Delaunay algorithm and principal component analysis for 3D visualization of mitochondrial DNA nucleoids by Biplane FPALM/dSTORM
Language English Country Germany Media print-electronic
Document type Journal Article
PubMed
26846371
DOI
10.1007/s00249-016-1114-5
PII: 10.1007/s00249-016-1114-5
Knihovny.cz E-resources
- Keywords
- 3D object segmentation, 3D super-resolution microscopy, Delaunay algorithm, Mitochondrial DNA replication, Nucleoids, Principal component analysis,
- MeSH
- Algorithms * MeSH
- Principal Component Analysis * MeSH
- Hep G2 Cells MeSH
- DNA-Binding Proteins metabolism MeSH
- Microscopy, Fluorescence * MeSH
- Nucleic Acid Conformation MeSH
- Humans MeSH
- DNA, Mitochondrial chemistry metabolism MeSH
- Mitochondrial Proteins metabolism MeSH
- Models, Molecular MeSH
- Imaging, Three-Dimensional * MeSH
- Check Tag
- Humans MeSH
- Publication type
- Journal Article MeSH
- Names of Substances
- DNA-Binding Proteins MeSH
- DNA, Mitochondrial MeSH
- Mitochondrial Proteins MeSH
- NABP2 protein, human MeSH Browser
Data segmentation and object rendering is required for localization super-resolution microscopy, fluorescent photoactivation localization microscopy (FPALM), and direct stochastic optical reconstruction microscopy (dSTORM). We developed and validated methods for segmenting objects based on Delaunay triangulation in 3D space, followed by facet culling. We applied them to visualize mitochondrial nucleoids, which confine DNA in complexes with mitochondrial (mt) transcription factor A (TFAM) and gene expression machinery proteins, such as mt single-stranded-DNA-binding protein (mtSSB). Eos2-conjugated TFAM visualized nucleoids in HepG2 cells, which was compared with dSTORM 3D-immunocytochemistry of TFAM, mtSSB, or DNA. The localized fluorophores of FPALM/dSTORM data were segmented using Delaunay triangulation into polyhedron models and by principal component analysis (PCA) into general PCA ellipsoids. The PCA ellipsoids were normalized to the smoothed volume of polyhedrons or by the net unsmoothed Delaunay volume and remodeled into rotational ellipsoids to obtain models, termed DVRE. The most frequent size of ellipsoid nucleoid model imaged via TFAM was 35 × 45 × 95 nm; or 35 × 45 × 75 nm for mtDNA cores; and 25 × 45 × 100 nm for nucleoids imaged via mtSSB. Nucleoids encompassed different point density and wide size ranges, speculatively due to different activity stemming from different TFAM/mtDNA stoichiometry/density. Considering twofold lower axial vs. lateral resolution, only bulky DVRE models with an aspect ratio >3 and tilted toward the xy-plane were considered as two proximal nucleoids, suspicious occurring after division following mtDNA replication. The existence of proximal nucleoids in mtDNA-dSTORM 3D images of mtDNA "doubling"-supported possible direct observations of mt nucleoid division after mtDNA replication.
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