Automated quantification and integrative analysis of 2D and 3D mitochondrial shape and network properties

PLoS ONE

Volumn 9, Issue 7, 2014, Pages

  Nikolaisen, Julie ^a   Nilsson, Linn I H ^a   Pettersen, Ina K N ^a   Willems, Peter H G M ^b   Lorens, James B ^a   Koopman, Werner J H ^b   Tronstad, Karl J ^a  

^a UNIVERSITY OF BERGEN   (Norway)

^b RADBOUD UNIVERSITY MEDICAL CENTER   (Netherlands)

Author keywords

[No Author keywords available]

Indexed keywords

GREEN FLUORESCENT PROTEIN; MITOCHONDRIA GREEN FLUORESCENT PROTEIN; ROTENONE; UNCLASSIFIED DRUG;

ARTICLE; AUTOMATION; BIOMASS; CELL ORGANELLE; CELL STRUCTURE; CLASSIFICATION ALGORITHM; CONFOCAL MICROSCOPY; CONTROLLED STUDY; DNA FRAGMENTATION; ENDOTHELIUM CELL; HUMAN; HUMAN CELL; IMAGE ANALYSIS; INFORMATION PROCESSING; MEMBRANE STRUCTURE; METABOLIC STRESS; MITOCHONDRIAL VOLUME; ORGANELLE SIZE; THREE DIMENSIONAL ANALYSIS; TWO DIMENSIONAL ANALYSIS; ALGORITHM; COMPUTER PROGRAM; FOURIER ANALYSIS; MITOCHONDRION; PROCEDURES; THREE DIMENSIONAL IMAGING; ULTRASTRUCTURE; UMBILICAL VEIN ENDOTHELIAL CELL;

ALGORITHMS; FOURIER ANALYSIS; GREEN FLUORESCENT PROTEINS; HUMAN UMBILICAL VEIN ENDOTHELIAL CELLS; HUMANS; IMAGING, THREE-DIMENSIONAL; MICROSCOPY, CONFOCAL; MITOCHONDRIA; SOFTWARE;

EID: 84903775307     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0101365     Document Type: Article

References (47)

1. Mitchell P (1961) Coupling of phosphorylation to electron and hydrogen transfer by a chemi-osmotic type of mechanism. Nature 191: 144-148.
2. Hagland H, Nikolaisen J, Hodneland LI, Gjertsen BT, Bruserud O, et al. (2007) Targeting mitochondria in the treatment of human cancer: a coordinated attack against cancer cell energy metabolism and signalling. Expert Opin Ther Targets 11: 1055-1069. (Pubitemid 47232621)
3. Carew JS, Huang P (2002) Mitochondrial defects in cancer. Mol Cancer 1: 9.
4. Civitarese AE, Carling S, Heilbronn LK, Hulver MH, Ukropcova B, et al. (2007) Calorie restriction increases muscle mitochondrial biogenesis in healthy humans. PLoS med 4: e76.
5. Supale S, Li N, Brun T, Maechler P (2012) Mitochondrial dysfunction in pancreatic beta cells. Trends Endocrinol Metab 23: 477-487.
6. Tronstad KJ, Nooteboom M, Nilsson LIH, Nikolaisen J, Sokolewicz M, et al. (2014) Regulation and quantification of cellular mitochondrial morphology and content. Curr Pharm Des.
7. Ryan MT, Hoogenraad NJ (2007) Mitochondrial-nuclear communications. Annu Rev Biochem 76: 701-722.
8. Kornmann B, Currie E, Collins SR, Schuldiner M, Nunnari J, et al. (2009) An ER-mitochondria tethering complex revealed by a synthetic biology screen. Science 325: 477-481.
9. Pucci B, Bertani F, Karpinich NO, Indelicato M, Russo MA, et al. (2008) Detailing the role of Bax translocation, cytochrome c release, and perinuclear clustering of the mitochondria in the killing of HeLa cells by TNF. J Cell Physiol 217: 442-449.
10. Frederick RL, Shaw JM (2007) Moving mitochondria: establishing distribution of an essential organelle. Traffic 8: 1668-1675. (Pubitemid 350066679)
11. Cereghetti GM, Scorrano L (2006) The many shapes of mitochondrial death. Oncogene 25: 4717-4724. (Pubitemid 44187621)
12. Benard G, Bellance N, James D, Parrone P, Fernandez H, et al. (2007) Mitochondrial bioenergetics and structural network organization. J Cell Sci 120: 838-848. (Pubitemid 46523485)
13. Frazier AE, Kiu C, Stojanovski D, Hoogenraad NJ, Ryan MT (2006) Mitochondrial morphology and distribution in mammalian cells. Biol Chem 387: 1551-1558. (Pubitemid 44837579)
14. Frank S, Gaume B, Bergmann-Leitner ES, Leitner WW, Robert EG, et al. (2001) The role of dynamin-related protein 1, a mediator of mitochondrial fission, in apoptosis. Dev Cell 1: 515-525. (Pubitemid 33586103)
15. Liesa M, Borda-d'Agua B, Medina-Gomez G, Lelliott CJ, Paz JC, et al. (2008) Mitochondrial fusion is increased by the nuclear coactivator PGC-1beta. PloS one 3: e3613.
16. Egner A, Jakobs S, Hell SW (2002) Fast 100-nm resolution three-dimensional microscope reveals structural plasticity of mitochondria in live yeast. PNAS 99: 3370-3375. (Pubitemid 34252116)
17. Nunnari J, Suomalainen A (2012) Mitochondria: in sickness and in health. Cell 148: 1145-1159.
18. Koopman WJ, Willems PH, Smeitink JA (2012) Monogenic mitochondrial disorders. N Engl J Med 366: 1132-1141.
19. Bindoff LA, Desnuelle C, Birch-Machin MA, Pellissier JF, Serratrice G, et al. (1991) Multiple defects of the mitochondrial respiratory chain in a mitochondrial encephalopathy (MERRF): a clinical, biochemical and molecular study. J Neurol Sci 102: 17-24.
20. Willems PH, Smeitink JA, Koopman WJ (2009) Mitochondrial dynamics in human NADH: ubiquinone oxidoreductase deficiency. Int J Biochem Cell Biol 41: 1773-1782.
21. Koopman WJ, Verkaart S, Visch HJ, van Emst-de Vries S, Nijtmans LG, et al. (2007) Human NADH: ubiquinone oxidoreductase deficiency: radical changes in mitochondrial morphology? Am J Physiol Cell Physiol 293: C22-29. (Pubitemid 47105004)
22. Giedt RJ, Pfeiffer DR, Matzavinos A, Kao CY, Alevriadou BR (2012) Mitochondrial dynamics and motility inside living vascular endothelial cells: role of bioenergetics. Ann Biomed Eng 40: 1903-1916.
23. Knott AB, Perkins G, Schwarzenbacher R, Bossy-Wetzel E (2008) Mitochondrial fragmentation in neurodegeneration. Nat Rev Neurosci 9: 505-518. (Pubitemid 351873464)
24. Koopman WJ, Visch HJ, Verkaart S, van den Heuvel LW, Smeitink JA, et al. (2005) Mitochondrial network complexity and pathological decrease in complex I activity are tightly correlated in isolated human complex I deficiency. Am J Physiol Cell Physiol 289: C881-890. (Pubitemid 41361644)
25. Mitra K, Lippincott-Schwartz J (2010) Analysis of mitochondrial dynamics and functions using imaging approaches. Curr Protoc Cell Biol Chapter 4: Unit 4 25 21-21.
26. Duchen MR, Surin A, Jacobson J (2003) Imaging mitochondrial function in intact cells. Methods Enzymol 361: 353-389. (Pubitemid 36241007)
27. Koopman WJ, Visch HJ, Smeitink JA, Willems PH (2006) Simultaneous quantitative measurement and automated analysis of mitochondrial morphology, mass, potential, and motility in living human skin fibroblasts. Cytometry A 69: 1-12. (Pubitemid 43062691)
28. Song W, Bossy B, Martin OJ, Hicks A, Lubitz S, et al. (2008) Assessing mitochondrial morphology and dynamics using fluorescence wide-field microscopy and 3D image processing. Methods 46: 295-303.
29. Campanella M, Seraphim A, Abeti R, Casswell E, Echave P, et al. (2009) IF1, the endogenous regulator of the F(1)F(o)-ATPsynthase, defines mitochondrial volume fraction in HeLa cells by regulating autophagy. Biochim Biophys Acta 1787: 393-401.
30. Chevrollier A, Cassereau J, Ferre M, Alban J, Desquiret-Dumas V, et al. (2012) Standardized mitochondrial analysis gives new insights into mitochondrial dynamics and OPA1 function. Int J Biochem Cell Biol 44: 980-988.
31. Lihavainen E, Makela J, Spelbrink JN, Ribeiro AS (2012) Mytoe: automatic analysis of mitochondrial dynamics. Bioinformatics 28: 1050-1051.
32. Zhu M, Li W, Lu C (2012) Role of alpha-synuclein protein levels in mitochondrial morphology and cell survival in cell lines. PloS One 7: e36377.
33. Koopman WJ, Verkaart S, Visch HJ, van der Westhuizen FH, Murphy MP, et al. (2005) Inhibition of complex I of the electron transport chain causes O2-. - mediated mitochondrial outgrowth. Am J Physiol Cell Physiol 288: C1440-1450. (Pubitemid 40991081)
34. Distelmaier F, Koopman WJ, Testa ER, de Jong AS, Swarts HG, et al. (2008) Life cell quantification of mitochondrial membrane potential at the single organelle level. Cytometry A 73: 129-138.
35. Koopman WJ, Distelmaier F, Esseling JJ, Smeitink JA, Willems PH (2008) Computer-assisted live cell analysis of mitochondrial membrane potential, morphology and calcium handling. Methods 46: 304-311.
36. Mortiboys H, Thomas KJ, Koopman WJ, Klaffke S, Abou-Sleiman P, et al. (2008) Mitochondrial function and morphology are impaired in parkin-mutant fibroblasts. Ann Neurol 64: 555-565.
37. Eisenberg I, Novershtern N, Itzhaki Z, Becker-Cohen M, Sadeh M, et al. (2008) Mitochondrial processes are impaired in hereditary inclusion body myopathy. Hum Mol Genet 17: 3663-3674.
38. Heeman B, Van den Haute C, Aelvoet SA, Valsecchi F, Rodenburg RJ, et al. (2011) Depletion of PINK1 affects mitochondrial metabolism, calcium homeostasis and energy maintenance. J Cell Sci 124: 1115-1125.
39. Distelmaier F, Valsecchi F, Forkink M, van Emst-de Vries S, Swarts HG, et al. (2012) Trolox-sensitive reactive oxygen species regulate mitochondrial morphology, oxidative phosphorylation and cytosolic calcium handling in healthy cells. Antioxid Redox Signal 17: 1657-1669.
40. Willems P, Wanschers BF, Esseling J, Szklarczyk R, Kudla U, et al. (2013) BOLA1 is an aerobic protein that prevents mitochondrial morphology changes induced by glutathione depletion. Antioxid Redox Signal 18: 129-138.
41. Swift S, Lorens J, Achacoso P, Nolan GP (2001) Rapid production of retroviruses for efficient gene delivery to mammalian cells using 293T cell-based systems. Curr Protoc Immunol Chapter 10: Unit 10 17C.
42. Lorens JB, Bennett MK, Pearsall DM, Throndset WR, Rossi AB, et al. (2000) Retroviral delivery of peptide modulators of cellular functions. Mol Ther 1: 438-447.
43. Biggs DS (2010) 3D deconvolution microscopy. Curr Protoc Cytom Chapter 12: Unit 12 19 11-20.
44. Collins TJ, Berridge MJ, Lipp P, Bootman MD (2002) Mitochondria are morphologically and functionally heterogeneous within cells. Embo j 21: 1616-1627. (Pubitemid 34614618)
45. Shirure VS, Reynolds NM, Burdick MM (2012) Mac-2 binding protein is a novel E-selectin ligand expressed by breast cancer cells. PLoS One 7: e44529.
46. Lee JS, Wee TL, Brown CM (2014) Calibration of wide-field deconvolution microscopy for quantitative fluorescence imaging. J Biomol Tech 25: 31-40.
47. Matthews GD, Gur N, Koopman WJ, Pines O, Vardimon L (2010) Weak mitochondrial targeting sequence determines tissue-specific subcellular localization of glutamine synthetase in liver and brain cells. J Cell Sci 123: 351-359.