSs are filtered based on backward tracing and path density analysis. Finally, neighboring CFSs are fused based on a collinearity criterion to bridge any noise artifacts in the 3D map that would otherwise fractionalize the tracing. We validate our proposed framework on simulated tomograms that closely mimic the features and appearance of experimental maps.
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Affiliation(s)
- Salim Sazzed
- Department of Computer Science, Old Dominion University, Norfolk, VA 23529
| | - Peter Scheible
- Department of Computer Science, Old Dominion University, Norfolk, VA 23529
| | - Jing He
- Department of Computer Science, Old Dominion University, Norfolk, VA 23529
| | - Willy Wriggers
- Department of Mechanical and Aerospace Engineering, Old Dominion University, Norfolk, VA 23529
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Palermo G, Sugita Y, Wriggers W, Amaro RE. Faces of Contemporary CryoEM Information and Modeling. J Chem Inf Model 2021; 60:2407-2409. [PMID: 32452204 DOI: 10.1021/acs.jcim.0c00481] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Giulia Palermo
- Department of Bioengineering, University of California Riverside, Riverside, California 92521, United States
| | - Yuji Sugita
- Theoretical Molecular Science Laboratory, RIKEN Cluster for Pioneering Research, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan.,Computational Biophysics Research Team, RIKEN Center for Computational Science, 7-1-26 Minatojima-Minamimachi, Chuo-ku, Kobe, Hyogo 650-0047, Japan.,Laboratory for Biomolecular Function Simulation, RIKEN Center for Biosystems Dynamics Research, 1-6-5 Minatojima-Minamimachi, Chuo-ku, Kobe, Hyogo 650-0047, Japan
| | - Willy Wriggers
- Department of Mechanical and Aerospace Engineering, Old Dominion University, Norfolk, Virginia 23529, United States
| | - Rommie E Amaro
- Department of Chemistry and Biochemistry, University of California San Diego, San Diego, California 92093-0340, United States
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