Delaunay algorithm and principal component analysis for 3D visualization of mitochondrial DNA nucleoids by Biplane FPALM/dSTORM
Jazyk angličtina Země Německo Médium print-electronic
Typ dokumentu časopisecké články
PubMed
26846371
DOI
10.1007/s00249-016-1114-5
PII: 10.1007/s00249-016-1114-5
Knihovny.cz E-zdroje
- Klíčová slova
- 3D object segmentation, 3D super-resolution microscopy, Delaunay algorithm, Mitochondrial DNA replication, Nucleoids, Principal component analysis,
- MeSH
- algoritmy * MeSH
- analýza hlavních komponent * MeSH
- buňky Hep G2 MeSH
- DNA vazebné proteiny metabolismus MeSH
- fluorescenční mikroskopie * MeSH
- konformace nukleové kyseliny MeSH
- lidé MeSH
- mitochondriální DNA chemie metabolismus MeSH
- mitochondriální proteiny metabolismus MeSH
- molekulární modely MeSH
- zobrazování trojrozměrné * MeSH
- Check Tag
- lidé MeSH
- Publikační typ
- časopisecké články MeSH
- Názvy látek
- DNA vazebné proteiny MeSH
- mitochondriální DNA MeSH
- mitochondriální proteiny MeSH
- NABP2 protein, human MeSH Prohlížeč
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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Trends Biochem Sci. 2009 Jul;34(7):358-65 PubMed
J Biol Chem. 2013 Oct 25;288(43):31386-99 PubMed
Mitochondrion. 2011 Jan;11(1):191-9 PubMed
Annu Rev Biochem. 2007;76:679-99 PubMed
J Cell Biol. 2008 Jun 30;181(7):1117-28 PubMed
Opt Express. 2011 Aug 1;19(16):15009-19 PubMed
Proc Natl Acad Sci U S A. 2012 Apr 17;109(16):6136-41 PubMed
J Biol Chem. 2003 Dec 5;278(49):48627-32 PubMed
Physiol Rev. 2008 Apr;88(2):611-38 PubMed
Nat Methods. 2008 Jun;5(6):527-9 PubMed
J Microsc. 2009 Oct;236(1):35-43 PubMed
Opt Express. 2012 Sep 10;20(19):20998-1009 PubMed
Biochim Biophys Acta. 2012 Sep-Oct;1819(9-10):1075-9 PubMed
Nat Methods. 2011 Apr;8(4):353-9 PubMed
Biochim Biophys Acta. 2008 Jul-Aug;1777(7-8):834-46 PubMed
Cell Metab. 2013 Mar 5;17(3):386-98 PubMed
Int J Biochem Cell Biol. 2013 Mar;45(3):593-603 PubMed
Trends Genet. 2010 Mar;26(3):103-9 PubMed
J Bioenerg Biomembr. 2015 Jun;47(3):255-63 PubMed
Opt Lett. 2015 Jun 1;40(11):2653-6 PubMed
Biochim Biophys Acta. 2010 Aug;1803(8):931-9 PubMed
Genome Res. 2011 Jan;21(1):12-20 PubMed
Nano Lett. 2009 Jun;9(6):2508-10 PubMed
Hum Mol Genet. 2013 May 15;22(10):1983-93 PubMed
Arch Biochem Biophys. 1990 Oct;282(1):116-24 PubMed
Proc Natl Acad Sci U S A. 2009 Dec 29;106(52):22275-80 PubMed
Biochim Biophys Acta. 2012 Sep-Oct;1819(9-10):914-20 PubMed
Proc Natl Acad Sci U S A. 2011 Aug 16;108(33):13534-9 PubMed
Cell Biochem Biophys. 2013 Jul;66(3):489-97 PubMed
Cell Metab. 2009 Aug;10(2):110-8 PubMed
Nat Struct Mol Biol. 2011 Oct 30;18(11):1290-6 PubMed
J Biol Chem. 2008 Feb 8;283(6):3665-75 PubMed
IUBMB Life. 2010 Jan;62(1):19-32 PubMed
Opt Express. 2014 Mar 24;22(6):7028-39 PubMed
Annu Rev Biochem. 2004;73:293-320 PubMed
Proc Natl Acad Sci U S A. 2015 Sep 8;112(36):11288-93 PubMed
Mitochondrion. 2007 Sep;7(5):311-21 PubMed
Trends Biochem Sci. 2007 Mar;32(3):111-7 PubMed
J Cell Biol. 1985 Jan;100(1):251-7 PubMed
Biochim Biophys Acta. 2010 Jun-Jul;1797(6-7):1327-41 PubMed
Cancer Res. 2004 Feb 1;64(3):985-93 PubMed
Mol Cell Biol. 2011 Dec;31(24):4994-5010 PubMed
Biochim Biophys Acta. 2012 Sep-Oct;1819(9-10):921-9 PubMed
