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exist together
coexist peacefully, as of nations
existing peacefully together

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(…と)共存する,両立する《+『with』+『名』》
共存,併立

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出典(authority):フリー百科事典『ウィキペディア（Wikipedia）』「2012/06/01 12:01:50」(JST)

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In fluorescence microscopy, colocalization refers to observation of the spatial overlap between two (or more) different fluorescent labels, each having a separate emission wavelength, to see if the different "targets" are located in the same area of the cell or very near to one another. The definition can be split into two different phenomena, co-occurrence, which refers to the presence of two (possibly unrelated) fluorophores in the same pixel, and correlation, a much more significant statistical relationship between the fluorophores indicative of a biological interaction.^[1]. This technique is important to many cell biological and physiological studies during the demonstration of a relationship between pairs of bio-molecules.

History of Colocalization

The ability to demonstrate a correlation between a pair of bio-molecules was greatly enhanced by Erik Manders of the University of Amsterdam who introduced Pearson's Correlation Coefficient to microscopists^[2], along with other coefficients of which the "overlap coefficients" M1 and M2 have proved to be the most popular and useful ^[3]^[4]. The purpose of using coefficients is to characterize the degree of overlap between images, usually two channels in a multidimensional microscopy image recorded at different emission wave lengths. A popular approach was introduced by Sylvain Costes, who utilized Pearson's Correlation Coefficient as a tool for setting the thresholds required by M1 and M2 in an objective fashion ^[5]. Costes approach makes the assumption that only positive correlations are of interest, and does not provide a useful measurement of PCC.

Although the use of coefficients can significantly improve the reliability of colocalization detection, it depends on the number of factors, including the conditions of how samples with fluorescence were prepared and how images with colocalization were acquired and processed. Studies should be conducted with great caution, and after careful background reading. Currently the field is dogged by confusion and a standardized approach is yet to be firmly established ^[6]. Attempts to rectify this include re-examination and revision of some of the coefficients ^[7], application of a factor to correct for noise^[1], and the proposal of further protocols^[8] which were thoroughly reviewed by Bolte and Cordelieres (2006)^[9]. In addition, due to the tendency of fluorescence images to contain a certain amount of out-of-focus signal, and poisson shot and other noise, they usually require pre-processing prior to quantification.^[10]. Careful image restoration by deconvolution removes noise and increases contrast in images, improving the quality of colocalization analysis results.

Examples of use

Some impermeable fluorescent zinc dyes can detectably label the cytosol and nuclei of apoptizing and necrotizing cells among each of four different tissue types examined. Namely: the cerebral cortex, the hippocampus, the cerebellum, and it was also demonstrated that colocalized detection of zinc increase and the well accepted cell death indicator propidium iodide also occurred in kidney cells. Using the principles of fluorescent colocalization. coincident detection of zinc accumulation and propidium iodide (a traditional cell death indicator) uptake in multiple cell types was demonstrated. (Stork & Li, The Journal of Neuroscience Methods, 2006). Various examples of quantification of colocalization in the field of neuroscience can be found in a review.^[11]

Related techniques

Förster resonance energy transfer (FRET): 10 nm proximity
- (Light microscopy: only 250 nm resolution; no certainty of effective interaction)
Immuno precipitation (IP) dropdowns / pulldowns
Yeast 2 hybrid - protein interaction mapping

Software implementations

open source

FIJI is just ImageJ - batteries included [9]
BioImage XD [10]

closed source

AxioVision Colocalization Module [11]
Colocalization Research Software [12]
CoLocalizer Pro CoLocalizer Pro
Elements Colocalization Module [13]
Huygens Colocalization Analyzer [14]
Volocity [15]
Volocity Demo [16]
Image Pro [17]
Bitplane Imaris [18]

References

^ ^a ^b Adler et al (2008). "Replicate based noise corrected correlations for accurate measurements of colocalization". [1]
^ Manders et al (1992). "Dynamics of three-dimensional replication patterns during the S-phase, analysed by double labelling of DNA and confocal microscopy." [2]
^ Manders et al (1993). "Measurement of co-localisation of objects in dual-colour confocal images. Journal of Microscopy 169:375-382
^ Zinchuk V et al (2007). "Quantitative colocalization analysis of multicolor confocal immunofluorescence microscopy images: pushing pixels to explore biological phenomena." Acta Histochem Cytochem 40:101-111.
^ Costes et al (2004) "Automatic and Quantitative Measurement of Protein-Protein Colocalization in Live Cells." [3]
^ BOLTE and CORDELIÈRES (2006) "A guided tour into subcellular colocalization analysis in light microscopy." [4]
^ Adler and Parmryd (2010)"Quantifying colocalization by correlation: The Pearson correlation coefficient is superior to the Mander's overlap coefficient." [5]
^ Curr Protoc Cell Biol "Quantitative colocalization analysis of confocal fluorescence microscopy images."
^ BOLTE and CORDELIÈRES (2006) "A guided tour into subcellular colocalization analysis in light microscopy." [6]
^ Pawley JB (2006). Handbook of Biological Confocal Microscopy. [7]
^ Zinchuk V & Grossenbacher-Zinchuk O (2009). "Recent advances in quantitative colocalization analysis: Focus on neuroscience". [8]

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English Journal

Extramitochondrial tricarboxylic acid cycle in retinal rod outer segments.

Panfoli I, Calzia D, Ravera S, Bruschi M, Tacchetti C, Candiani S, Morelli A, Candiano G.SourceDepartment of Biology, University of Genoa, Viale Benedetto XV, 5, 16132 Genova, Italy.
Biochimie.Biochimie.2011 Sep;93(9):1565-75. Epub 2011 Jun 13.
Vertebrate retinal rod Outer Segments (OS) are the site of visual transduction, an energy demanding process for which mechanisms of ATP supply are still poorly known. Glycolysis or diffusion of either ATP or phosphocreatine from the Inner Segment (IS) does not seem to display adequate timing to supp
PMID 21683117

Colocalization of hyperpolarization-activated, cyclic nucleotide-gated channel subunits in rat retinal ganglion cells.

Stradleigh TW, Ogata G, Partida GJ, Oi H, Greenberg KP, Krempely KS, Ishida AT.SourceDepartment of Neurobiology, Physiology and Behavior, University of California, Davis, California 95616.
The Journal of comparative neurology.J Comp Neurol.2011 Sep 1;519(13):2546-73. doi: 10.1002/cne.22638.
The current-passing pore of mammalian hyperpolarization-activated, cyclic nucleotide-gated (HCN) channels is formed by subunit isoforms denoted HCN1-4. In various brain areas, antibodies directed against multiple isoforms bind to single neurons, and the current (I(h) ) passed during hyperpolarizatio
PMID 21456027

Japanese Journal

Colocalization of 14-3-3 Proteins with SOD1 in Lewy Body-Like Hyaline Inclusions in Familial Amyotrophic Lateral Sclerosis Cases and the Animal Model.

Okamoto Yoko,Shirakashi Yoshitomo,Ihara Masafumi,Urushitani Makoto,Oono Miki,Kawamoto Yasuhiro,Yamashita Hirofumi,Shimohama Shun,Kato Shinsuke,Hirano Asao,Tomimoto Hidekazu,Ito Hidefumi,Takahashi Ryosuke
PloS one 6(5), 2011-05
Cu/Zn superoxide dismutase (SOD1) is a major component of Lewy body-like hyaline inclusion (LBHI) found in the postmortem tissue of SOD1-linked familial amyotrophic lateral sclerosis (FALS) patients. …
NAID 120003163709

Localization of Alkaline Phosphatase and Cathepsin D during Cell Restoration after Colchicine Treatment in Primary Cultures of Fetal Rat Hepatocytes

Chida Kohsuke,Taguchi Meiko
ACTA HISTOCHEMICA ET CYTOCHEMICA 44(3), 155-158, 2011
… At 3 hr and 24 hr after colchicine treatment, numerous coarse dots containing ALP were observed throughout the cytoplasm, and some of these showed colocalization with CAPD. …
NAID 130000722779