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Imaging cycler microscopy

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An imaging cycler microscope (ICM) is a fully automated (epi)fluorescence microscope which overcomes the spectral resolution limit resulting in parameter- and dimension-unlimited fluorescence imaging. The principle and robotic device was described by Walter Schubert in 1997 [1] and eversince has been further developed with his co-workers within the human toponome project.[2][3][4][5] The ICM runs robotically controlled repetitive incubation-imaging-bleaching cycles with dye-conjugated probe libraries recognizing target structures in situ (biomolecules in fixed cells or tissue sections). This results in the transmission of a randomly large number of distinct biological informations by re-using the same fluorescence channel after bleaching for the transmission of another biological information using the same dye which is conjugated to another specific probe, a.s.o. Thereby noise-reduced quasi-multi channel fluorescence images with reproducible physical, geometrical, and biophyscial stabilities are generated. The resulting power of combinatorial molecular discrimination (PCMD) per data point is given by 65,536k, where 65,536 is the number of grey value levels (output of a 16-bit CCD camera) and k is the number of co-mapped biomolecules and/or subdomains per biomolecule(s). High PCMD has been shown for k = 100,[3][5] and in principle can be expanded for much higher numbers of k. In contrast to traditional multi-channel-few parameter fluorescence microscopy (Fig 1a) high PCMDs in an ICM lead to high functional and spatial resolution (Fig 1b). Systematic ICM analysis of biological systems reveals the supramolecular segregation law that describes the pinciple of order of large, hierarchically organized biomolecular networks in situ (toponome).[6] The ICM is the core technology for the systematic mapping of the complete protein network code in tissues (human toponome project).[2] The original ICM method [1] includes any modification of the bleaching step. Corresponding modifications have been reported for antibody retrieval [7] and chemical dye-quenching [8] debated recently.[9][10] The Toponome Imaging Systems (TIS) and Multi-Epitope-Ligand cartographs (MELC) represent different stages of the ICM technological development. Imaging Cycler Microscopy received the American ISAC best paper award in 2008 for the three symbol code of organized proteomes.[11]

Comparison of dimension-unlimited fluorescence imaging cycler microscopy (ICM) and standard three-parameter fluorescence microscopy.

Citations

  1. ^ a b Schubert W (1997) Automated device and method for measuring and identifying molecules or fragments thereof. European patent EP 0810428 B1 [see also Schubert W. US patent 6,150,173 (2000); Japanese patent 3739528 (1998)].
  2. ^ a b Cottingham, Katie (May 2008). "Human Toponome Project | Human Proteinpedia is open for (free) business". Journal of Proteome Research. 7 (5): 1806–1806. doi:10.1021/pr083701k.
  3. ^ a b Schubert, Walter; Bonnekoh, Bernd; Pommer, Ansgar J; Philipsen, Lars; Böckelmann, Raik; Malykh, Yanina; Gollnick, Harald; Friedenberger, Manuela; Bode, Marcus; Dress, Andreas W M (1 October 2006). "Analyzing proteome topology and function by automated multidimensional fluorescence microscopy". Nature Biotechnology. 24 (10): 1270–1278. doi:10.1038/nbt1250.
  4. ^ Friedenberger, Manuela; Bode, Marcus; Krusche, Andreas; Schubert, Walter (September 2007). "Fluorescence detection of protein clusters in individual cells and tissue sections by using toponome imaging system: sample preparation and measuring procedures". Nature Protocols. 2 (9): 2285–2294. doi:10.1038/nprot.2007.320.
  5. ^ a b Schubert, W. "Direct, spatial imaging of randomly large supermolecules by using parameter unlimited TIS imaging cycler microscopy" (PDF). International Microscopy Conference 2013. Retrieved 2013-09-23.
  6. ^ Schubert, W (2014). "Systematic, spatial imaging of large multimolecular assemblies and the emerging principles of supramolecular order in biological systems". Journal of Molecular Recognition. 27 (1): 3–18. doi:10.1002/jmr.2326.
  7. ^ Micheva, Kristina D.; Smith, Stephen J (July 2007). "Array Tomography: A New Tool for Imaging the Molecular Architecture and Ultrastructure of Neural Circuits". Neuron. 55 (1): 25–36. doi:10.1016/j.neuron.2007.06.014.
  8. ^ Gerdes, M. J. (1 July 2013). "Highly multiplexed single-cell analysis of formalin-fixed, paraffin-embedded cancer tissue". Proceedings of the National Academy of Sciences. 110 (29): 11982–11987. doi:10.1073/pnas.1300136110. {{cite journal}}: Unknown parameter |coauthors= ignored (|author= suggested) (help)
  9. ^ Schubert, W.; Dress, A.; Ruonala, M.; Krusche, A.; Hillert, R.; Gieseler, A.; Walden, P. (7 January 2014). "Imaging cycler microscopy". Proceedings of the National Academy of Sciences. 111 (2): E215–E215. doi:10.1073/pnas.1319017111.
  10. ^ Gerdes, M. J. (7 January 2014). "Reply to Schubert et al.: Regarding critique of highly multiplexed technologies". Proceedings of the National Academy of Sciences. 111 (2): E216–E216. doi:10.1073/pnas.1319622111.
  11. ^ Schubert, Walter (June 2007). "A three-symbol code for organized proteomes based on cyclical imaging of protein locations". Cytometry Part A. 71A (6): 352–360. doi:10.1002/cyto.a.20281.

References

Further reading

  • Abott, A (12 October 2006). "Research highlights". Nature. 443 (7112): 608–609. doi:10.1038/443608a.
  • Ademmer; Ebert,; Müller-Ostermeyer,; Friess,; Büchler,; Schubert,; Malfertheiner, (April 1998). "Effector T lymphocyte subsets in human pancreatic cancer: detection of CD8+ CD18+ cells and CD8+ CD103+ cells by multi-epitope imaging". Clinical and Experimental Immunology. 112 (1): 21–26. doi:10.1046/j.1365-2249.1998.00546.x.{{cite journal}}: CS1 maint: extra punctuation (link)
  • Barysenka, Andrei; Dress, Andreas W.M.; Schubert, Walter (1 September 2010). "An information theoretic thresholding method for detecting protein colocalizations in stacks of fluorescence images". Journal of Biotechnology. 149 (3): 127–131. doi:10.1016/j.jbiotec.2010.01.009.
  • Bedner, Elzbieta; Du, Litong; Traganos, Frank; Darzynkiewicz, Zbigniew (1 January 2001). "Caffeine dissociates complexes between DNA and intercalating dyes: Application for bleaching fluorochrome-stained cells for their subsequent restaining and analysis by laser scanning cytometry". Cytometry. 43 (1): 38–45. doi:10.1002/1097-0320(20010101)43:1<38::AID-CYTO1017>3.0.CO;2-S.
  • Berndt, Uta; Philipsen, Lars; Bartsch, Sebastian; Hu, Yuqin; Röcken, Christoph; Bertram, Wiedenmann; Hämmerle, Marcus; Rösch, Thomas; Sturm, Andreas (2010). "Comparative Multi-Epitope-Ligand-Cartography reveals essential immunological alterations in Barrett's metaplasia and esophageal adenocarcinoma". Molecular Cancer. 9 (1): 177. doi:10.1186/1476-4598-9-177.{{cite journal}}: CS1 maint: unflagged free DOI (link)
  • Bhattacharya, Sayantan; Mathew, George; Ruban, Ernie; Epstein, David B. A.; Krusche, Andreas; Hillert, Reyk; Schubert, Walter; Khan, Michael (3 December 2010). "Toponome Imaging System: Protein Network Mapping in Normal and Cancerous Colon from the Same Patient Reveals More than Five-Thousand Cancer Specific Protein Clusters and Their Subcellular Annotation by Using a Three Symbol Code". Journal of Proteome Research. 9 (12): 6112–6125. doi:10.1021/pr100157p.
  • Bode, Marcus (March 2008). "Interlocking transcriptomics, proteomics and toponomics technologies for brain tissue analysis in murine hippocampus". Proteomics. 8 (6): 1170–1178. doi:10.1002/pmic.200700742. {{cite journal}}: Unknown parameter |coauthors= ignored (|author= suggested) (help)
  • Bonnekoh, B. (2007). "The CD11a Binding Site of Efalizumab in Psoriatic Skin Tissue as Analyzed by Multi-Epitope Ligand Cartography Robot Technology". Skin Pharmacology and Physiology. 20 (2): 96–111. doi:10.1159/000097982. {{cite journal}}: Unknown parameter |coauthors= ignored (|author= suggested) (help)
  • Bonnekoh, Bernd; Malykh, Yanina; Böckelmann, Raik; Bartsch, Sebastian; Pommer, Ansgar J.; Gollnick, Harald. (2006). "Profiling lymphocyte subpopulations in peripheral blood under efalizumab treatment of psoriasis by multi epitope ligand cartography (MELC) robot microscopy". Eur J Dermatol. 16 (6): 623–635. doi:10.1684/ejd.2006.0005.
  • Bonnekoh, B. (2007). "Topo-Proteomic in situ Analysis of Psoriatic Plaque under Efalizumab Treatment". Skin Pharmacology and Physiology. 20 (5): 237–252. doi:10.1159/000104422. {{cite journal}}: Unknown parameter |coauthors= ignored (|author= suggested) (help)
  • Bonnekoh, Bernd; Pommer, Ansgar J.; Böckelmann, Raik; Philipsen, Lars; Hofmeister, Henning; Gollnick, Harald (June 2008). "In-situ-topoproteome analysis of cutaneous lymphomas: Perspectives of assistance for dermatohistologic diagnostics by Multi Epitope Ligand Cartography (MELC)". Journal der Deutschen Dermatologischen Gesellschaft. doi:10.1111/j.1610-0387.2007.06754.x.
  • Coste, O.; Brenneis, C.; Linke, B.; Pierre, S.; Maeurer, C.; Becker, W.; Schmidt, H.; Gao, W.; Geisslinger, G.; Scholich, K. (10 September 2008). "Sphingosine 1-Phosphate Modulates Spinal Nociceptive Processing". Journal of Biological Chemistry. 283 (47): 32442–32451. doi:10.1074/jbc.M806410200.{{cite journal}}: CS1 maint: unflagged free DOI (link)
  • Dress, Andreas W. M.; Lokot, T.; Pustyl’nikov, L. D.; Schubert, W. (January 2005). "Poisson Numbers and Poisson Distributions in Subset Surprisology". Annals of Combinatorics. 8 (4): 473–485. doi:10.1007/s00026-004-0234-2.
  • Dress, Andreas; Lokot, Tatjana; Schubert, Walter; Serocka, Peter (3 October 2008). "Two Theorems about Similarity Maps". Annals of Combinatorics. 12 (3): 279–290. doi:10.1007/s00026-008-0351-4.
  • Ebert, Matthias P.A.; Ademmer, Karin; Muller-Ostermeyer, Frauke; Friess, Helmut; Buchler, Markus W.; Schubert, Walter; Malfertheiner, Peter (November 1998). "CD8+CD103+ T cells analogous to intestinal intraepithelial lymphocytes infiltrate the pancreas in chronic pancreatitis". The American Journal of Gastroenterology. 93 (11): 2141–2147. doi:10.1111/j.1572-0241.1998.00610.x.
  • Ecker, Rupert C.; Rogojanu, Radu; Streit, Marc; Oesterreicher, Katja; Steiner, Georg E. (March 2006). "An improved method for discrimination of cell populations in tissue sections using microscopy-based multicolor tissue cytometry". Cytometry Part A. 69A (3): 119–123. doi:10.1002/cyto.a.20219.
  • Eckhardt, J.; Ostalecki, C.; Kuczera, K.; Schuler, G.; Pommer, A. J.; Lechmann, M. (16 November 2012). "Murine Whole-Organ Immune Cell Populations Revealed by Multi-epitope-Ligand Cartography". Journal of Histochemistry & Cytochemistry. 61 (2): 125–133. doi:10.1369/0022155412470140.
  • Eyerich, Kilian (15 September 2009). "Comparative in situ topoproteome analysis reveals differences in patch test-induced eczema: cytotoxicity-dominated nickel versus pleiotrope pollen reaction". Experimental Dermatology. 19 (6): 511–517. doi:10.1111/j.1600-0625.2009.00980.x. {{cite journal}}: Unknown parameter |coauthors= ignored (|author= suggested) (help)
  • Gieseler, A (2013). "Cell Membrane Toponomics" in Dubitzky, Wolkenhauer, Cho, Yokota. Encyclopedia of Systems Biology. Springer New York. pp. 364–366. doi:10.1007/978-1-4419-9863-7_1568. ISBN 978-1-4419-9862-0.
  • Gieseler, A (2013). "Synaptic proteins" in Dubitzky, Wolkenhauer, Cho, Yokota. Encyclopedia of Systems Biology. Springer New York. pp. 2034–2036. doi:10.1007/978-1-4419-9863-7_632. ISBN 978-1-4419-9862-0.
  • Gieseler, A (2013). "Synaptic toponome" in Dubitzky, Wolkenhauer, Cho, Yokota. Encyclopedia of Systems Biology. Springer New York. pp. 2036–2038. doi:10.1007/978-1-4419-9863-7_633. ISBN 978-1-4419-9862-0.
  • Haars, Regina; Schneider, Abidat; Bode, Marcus; Schubert, W. (2000). "Secretion and differential localization of the proteolytic cleavage products Abeta40 and Abeta42 of the Alzheimer amyloid precursor protein in human fetal myogenic cells". European Journal of Cell Biology. 79 (6): 400–406. doi:10.1078/0171-9335-00064. PMID 10928455.
  • Herold, Julia; Schubert, Walter; Nattkemper, Tim W. (15 September 2010). "Automated detection and quantification of fluorescently labeled synapses in murine brain tissue sections for high throughput applications". Journal of Biotechnology. 149 (4): 299–309. doi:10.1016/j.jbiotec.2010.03.004.
  • Hillert, R (2013). "Combinatorial molecular phenotypes (CMPs)" in Dubitzky, Wolkenhauer, Cho, Yokota. Encyclopedia of Systems Biology. Springer New York. pp. 440–441. doi:10.1007/978-1-4419-9863-7_634. ISBN 978-1-4419-9862-0.
  • Hillert, R (2013). "Toponome analysis" in Dubitzky, Wolkenhauer, Cho, Yokota. Encyclopedia of Systems Biology. Springer New York. pp. 2188–2191. doi:10.1007/978-1-4419-9863-7_635. ISBN 978-1-4419-9862-0.
  • Kovacheva, V. N.; Khan, A. M.; Khan, M.; Epstein, D. B. A.; Rajpoot, N. M. (21 November 2013). "DiSWOP: a novel measure for cell-level protein network analysis in localized proteomics image data". Bioinformatics. 30 (3): 420–427. doi:10.1093/bioinformatics/btt676.
  • Krusche, A (2013). "TIS robot" in Dubitzky, Wolkenhauer, Cho, Yokota. Encyclopedia of Systems Biology. Springer New York. pp. 2172–2174. doi:10.1007/978-1-4419-9863-7_636. ISBN 978-1-4419-9862-0.
  • Laffers, Wiebke; Mittag, Anja; Lenz, Dominik; Tárnok, Attila; Gerstner, Andreas O. H. (March 2006). "Iterative restaining as a pivotal tool for n-color immunophenotyping by slide-based cytometry". Cytometry Part A. 69A (3): 127–130. doi:10.1002/cyto.a.20216.
  • Mittag, Anja; Lenz, Dominik; Gerstner, Andreas O. H.; Tárnok, Attila (July 2006). "Hyperchromatic cytometry principles for cytomics using slide based cytometry". Cytometry Part A. 69A (7): 691–703. doi:10.1002/cyto.a.20285.
  • Murphy, Robert F (October 2006). "Putting proteins on the map". Nature Biotechnology. 24 (10): 1223–1224. doi:10.1038/nbt1006-1223.
  • Nattkemper, T.W.; Ritter, H.J.; Schubert, W. (June 2001). "A neural classifier enabling high-throughput topological analysis of lymphocytes in tissue sections". IEEE Transactions on Information Technology in Biomedicine. 5 (2): 138–149. doi:10.1109/4233.924804.
  • Nattkemper, Tim W.; Twellmann, Thorsten; Ritter, Helge; Schubert, Walter (January 2003). "Human vs. machine: evaluation of fluorescence micrographs". Computers in Biology and Medicine. 33 (1): 31–43. doi:10.1016/s0010-4825(02)00060-4.
  • Oeltze, S.; Freiler, W.; Hillert, Reyk; Doleisch, Helmut; Preim, Bernhard; Schubert, Walter (December 2011). "Interactive, Graph-based Visual Analysis of High-dimensional, Multi-parameter Fluorescence Microscopy Data in Toponomics". IEEE Transactions on Visualization and Computer Graphics. 17 (12): 1882–1891. doi:10.1109/TVCG.2011.217.
  • Ostalecki, Christian; Konrad, Andreas; Thurau, Elisabeth; Schuler, Gerold; Croner, Roland S.; Pommer, Ansgar J.; Stürzl, Mich ael (August 2013). "Combined multi-gene analysis at the RNA and protein levels in single FFPE tissue sections". Experimental and Molecular Pathology. 95 (1): 1–6. doi:10.1016/j.yexmp.2013.03.008.
  • Philipsen, L.; Engels, T.; Schilling, K.; Gurbiel, S.; Fischer, K.-D.; Tedford, K.; Schraven, B.; Gunzer, M.; Reichardt, P. (10 June 2013). "Multimolecular Analysis of Stable Immunological Synapses Reveals Sustained Recruitment and Sequential Assembly of Signaling Clusters". Molecular & Cellular Proteomics. 12 (9): 2551–2567. doi:10.1074/mcp.M112.025205.{{cite journal}}: CS1 maint: unflagged free DOI (link)
  • Ruetze, Martin; Gallinat, Stefan; Wenck, Horst; Deppert, Wolfgang; Knott, Anja (2010). "In situ localization of epidermal stem cells using a novel multi epitope ligand cartography approach". Integrative Biology. 2 (5–6): 241. doi:10.1039/b926147h.
  • Sage, Linda (5 June 2009). "The molecular face of prostate cancer". Journal of Proteome Research. 8 (6): 2616–2616. doi:10.1021/pr9003129.
  • Schmid, Eva M.; McMahon, Harvey T. (23 August 2007). "Integrating molecular and network biology to decode endocytosis". Nature. 448 (7156): 883–888. doi:10.1038/nature06031.
  • Schubert, Walter (2002). "Polymyositis, Topological Proteomics Technology and Paradigm for Cell Invasion Dynamics". Journal of Theoretical Medicine. 4 (1): 75–84. doi:10.1080/10273660290015224.
  • Schubert, W. (2003). "Topological Proteomics, Toponomics, MELK-Technology". Adv Biochem Eng Biotechnol. 83: 189–209. doi:10.1007/3-540-36459-5_8.
  • Schubert, Walter (April 2006). "Cytomics in characterizing Toponomes: Towards the biological code of the cell". Cytometry Part A. 69A (4): 209–211. doi:10.1002/cyto.a.20203.
  • Schubert, Walter (March 2006). "Exploring molecular networks directly in the cell". Cytometry Part A. 69A (3): 109–112. doi:10.1002/cyto.a.20234.
  • Schubert, Walter (October 2007). "Breaking the biological code". Cytometry Part A. 71A (10): 771–772. doi:10.1002/cyto.a.20466.
  • Schubert, Walter (15 September 2010). "On the origin of cell functions encoded in the toponome". Journal of Biotechnology. 149 (4): 252–259. doi:10.1016/j.jbiotec.2010.03.009.
  • Schubert, W (2012). "Toponomanalyse" in Lottspeich, Engels. Bioanalytik (3rd ed.). Spektrum Heidelberg. pp. 1139–1151. ISBN 978-3-8274-2942-1.
  • Schubert, Walter; Bode, Marcus; Hillert, Reyk; Krusche, Andreas; Friedenberger, Manuela (April 2008). "Toponomics and neurotoponomics: a new way to medical systems biology". Expert Review of Proteomics. 5 (2): 361–369. doi:10.1586/14789450.5.2.361.
  • Schubert, Walter; Friedenberger, Manuela; Bode, Marcus; Krusche, Andreas; Hillert, Reyk (November 2008). "Functional architecture of the cell nucleus: Towards comprehensive toponome reference maps of apoptosis". Biochimica et Biophysica Acta (BBA) - Molecular Cell Research. 1783 (11): 2080–2088. doi:10.1016/j.bbamcr.2008.07.019.
  • Schubert, W.; Friedenberger, M.; Haars, R.; Bode, M.; Philipsen, L.; Nattkemper, T.; Ritter, H. (2002). "Automatic Recognition of Muscle-Invasive T-Lymphocytes Expressing Dipeptidyl-Peptidase IV (CD26) and Analysis of the Associated Cell Surface Phenotypes". Journal of Theoretical Medicine. 4 (1): 67–74. doi:10.1080/10273660290015189.
  • Schubert, Walter; Gieseler, Anne; Krusche, Andreas; Hillert, Reyk (5 June 2009). "Toponome Mapping in Prostate Cancer: Detection of 2000 Cell Surface Protein Clusters in a Single Tissue Section and Cell Type Specific Annotation by Using a Three Symbol Code". Journal of Proteome Research. 8 (6): 2696–2707. doi:10.1021/pr800944f.
  • Schubert, Walter; Gieseler, Anne; Krusche, Andreas; Serocka, Peter; Hillert, Reyk (June 2012). "Next-generation biomarkers based on 100-parameter functional super-resolution microscopy TIS". New Biotechnology. 29 (5): 599–610. doi:10.1016/j.nbt.2011.12.004.
  • Schubert, W (2013). "Toponomics" in Dubitzky, Wolkenhauer, Cho, Yokota. Encyclopedia of Systems Biology. Springer New York. pp. 2191–2212. doi:10.1007/978-1-4419-9863-7_631. ISBN 978-1-4419-9862-0.
  • Schubert, Walter (January 2014). "Systematic, spatial imaging of large multimolecular assemblies and the emerging principles of supramolecular order in biological systems". Journal of Molecular Recognition. 27 (1): 3–18. doi:10.1002/jmr.2326.
  • Schubert, W. (2013). "Systems Biology of Cancer" in Pelengaris, Khan. Molecular biology of cancer: a bridge from bench to bedside (2nd ed.). Wiley-Blackwell New York. pp. 554–584. ISBN 978-1-118-02287-0. {{cite book}}: Unknown parameter |coauthors= ignored (|author= suggested) (help)
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