Skip to main content Accessibility help

We use cookies to distinguish you from other users and to provide you with a better experience on our websites. Close this message to accept cookies or find out how to manage your cookie settings.

Close cookie message
×
Hostname: page-component-8448b6f56d-cfpbc Total loading time: 0 Render date: 2024-04-20T15:11:18.069Z Has data issue: false hasContentIssue false

Part I - Super-Resolution Microscopy and Molecular Imaging Techniques to Probe Biology

Published online by Cambridge University Press:  05 May 2022

Edited by
Krishnarao Appasani  and
Raghu Kiran Appasani
Krishnarao Appasani
Affiliation:
GeneExpression Systems, Inc.
Raghu Kiran Appasani
Affiliation:
Psychiatrist, Neuroscientist, & Mental Health Advocate
Get access

Summary

A summary is not available for this content so a preview has been provided. Please use the Get access link above for information on how to access this content.
Image of the first page of this content. For PDF version, please use the ‘Save PDF’ preceeding this image.'
Type
Chapter
Information
Single-Molecule Science
From Super-Resolution Microscopy to DNA Mapping and Diagnostics
 , pp. 1 - 64
Publisher: Cambridge University Press
Print publication year: 2022

Access options

Get access to the full version of this content by using one of the access options below. (Log in options will check for institutional or personal access. Content may require purchase if you do not have access.)

References

References

Aitken, C. E., Petrov, A., Puglisi, J. D., et al. (2010). Single Ribosome Dynamics and the Mechanism of Translation. Annual Reviews of Biophysics, 39 , 491–513.CrossRefGoogle ScholarPubMed
Albrecht, T., Slabaugh, G., Alonso, E., et al. (2017). Deep Learning for Single-Molecule Science. Nanotechnology, 28, 42.Google Scholar
Ashkin, A. 1970. Acceleration and Trapping of Particles by Radiation Pressure. Physical Review Letters, 24 , 156–159.Google Scholar
Ashkin, A., Dziedzic, J. M., Bjorkholm, J. E., and Chu, S. (1986). Observation of a Single-Beam Gradient Force Optical Trap for Dielectric Particles. Optics Letters, 11 , 288–290.Google Scholar
Benesch, R. E. and Benesch, R. (1953). Enzymatic Removal of Oxygen for Polarography and Related Methods. Science, 118 , 447–448.Google Scholar
Betzig, E. and Chichester, R. J. (1993). Single Molecules Observed by Near-Field Scanning Optical Microscopy. Science, 262 , 1422–1425.Google Scholar
Betzig, E. and Trautman, J. K. (1992). Near-Field Optics: Microscopy, Spectroscopy, and Surface Modification beyond the Diffraction Limit. Science, 257, 189–195.Google Scholar
Binnig, G. and Rohrer, H. (1982). Scanning Tunnelling Microscopy. Helvetica Physics Acta, 55, 726–735.Google Scholar
Binnig, G., Quate, C. F., and Gerber, C. (1986). Atomic Force Microscope. Physical Reviews Letters, 56 , 930–933.CrossRefGoogle ScholarPubMed
Birk, U. J. (2019). Super-Resolution Microscopy of Chromatin. Genes (Basel), 10 , 493.Google Scholar
Block, S. M., Goldstein, L. S. B., Schnapp, B. J., et al. (1990). Bead Movement by Single Kinesin Molecules Studied with Optical Tweezers. Nature, 348 , 348–352. doi: 10.1038/348348a0CrossRefGoogle ScholarPubMed
Bokinsky, G. and Zhuang, X. W. (2005). Single-Molecule RNA Folding. Accounts of Chemical Research, 38 , 566–573.CrossRefGoogle ScholarPubMed
Brower-Toland, B. D., Smith, C. L., Yeh, R. C., et al. (2002). Mechanical Disruption of Individual Nucleosomes Reveals a Reversible Multistage Release of DNA. Proceedings of the National Academy of Sciences United States of America, 99 , 1960–1965.Google Scholar
Bustamante, C., Chemla, Y. R, Forde, N. R., et al. (2004). Mechanical Processes in Biochemistry. Annual Reviews of Biochemistry, 73, 705–748.CrossRefGoogle ScholarPubMed
Chemla, Y. R., Anderson, D. L., and Bustmante, C. (2005). Mechanism of Force Generation of a Viral DNA Packaging Motor. Cell, 122 , 683–692.CrossRefGoogle ScholarPubMed
Chen, J., Miller, J., Kirchmaier, A., et al. (2012). Single-Molecule Tools Elucidate H2A.Z Nucleosome Composition. Journal of Cell Science, 125, 2954–2964.Google ScholarPubMed
DeHaven, A. C., Norden, I. S., and Hoskins, A. A. (2016). Lights, Camera, Action! Capturing the Spliceosome and Pre-mRNA Splicing with Single-Molecule Fluorescence Microscopy. Wiley Interdisciplinary Reviews in RNA, 5, 683–701.Google Scholar
Dufrêne, Y. F., Ando, T., Garcia, R., et al. (2017). Imaging Modes of Atomic Force Microscopy for Application in Molecular and Cell Biology. Nature Nanotechnology, 12, 295–307.Google Scholar
Engel, A. (1991). Biological applications of scanning probe microscopes. Annual Reviews Biophysics and Biophysical Chemistry, 20, 79–108.CrossRefGoogle ScholarPubMed
Engel, A. and Muller, D. J. (2000). Observing Single Biomolecules at Work with the Atomic Force Microscope.Nature Structural Biology, 7 , 715–718.Google Scholar
Förster, T. (1948). Zwischenmolekulareenergiewanderung und fluoreszenz. Annalen Der Physik, 2 , 55–75.CrossRefGoogle Scholar
Frank, J. and Agarwal, R. K. (2000). A Ratchet-Like Inter-Subunit Reorganization of the Ribosome during Translocation. Nature, 406, 318–322.Google Scholar
Frank, J. and Gonzalez, R. L. Jr. (2010). Structure and Dynamics of a Processive Brownian Motor: The Tyranslating Ribosome. Annual Reviews of Biochemistry, 79 , 381–412.Google Scholar
Fu, X., Moonschi, F. H., Fox-Loe, A. M., et al. (2019). Brain Region-Specific Single Molecule Fluorescence Imaging. Analytical Chemistry. doi: 10.1021/acs.analchem.9b02133.Google Scholar
Funatsu, T., Harada, Y., Higuchi, H., et al. (1997). Imaging and Nano-Manipulation of Single Biomolecules. Biophysical Chemistry, 68, 63–72.Google Scholar
Ha, T., Enderle, T., Weiss, S., et al. (1996). Probing the Interaction between Two Single Molecules: Fluorescence Resonance Energy Transfers between a Single Donor and a Single Acceptor. Proceedings of the National Academy of Sciences United States of America, 93 , 6264–6268.Google Scholar
Ha, T., Zhuang, X. W., Kim, H. D., et al. (1999). Ligand-Induced Conformational Changes Observed in Single RNA Molecules. Proceedings of the National Academy of Sciences United States of America, 96, 9077–9082.Google Scholar
Hell, S. W. 2007. Far-Field Optical Nanoscopy. Science, 316 , 1153–1158.CrossRefGoogle ScholarPubMed
Hell, S. W., Byba, M., and Jakobs, S. (2004). Concepts for Nanoscale Resolution in Fluorescence Microscopy. Current Opinions in Neurobiology, 14 , 599–609.Google Scholar
Hirschfield, T. (1976). Optical Microscopic Observation of Single Small Molecules. Applied Optics, 15 , 2965–2966.CrossRefGoogle Scholar
Howard, J., Hudspeth, A. J., Vale, R. D., et al. (1989). Movement of Microtubules by Single Kinesin Molecules.Nature, 342, 154–158.Google Scholar
Huang, B., Babcock, H., and Zhuang, X. (2010). Breaking the Diffraction Barrier: Super-Resolution Imaging of Cells. Cell, 143, 1047–1058.CrossRefGoogle ScholarPubMed
Hugel, T., Michaelis, J., Walter, J. M., et al. (2007). Experimental Test of Connector Rotation during DNA Packaging into Bacteriophage Varphi29 Capsids. Public Library of Sciences Biology, 5 , e59. doi:10.1371/journal.pbio.0050059.Google Scholar
Kaledhonkar, S., Fu, Z., Caban, K., et. al. (2019). Late Steps in Bacterial Translation Initiation Visualized Using Time-Resolved Cryo-EM. Nature, 570, 400–404.Google Scholar
Kapanidis, A. N. and Weiss, S. (2004). Fluorescence-Aided Molecule Sorting: Analysis of Structure and Interactions by Alternating-Laser Excitation of Single Molecules. Proceedings of the National Academy of Sciences United States of America, 101 , 8936–8941.Google Scholar
Kapanidis, A. N., Laurence, T. A., Lee, N. K., et al. (2005). Alternating-Laser Excitation of Single Molecules. Accounts of Chemical Research, 38 , 523–533.Google Scholar
Kapanidis, A. N, Margeat, E., Weiss, S., et al. (2006). Initial Transcription by RNA Polymerase Proceeds through a DNA-Scrunching Mechanism. Science, 314 , 1144–1147.Google Scholar
Kim, P. S. and Baldwin, R. L. (1982). Specific Intermediates in the Folding Reactions of Small Proteins and the Mechanism of Protein Folding. Annual Reviews of Biochemistry, 51 , 459–489.Google Scholar
Kinosita, K., Itoh, H., Yoshida, M., et al. (2004). Mechanically Driven ATP Synthesis by F-1-ATPase. Nature, 427 , 465–468.Google Scholar
Ladoux, B., Quivy, J. P., Doyle, P., et al. (2000). Fast Kinetics of Chromatin Assemble Revealed by Single-Molecule Video-Microscopy and Scanning Force Microscopy. Proceedings of the National Academy of Sciences United States of America, 97 , 14251–14256.Google Scholar
Lindsay, S. M., Thundat, T., and Nagahara, L. (1988). Adsorbate Deformation as a Contrast Mechanism in STM Images of Bio-Polymers in an Aqueous Environment – Images of the Unstained. Hydrated DNA Double Helix. Journal of Microscopy, 152, 213–220.Google Scholar
Lindsay, S. M., Thundat, T., Nagahara, L., et al. (1989). Images of the DNA double helix in water. Science, 244, 1063–1064.Google Scholar
Lu, H. P., Xun, L. Y., and Xie, X. S. (1998). Single-Molecule Enzymatic Dynamics. Science, 282, 1877–1882.Google Scholar
Mallik, R., Gross, S. P., et al. (2004). Molecular Motors: Strategies to Get Along. Current Biology, 14 , R971–R982.CrossRefGoogle ScholarPubMed
Mashanov, G. I., Tacon, D., Knight, A. E., et al. (2003). Visualizing Single Molecules inside Living Cells Using Total Internal Reflection Fluorescence Microscopy. Methods, 29 , 142–152.Google Scholar
Michalet, X. and Weiss, S. (2002). Critical Reviews in Physique, 3, 619–644.Google Scholar
Mir, M., Reimer, A., Stadler, M., et al. (2018). Single Molecule Imaging in Live Embryos Using Lattice Light-Sheet Microscopy. Methods in Molecular Biology, 1814, 541–559.Google Scholar
Moerner, W. E. (1994). Examining Nano-Environments in Solids on the Scale of a Single, Isolated Impurity Molecule. Science, 265, 46–53.CrossRefGoogle Scholar
Moerner, W. E. and Kador, L. (1989). Finding a Single Molecule in a Haystack – Optical Detection and Spectroscopy of Single Absorbers in Solids. Analytical Chemistry, 61 , A1217-A1223.Google Scholar
Moerner, W. E. and Orrit, M. (1999). Illuminating Single Molecules in Condensed Matter. Science, 283, 1670–1676.Google Scholar
Morisaki, T., Lyon, K., Deluca, K. F., et al. (2016). Real-time Quantification of Single translation dynamics in living cells. Science, 352, 1425–1429.CrossRefGoogle ScholarPubMed
Neher, E. and Sakmann, B. (1976). Single-Channel Currents Recorded from Membrane of Denervated Frog Muscle-Fibers. Nature, 260, 799–802.CrossRefGoogle Scholar
Orrit, M. and Bernard, J. (1990). Single Pentacene Molecules Detected by Fluorescence Excitation in a P-Terphenyl Crystal. Physical Review Letters, 65, 2716–2719.Google Scholar
Perkins, T. T., Smith, D. E., and Chu, S. (1994). Direct Observation of Tube-Like Motion of a Single Polymer-Chain. Science, 264, 819–822.CrossRefGoogle ScholarPubMed
Perrin, J. (1918). La fluorescence. Annals of Physics, 10 , 133–159.Google Scholar
Psaltis, D., Quake, S. R., Yang, C. H., et al. (2006). Developing Optofluidic Technology through the Fusion of Microfluidics and Optics. Nature, 442, 381–386.Google Scholar
Revyakin, A., Liu, C. Y., Ebright, R. H., et al. (2006). Abortive Initiation and Productive Initiation by RNA Polymerase Involve DNA Scrunching. Science, 314 , 1139–1143.CrossRefGoogle ScholarPubMed
Rotman, B. (1961). Measurement of Activity of Single Molecules of ß-d-Galactosidase. Proceedings of the National Academy of Sciences United States of America, 47 , 1981-1991.Google Scholar
Rusimova, K. R., Purkiss, R. M., Howes, R., et al. (2018). Regulating the Femtosecond Excited-State Lifetime of a Single Molecule. Science, 361, 1012–1016.Google Scholar
Selvin, P. R. and Ha, T., eds. (2008). Single-Molecule Techniques, a Laboratory Manual. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY.Google Scholar
Squires, T. M. and Quake, S. R. (2005). Microfluidics: Fluid Physics at the Nanoliter Scale. Reviews in Modern Physics, 77 , 977–1026.Google Scholar
Shashkova, S. and Leake, M. C. (2017). Single-Molecule Fluorescence Microscopy Review: Shedding New Light on Old Problems. Biosciences Reports, 37, pii: BSR20170031.Google Scholar
Sternberg, S. H., Redding, S., Jinek, M., et al. (2014). DNA Interrogation by the CRISPR RNA Guided Endonuclease Cas9. Nature, 507, 62–67.Google Scholar
Vale, R. D., Funatsu, T., Pierce, D. W., et al. (1996). Direct Observation of Single Kinesin Molecules Moving along Microtubules. Nature, 380 , 451–453.Google Scholar
Walter, N. G., Huang, C-Y., Manzo, A. J, and Sobhy, M. A. (2008). Do-It-Yourself Guide: How to Use Modern Single-Molecule Toolkit. Nature Methods, 5, 475–489.Google Scholar
Weiss, S. (2004). Photon Arrival-Time Interval Distribution (PAID): A Novel Tool for Analysing Interactions. Journal of Physical Chemistry B, 108 , 3051–3067.Google Scholar
Wollman, A. J. M., Hedlund, E. G., Shashkova, S., et al. (2019). Towards Mapping the 3D Genome through High Speed Single-Molecule Tracking of Functional Transcription Factors in Single Living Cells. Methods, pii, S1046–2023, 30473–30480.Google Scholar
Yanagida, T. (2000). Single-Molecule Imaging of EGFR Signalling on the Surface of Living Cells. Nature Cell Biology, 2 , 168–172.Google Scholar
Zhang, Y., Smith, C. L, Grill, S. W., et al. (2006). DNA Translocation and Loop Formation Mechanism of Chromatin Remodelling by SWI/SNF and RSC. Molecular Cell, 24 , 559–568.Google Scholar
Zhuang, X. B., Bartley, L. E., Babcock, H. P., et al. (2000). A Single-Molecule Study of RNA Catalysis and Folding. Science, 288 , 2048–2051.CrossRefGoogle ScholarPubMed
Zhuang, X. W. (2003). Visualizing Infection of Individual Influenza Viruses. Proceedings of the National Academy of Sciences United States of America, 100 , 9280–9285.Google Scholar
Zlatanova, J. and Leuba, S. H. (2003). Chromatin Fibers, One-at-a-Time. Journal of Molecular Biology, 331, 1–19.Google Scholar
Zlatanova, J., Lindsay, S. M., and Leuba, S. H. (2000). Single Molecule Force Spectroscopy in Biology Using the Atomic Force Microscope. Progresses in Biophysics and Molecular Biology, 74 , 37–61.Google Scholar
Zlatanova, J., McAllister, W. T, Leuba, S. H., et al. 2006. Single-Molecule Approaches Reveal the Idiosyncrasies of RNA Polymerases. Structure, 14 , 953–966.Google Scholar

References

Achtert, E., Bohm, C., and Kroger, P. (2006). DeLiClu: Boosting Robustness, Completeness, Usability, and Efficiency of Hierarchical Clustering by a Closest Pair Ranking. Advances in Knowledge Discovery and Data Mining, Proceedings, 3918, 119–128.CrossRefGoogle Scholar
Andrews, J. O., Conway, W., Cho, W., et al. (2018). qSR: A Quantitative Super-Resolution Analysis Tool Reveals the Cell-Cycle Dependent Organization of RNA Polymerase I in Live Human Cells. International Journal of Science Reports, 8, 7424.Google Scholar
Andronov, L., Lutz, Y., Vonesch, J. L., and Klaholz, B. P. (2016a). SharpViSu: Integrated Analysis and Segmentation of Super-Resolution Microscopy Data. Bioinformatics, 32, 2239–2241.Google Scholar
Andronov, L., Orlov, I., Lutz, Y., Vonesch, J. L. and Klaholz, B. P. (2016b). ClusterViSu, a Method for Clustering of Protein Complexes by Voronoi Tessellation in Super-Resolution Microscopy. International Journal of Science Reports, 6, 24084.Google ScholarPubMed
Ankerst, M., Breunig, M. M., Kriegel, H. P., and Sander, J. (1999). OPTICS: Ordering Points to Identify the Clustering Structure. Sigmod Record, 28 (2), 49–60.Google Scholar
Annibale, P., Vanni, S., Scarselli, M., Rothlisberger, U., and Radenovic, A. (2011a). Identification of clustering artifacts in photoactivated localization microscopy. Nature Methods, 8, 527–528.Google Scholar
Annibale, P., Vanni, S., Scarselli, M., Rothlisberger, U., and Radenovic, A., A. (2011b). Quantitative Photo Activated Localization Microscopy: Unraveling the Effects of Photoblinking. PLoS One, 6, e22678.Google Scholar
Baddeley, A., Rubak, E., and Turner, R. (2015). Correlation. In Spatial Point Patterns: Methodology and Applications with R. Chapman and Hall/CRC.Google Scholar
Bates, M., Huang, B., Dempsey, G. T., and Zhuang, X. (2007). Multicolor Super-Resolution Imaging with Photo-Switchable Fluorescent Probes. Science, 317, 1749–1753.CrossRefGoogle ScholarPubMed
Betzig, E., Patterson, G. H., Sougrat, R., et al. (2006). Imaging Intracellular Fluorescent Proteins at Nanometer Resolution. Science, 313, 1642–1645.Google Scholar
Bhuvanendran, S., Salka, K., Rainey, K., et al. (2014). Superresolution Imaging of Human Cytomegalovirus vMIA Localization in Sub-Mitochondrial Compartments. Viruses, 6, 1612–1636.Google Scholar
Caetano, F. A., Dirk, B. S., Tam, J. H., et al. (2015). MIiSR: Molecular Interactions in Super-Resolution Imaging Enables the Analysis of Protein Interactions, Dynamics and Formation of Multi-Protein Structures. PLoS Computational Biology, 11, e1004634.Google Scholar
Carter, A. R., King, G. M., Ulrich, T. A., Halsey, W., Alchenberger, D., and Perkins, T. T. (2007). Stabilization of an Optical Microscope to 0.1 nm in Three Dimensions. Applied Optics, 46, 421–427.Google Scholar
Chenouard, N., Smal, I. de Chaumont, F. , et al. (2014). Objective Comparison of Particle Tracking Methods. Nature Methods, 11, 281–289.Google Scholar
Churchman, L. S., Okten, Z., Rock, R. S., Dawson, J. F., and Spudich, J. A. (2005). Single Molecule High-Resolution Colocalization of Cy3 and Cy5 Attached to Macromolecules Measures Intramolecular Distances through Time. Proceedings of the National Academy of Sciences of the United States of America, 102, 1419–1423.Google Scholar
Clark, P. J. and Evans,. F. C. (1954). Distance to Nearest Neighbor as a Measure of Spatial Relationships in Populations. Ecology, 35, 445–453.Google Scholar
Coltharp, C., Kessler, R. P., and Xiao, J. (2012). Accurate Construction of Photoactivated Localization Microscopy (PALM) Images for Quantitative Measurements. PLoS One, 7, e51725.Google Scholar
Coltharp, C., Yang, X., and Xiao, J. (2014). Quantitative Analysis of Single-Molecule Superresolution Images. Current Opinion in Structural Biology, 28, 112–121.CrossRefGoogle ScholarPubMed
Dani, A., Huang, B., Bergan, J., Dulac, C., and Zhuang, X. (2010). Superresolution Imaging of Chemical Synapses in the Brain. Neuron, 68, 843–856.Google Scholar
Ester, M., Kriegel, H. P., Sander, J., and Xu, X. (1996). A Density-Based Alogorithm for Discovering Clusters in Large Spatial Databases with Noise. Second International Conference on Knowledge Discovery and Data Mining (KDD-96), 96, 226–331.Google Scholar
Georgieva, M., Cattoni, D. I., Fiche, J. B., Mutin, T., Chamousset, D., and Nollmann, M. (2016). Nanometer Resolved Single-Molecule Colocalization of Nuclear Factors by Two-Color Super Resolution Microscopy Imaging. Methods, 105, 44–55.Google Scholar
Gunewardene, M. S., Subach, F. V., Gould, T. J., et al. (2011). Superresolution Imaging of Multiple Fluorescent Proteins with Highly Overlapping Emission Spectra in Living Cells. Biophysical Journal, 101, 1522–1528.CrossRefGoogle ScholarPubMed
Gunzenhauser, J., Olivier, N., Pengo, T., and Manley, S. (2012). Quantitative Super-Resolution Imaging Reveals Protein Stoichiometry and Nanoscale Morphology of Assembling HIV-Gag Virions. Nano Letters, 12, 4705–4710.Google Scholar
Heilemann, M., van de Linde, S., Schuttpelz, M., et al. (2008). Subdiffraction-Resolution Fluorescence Imaging with Conventional Fluorescent Probes. Angewante Chemie International Edition England, 47, 6172–6176.Google Scholar
Hess, S. T., Girirajan, T. P., and Mason, M. D. (2006). Ultra-High Resolution Imaging by Fluorescence Photoactivation Localization Microscopy. Biophysical Journal, 91, 4258–4272.CrossRefGoogle ScholarPubMed
Huang, B., Wang, W., Bates, M., and Zhuang, X. (2008). Three-Dimensional Super-Resolution Imaging by Stochastic Optical Reconstruction Microscopy. Science, 319, 810–813.Google Scholar
Huang, F., Hartwich, T. M., Rivera-Molina, F. E., et al. (2013). Video-Rate Nanoscopy Using sCMOS Camera-Specific Single-Molecule Localization Algorithms. Nature Methods, 10, 653–658.Google Scholar
Kamiyama, D. and Huang, B. (2012). Development in the STORM. Developmental Cell, 23, 1103–1110.Google Scholar
Kiskowski, M. A., Hancock, J. F., and Kenworthy, A. K. (2009). On the Use of Ripley’s K-Function and Its Derivatives to Analyze Domain Size. Biophysical Journal, 97, 1095–1103.Google Scholar
Lagache, T., Lang, G., Sauvonnet, N., and Olivo-Marin, J. C. (2013). Analysis of the Spatial Organization of Molecules with Robust Statistics. PLoS One, 8, e80914.Google Scholar
Lee, S. H., Shin, J. Y., Lee, A., and Bustamante, C. (2012). Counting Single Photoactivatable Fluorescent Molecules by Photoactivated Localization Microscopy (PALM). Proceedings of the National Academy of Sciences of the United States of America, 109, 17436–17441.CrossRefGoogle ScholarPubMed
Lehmann, M., Lichtner, G., Klenz, H., and Schmoranzer, J. (2016). Novel Organic Dyes for Multicolor Localization-Based Super-Resolution Microscopy. Journal of Biophotonics, 9, 161–170.CrossRefGoogle ScholarPubMed
Lemmer, P., Gunkel, M., Baddeley, D., et al. (2008). SPDM: Light Microscopy with Single-Molecule Resolution at the Nanoscale. Applied Physics B-Lasers and Optics, 93, 1–12.Google Scholar
Malkusch, S. and Heilemann, M. (2016). Extracting Quantitative Information from Single-Molecule Super-Resolution Imaging Data with LAMA – LocAlization Microscopy Analyzer. Science Reports, 6, 34486.CrossRefGoogle ScholarPubMed
Malkusch, S., Endesfelder, U., Mondry, J., Gelleri, M., Verveer, P. J., and Heilemann, M. (2012). Coordinate-Based Colocalization Analysis of Single-Molecule Localization Microscopy Data. Histochemisty and Cell Biology, 137, 1–10.Google Scholar
Manley, S., Gillette, J. M., Patterson, G. H., et al. (2008). High-Density Mapping of Single-Molecule Trajectories with Photoactivated Localization Microscopy. Nature Methods, 5, 155–157.Google Scholar
Mazouchi, A. and Milstein, J. N. (2016). Fast Optimized Cluster Algorithm for Localizations (FOCAL): A Spatial Cluster Analysis for Super-Resolved Microscopy. Bioinformatics, 32, 747–754.Google Scholar
Mlodzianoski, M. J., Curthoys, N. M., Gunewardene, M. S., Carter, S., and Hess, S. T. (2016). Super-Resolution Imaging of Molecular Emission Spectra and Single Molecule Spectral Fluctuations. PLoS One, 11, e0147506.Google Scholar
Nan, X., Collisson, E. A., Lewis, S., et al. (2013). Single-Molecule Superresolution Imaging Allows Quantitative Analysis of RAF Multimer Formation and Signaling. Proceedings of the National Academy of Sciences of the United States of America, 110, 18519–18324.Google Scholar
Nicovich, P. R., Owen, D. M., and Gaus, K. (2017). Turning Single-Molecule Localization Microscopy into a Quantitative Bioanalytical Tool. Nature Protocols, 12, 453–460.Google Scholar
Ori, A., Banterle, N., Iskar, M., et al. (2013). Cell Type-Specific Nuclear Pores: A Case in Point for Context-Dependent Stoichiometry of Molecular Machines. Molecular Systems Biology, 9, 648.Google Scholar
Ovesny, M., Krizek, P., Borkovec, J., Svindrych, Z., and Hagen, G. M. (2014). ThunderSTORM: A Comprehensive ImageJ Plug-in for PALM and STORM Data Analysis and Super-Resolution Imaging. Bioinformatics, 30, 2389–2390.Google Scholar
Pageon, S. V., Nicovich, P. R., Mollazade, M., Tabarin, T., and Gaus, K. (2016). Clus-DoC: A Combined Cluster Detection and Colocalization Analysis for Single-Molecule Localization Microscopy Data. Molecular Biology of the Cell, 27, 3627–3636.Google Scholar
Patterson, G. H. (2009). Fluorescence Microscopy below the Diffraction Limit. Seminars in Cell and Developmental Biology, 20, 886–893.Google Scholar
Patterson, G. H. (2011). Highlights of the Optical Highlighter Fluorescent Proteins. Journal of Microscopy, 243, 1–7.Google Scholar
Pengo, T., Holden, S. J., and Manley, S. (2015). PALMsiever: A Tool to Turn Raw Data into Results for Single-Molecule Localization Microscopy. Bioinformatics, 31, 797–798.Google Scholar
Penttinen, A. and Stoyan, D. (2000). Recent Applications of Point Processes in Forestry Statistics. Statistical Science, 15, 61–78.Google Scholar
Renz, M., Daniels, B. R., Vamosi, G., Arias, I. M., and Lippincott-Schwartz, J. (2012). Plasticity of the Asialoglycoprotein Receptor Deciphered by Ensemble FRET Imaging and Single-Molecule Counting PALM Imaging. Proceedings of the National Academy of Sciences of the United States of America, 109, E2989–E2997.Google Scholar
Ripley, B. D. (1977). Modeling Spatial Patterns. Journal of the Royal Statistical Society Series B-Methodological, 39, 172–212.Google Scholar
Rollins, G. C., Shin, J. Y., Bustamante, C., and Presse, S. (2015). Stochastic Approach to the Molecular Counting Problem in Superresolution Microscopy. Proceedings of the National Academy of Sciences of the United States of America, 112, E110–E118.Google Scholar
Rossy, J., Cohen, E., Gaus, K., and Owen, D. M. (2014). Method for Co-Cluster Analysis in Multichannel Single-Molecule Localisation Data. Histochemistry and Cell Biology, 141, 605–612.Google Scholar
Rubin-Delanchy, P., Burn, G. L., Griffie, J., et al. (2015). Bayesian Cluster Identification in Single-Molecule Localization Microscopy Data. Nature Methods, 12, 1072–1076.CrossRefGoogle ScholarPubMed
Rust, M. J., Bates, M., and Zhuang, X. (2006). Sub-Diffraction-Limit Imaging by Stochastic Optical Reconstruction Microscopy (STORM). Nature Methods, 3, 793–795.Google Scholar
Sage, D., Kirshner, H., Pengo, T., et al. (2015). Quantitative Evaluation of Software Packages for Single-Molecule Localization Microscopy. Nature Methods, 12, 717–724.Google Scholar
Schnitzbauer, J., Wang, Y., Zhao, S., et al. (2018). Correlation Analysis Framework for Localization-Based Superresolution Microscopy. Proceedings of the National Academy of Sciences of the United States of America, 115, 3219–3224.Google Scholar
Sengupta, P., Jovanovic-Talisman, T., Skoko, D., Renz, M., Veatch, S. L., and Lippincott-Schwartz, J. (2011). Probing Protein Heterogeneity in the Plasma Membrane Using PALM and Pair Correlation Analysis. Nature Methods, 8, 969–975.Google Scholar
Shivanandan, A., Radenovic, A., and Sbalzarini, I. F. (2013). MosaicIA: An ImageJ/Fiji Plugin for Spatial Pattern and Interaction Analysis. BMC Bioinformatics, 14, 349.CrossRefGoogle ScholarPubMed
Shroff, H., Galbraith, C. G., Galbraith, J. A., et al. (2007). Dual-Color Superresolution Imaging of Genetically Expressed Probes within Individual Adhesion Complexes. Proceedings of the National Academy of Sciences of the United States of America, 104, 20308–20313.CrossRefGoogle ScholarPubMed
Shtengel, G., Galbraith, J. A., Galbraith, C. G., et al. (2009). Interferometric Fluorescent Super-Resolution Microscopy Resolves 3D Cellular Ultrastructure. Proceedings of the National Academy of Sciences of the United States of America, 106, 3125–3130.Google Scholar
Small, A. and Stahlheber, S. (2014). Fluorophore Localization Algorithms for Super-Resolution Microscopy. Nature Methods, 11, 267–279.Google Scholar
Stone, M. B. and Veatch, S. L. (2015). Steady-State Cross-Correlations for Live Two-Colour Super-Resolution Localization Data Sets. Nature Communications, 6, 7347.Google Scholar
Subach, F. V., Patterson, G. H. Manley, S., Gillette, J. M., Lippincott-Schwartz, J., and Verkhusha, V. V. (2009). Photoactivatable mCherry for High-Resolution Two-Color Fluorescence Microscopy. Nature Methods, 6, 153–159.Google Scholar
Subach, F. V., Patterson, G. H., Renz, M., Lippincott-Schwartz, J., and Verkhusha, V. V. (2010). Bright Monomeric Photoactivatable Red Fluorescent Protein for Two-Color Super-Resolution sptPALM of Live Cells. Journal of the American Chemical Society, 132, 6481–6491.CrossRefGoogle ScholarPubMed
van de Linde, S., Endesfelder, U., Mukherjee, A., et al. (2009). Multicolor Photoswitching Microscopy for Subdiffraction-Resolution Fluorescence Imaging. Photochemical and Photobiological Sciences, 8, 465–469.Google Scholar
van de Linde, S., Loschberger, A., Klein, T., et al. (2011). Direct Stochastic Optical Reconstruction Microscopy with Standard Fluorescent Probes. Nature Protocols, 6, 991–1009.CrossRefGoogle ScholarPubMed
Veatch, S. L., Machta, B. B., Shelby, S. A., Chiang, E. N., Holowka, D. A., and Baird, B. (2012). Correlation Functions Quantify Super-Resolution Images and Estimate Apparent Clustering Due to Over-Counting. PLoS One, 7, e31457.Google Scholar
Wang, Y., Schnitzbauer, J., Hu, Z., Li, X., Cheng, Y., Huang, Z. L., and Huang, B. (2014). Localization Events-Based Sample Drift Correction for Localization Microscopy with Redundant Cross-Correlation Algorithm. Optics Express, 22, 15982–15991.CrossRefGoogle ScholarPubMed
Yu, J. (2016). Single-Molecule Studies in Live Cells. Annual Review of Physical Chemistry, 67, 565–585.Google Scholar

References

Berthold, M. R., Cebron, N., Dill, F., et al. (2008). KNIME: The Konstanz Information Miner. Berlin, Heidelberg, Springer Berlin Heidelberg.Google Scholar
Conrad, C., Wünsche, A., Tan, T. H., et al. (2011). Micropilot: Automation of Fluorescence Microscopy-Based Imaging for Systems Biology. Nature Methods 8(3), 246–249.Google Scholar
Eberle, J. P., Muranyi, W., Erfle, H., and Gunkel, M. (2017). Fully Automated Targeted Confocal and Single-Molecule Localization Microscopy. In Erfle, H., ed., Super-Resolution Microscopy. Humana Press, New York, NY: 139–152.Google Scholar
Edelstein, A. D., Tsuchida, M. A., Amodaj, N., Pinkard, H., Vale, R. D., and Stuurman, N. (2014). Advanced Methods of Microscope Control Using μManager Software. Journal of Biological Methods 1(2), e10. doi: 10.14440/jbm.2014.36.Google Scholar
Gaj, T., Gersbach, C. A., and Barbas, C. F. III (2013). ZFN, TALEN, and CRISPR/Cas-Based Methods for Genome Engineering. Trends Biotechnol 31(7), 397–405.Google Scholar
Gunkel, M., Chung, I., Wörz, S., et al. (2017). Quantification of Telomere Features in Tumor Tissue Sections by an Automated 3D Imaging-Based Workflow. Methods 114, 60–73.Google Scholar
Hagen, G. M., Borkovec, J., Ovesný, M., Křížek, P., and Švindrych, Z. (2014). ThunderSTORM: A Comprehensive ImageJ Plug-in for PALM and STORM Data Analysis and Super-Resolution Imaging. Bioinformatics 30(16), 2389–2390.Google Scholar
Heintze, J., Luft, C., and Ketteler, R. (2013). A CRISPR Case for High-Throughput Silencing. Front Genet 4, 193.Google Scholar
Lenart, P., Petronczki, M., Steegmaier, M., et al. (2007). The Small-Molecule Inhibitor BI 2536 Reveals Novel Insights into Mitotic Roles of Polo-Like Kinase 1. Current Biology 17(4), 304–315.Google Scholar
Mali, P., Yang, L., Esvelt, K. M., et al. (2013). RNA-Guided Human Genome Engineering via Cas9. Science 339(6121), 823–826.Google Scholar
Neumann, B., Walter, T., Hériché, J.-K., et al. (2010). Phenotypic Profiling of the Human Genome by Time-Lapse Microscopy Reveals Cell Division Genes. Nature 464(7289), 721–727.CrossRefGoogle ScholarPubMed
Rust, M. J., Bates, M., and Zhuang, X. (2006). Sub-Diffraction-Limit Imaging by Stochastic Optical Reconstruction Microscopy (STORM). Nature Methods 3, 793.Google Scholar
Sander, J. D. and Joung, J. K. (2014). CRISPR-Cas Systems for Editing, Regulating and Targeting Genomes. Nature Biotechnology 32(4), 347–355.Google Scholar
Temple, G., Gerhard, D. S., Rasooly, R., et al. (2009). The Completion of the Mammalian Gene Collection (MGC). Genome Research 19(12), 2324–2333.Google Scholar
Tischer, C., Hilsenstein, V., Hanson, K., and Pepperkok, R. (2014). Adaptive Fluorescence Microscopy by Online Feedback Image Analysis. In Waters, J. C. and Wittman, T., eds., Methods in Cell Biology. Academic Press. Vol. 123, 489–503.Google Scholar

References

Anon., (n.d.) GeneCards. Human Genes | Gene Database | Gene Search. www.genecards.org/.Google Scholar
Baday, M., et al. (2012). Multi-Color Super-Resolution DNA Imaging for Genetic Analysis. Nano Letters, 12, 3861–3866.Google Scholar
Batzer, M. A. and Deininger, P. L. (2002). Alu Repeats and Human Genomic Diversity. Nature Reviews. Genetics, 3(5), 370–379. http://dx.doi.org/10.1038/nrg798.Google Scholar
Bensimon, A., et al. (1994). Alignment and Sensitive Detection of DNA by a Moving Interface. Science, 265(5181), 2096–2098.CrossRefGoogle ScholarPubMed
Cabianca, D. S. and Gabellini, D. (2010). The Cell Biology of Disease: FSHD: Copy Number Variations on the Theme of Muscular Dystrophy. The Journal of Cell Biology, 191(6), 1049–1060. www.pubmedcentral.nih.gov/articlerender.fcgi?artid=3002039&tool=pmcentrez&rendertype=abstract.Google Scholar
Cai, W., Jing, J., Irvin, B., et al. (1998). High-Resolution Restriction Maps of Bacterial Artificial Chromosome Constructed by Optical Mapping. Proceedings of the National Academy of Science USA, 95(March), 3390–3395.Google Scholar
Choudhuri, S. (2003). The Path from Nuclein to Human Genome: A Brief History of DNA with a Note on Human Genome Sequencing and Its Impact on Future Research in Biology. Bulletin of Science, Technology and Society, 23(5), 360–367. http://bst.sagepub.com/cgi/doi/10.1177/0270467603259770.Google Scholar
Dahm, R. (2005). Friedrich Miescher and the Discovery of DNA. Developmental Biology, 278(2), 274–288.Google Scholar
Dinsdale, E. A., et al. (2008). Functional Metagenomic Profiling of Nine Biomes. Nature, 452(7187), 629–632. www.ncbi.nlm.nih.gov/pubmed/18337718.Google Scholar
Gaillard, M.-C., et al. (2014). Differential DNA Methylation of the D4Z4 Repeat in Patients with FSHD and Asymptomatic Carriers. Neurology, 83(8), 733–742. www.ncbi.nlm.nih.gov/pubmed/25031281.Google Scholar
Grönlund, M. M., et al. (2000). Importance of Intestinal Colonisation in the Maturation of Humoral Immunity in Early Infancy: A Prospective Follow Up Study of Healthy Infants Aged 0–6 Months. Archives of Disease in Childhood. Fetal and Neonatal Edition, 83(3), F186–F192. www.ncbi.nlm.nih.gov/pubmed/11040166.Google Scholar
Grunwald, A., et al. (2015). Bacteriophage Strain Typing by Rapid Single Molecule Analysis. Nucleic Acids Research, 43(18), 1–8. www.ncbi.nlm.nih.gov/pubmed/26019180.Google Scholar
Handelsman, J. (2004). Metagenomics: Application of Genomics to Uncultured Microorganisms. Microbiology and Molecular Biology Reviews, 68(4), 669–685.Google Scholar
Hansen, K. D., et al. (2011). Increased Methylation Variation in Epigenetic Domains across Cancer Types. Nature Genetics, 43(8), 768–775. http://dx.doi.org/10.1038/ng.865.Google Scholar
Hanz, G. M., et al. (2014). Sequence-Specific Labeling of Nucleic Acids and Proteins with Methyltransferases and Cofactor Analogues. Journal of Visualized Experiments: JoVE, (93), 3–12. www.ncbi.nlm.nih.gov/pubmed/25490674.Google Scholar
Herrick, J. and Bensimon, A. (2009). Introduction to Molecular Combing: Genomics, DNA Replication, and Cancer. Methods in Molecular Biology, 521, 71–101.Google Scholar
Huichalaf, C., et al. (2014). DNA Methylation Analysis of the Macrosatellite Repeat Associated with FSHD Muscular Dystrophy at Single Nucleotide Level. PloS One, 9(12), p.e115278. http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0115278#s6.Google Scholar
Jeffet, J., et al. (2016). Super-Resolution Genome Mapping in Silicon Nanochannels. ACS Nano, 10(11), 9823–9830. http://pubs.acs.org/doi/abs/10.1021/acsnano.6b05398.Google Scholar
Jones, P. A. and Takai, D. (2001). The Role of DNA Methylation in Mammalian Epigenetics. Science, 293(5532), 1068–1070.Google Scholar
Kidd, J. M. et al. (2008). Mapping and Sequencing of Structural Variation from Eight Human Genomes. Nature, 453(7191), 56–64.Google Scholar
Kinkley, S., et al. (2009). SPOC1: A Novel PHD-Containing Protein Modulating Chromatin Structure and Mitotic Chromosome Condensation. Journal of Cell Science, 122(16), 2946–2956.Google Scholar
Klimasauskas, S. and Weinhold, E. (2007). A New Tool for Biotechnology: AdoMet-Dependent Methyltransferases. Trends in Biotechnology, 25(3), 99–104. www.ncbi.nlm.nih.gov/pubmed/17254657.Google Scholar
Laird, P. W. (2010). Principles and Challenges of Genome-Wide DNA Methylation Analysis. Nature Reviews Genetics, 11(3), 191. www.ncbi.nlm.nih.gov/pubmed/20125086.Google Scholar
Lam, E. T., et al. (2012). Genome Mapping on Nanochannel Arrays for Structural Variation Analysis and Sequence Assembly. Nature Biotechnology, 30(8), 771–776. www.nature.com/doifinder/10.1038/nbt.2303.CrossRefGoogle ScholarPubMed
Landan, G., et al. (2012). Epigenetic Polymorphism and the Stochastic Formation of Differentially Methylated Regions in Normal and Cancerous Tissues. Nature Genetics, 44(11), 1207–1214. www.nature.com/doifinder/10.1038/ng.2442.Google Scholar
Landau, D. A. et al. (2014). Locally Disordered Methylation Forms the Basis of Intratumor Methylome Variation in Chronic Lymphocytic Leukemia. Cancer Cell, 26(6), 813–825. www.ncbi.nlm.nih.gov/pubmed/25490447.Google Scholar
Levy-Sakin, M. and Ebenstein, Y. (2013). Beyond Sequencing: Optical Mapping of DNA in the Age of Nanotechnology and Nanoscopy. Current Opinion in Biotechnology, 24, 690–698. www.ncbi.nlm.nih.gov/pubmed/23428595.CrossRefGoogle ScholarPubMed
van der Maarel, S. M., et al. (2000). De Novo Facioscapulohumeral Muscular Dystrophy: Frequent Somatic Mosaicism, Sex-Dependent Phenotype, and the Role of Mitotic Transchromosomal Repeat Interaction between Chromosomes 4 and 10. American Journal of Human Genetics, 66(1), 26–35. www.sciencedirect.com/science/article/pii/S0002929707622307.Google Scholar
Mak, A. C. Y., et al. (2016). Genome-Wide Structural Variation Detection by Genome Mapping on Nanochannel Arrays. Genetics, 202(1), 351–362. www.pubmedcentral.nih.gov/articlerender.fcgi?artid=4701098&tool=pmcentrez&rendertype=abstract.Google Scholar
Mather, K. A., et al. (2011). Is Telomere Length a Biomarker of Aging? A Review. The Journals of Gerontology. Series A, Biological Sciences and Medical Sciences, 66(2), 202–213. www.ncbi.nlm.nih.gov/pubmed/21030466.Google Scholar
Mostovoy, Y., et al. (2016). A Hybrid Approach for De Novo Human Genome Sequence Assembly and Phasing. Nature Methods, 13(7), 587–590. www.nature.com/doifinder/10.1038/nmeth.3865%5Cnhttp://www.ncbi.nlm.nih.gov/pubmed/27159086.Google Scholar
Nilsson, A. N., et al. (2014). Competitive Binding-Based Optical DNA Mapping for Fast Identification of Bacteria – Multi-Ligand Transfer Matrix Theory and Experimental Applications on Escherichia Coli. Nucleic Acids Research, 42(15), E118.Google Scholar
Noble, C., et al. (2013). A Fast and Scalable Algorithm for Alignment of Optical DNA Mappings. PLoS One, 10(4), e0121905.Google Scholar
O'Boyle, C. J., et al. (1998). Microbiology of Bacterial Translocation in Humans. Gut, 42(1), 29–35. http://gut.bmj.com/cgi/doi/10.1136/gut.42.1.29.Google Scholar
Pendleton, M., et al. (2015a). Assembly and Diploid Architecture of an Individual Human Genome via Single-Molecule Technologies. Nature Methods, 12(8), 780–786. www.nature.com/nmeth/journal/v12/n8/full/nmeth.3454.html#affil-auth.Google Scholar
Pendleton, M., et al. (2015b). Assembly and diploid architecture of an individual human genome via single-molecule technologies. Nature Methods, 12(8), 780–786. http://dx.doi.org/10.1038/nmeth.3454.Google Scholar
Petell, C. J., et al. (2016). An Epigenetic Switch Regulates De Novo DNA Methylation at a Subset of Pluripotency Gene Enhancers during Embryonic Stem Cell Differentiation. Nucleic Acids Research, 44(16), 7605–7617.Google Scholar
Reinius, L. E., et al. (2012). Differential DNA Methylation in Purified Human Blood Cells: Implications for Cell Lineage and Studies on Disease Susceptibility. PLoS One, 7(7), e41361.Google Scholar
Schmid, C. W. and Prescott, L. D. (1975). Organization of the Human Genome Transcription. Cell, 6(November), 345–358.CrossRefGoogle Scholar
Sender, R., Fuchs, S., and Milo, R. (2016). Revised Estimates for the Number of Human and Bacteria Cells in the Body. PLOS Biology, 14(8), e1002533.Google Scholar
Thakur, A. K., et al. (2014). Gut-Microbiota and Mental Health: Current and Future Perspectives. Journal of Pharmacology and Clinical Toxicology, 2(1), 1–15.Google Scholar
Thomas Anantharaman, B. M., 2001. False Positives in Genomic Map Assembly and Sequence Validation. In Gascuel, O. and Moret, B. M. E., eds., Algorithms in Bioinformatics, Lecture Notes in Computer Science. Berlin, Heidelberg: Springer Berlin Heidelberg. http://link.springer.com/10.1007/3-540-44696-6.Google Scholar
Treangen, T. J. and Salzberg, S. L. (2012). Repetitive DNA and Next-Generation Sequencing: Computational Challenges and Solutions. Nature Reviews. Genetics, 13(1), 36–46. www.pubmedcentral.nih.gov/articlerender.fcgi?artid=3324860&tool=pmcentrez&rendertype=abstract.Google Scholar
Valinluck, V. and Sowers, L. C. (2007). Endogenous Cytosine Damage Products Alter the Site Selectivity of Human DNA Maintenance Methyltransferase DNMT1. Cancer Research, 67(3), 946–950.Google Scholar
Wooley, J. C. and Ye, Y. (2009). Metagenomics: Facts and Artifacts, and Computational Challenges. National Institutes of Health Public Access, 25(1), 71–81.Google Scholar
Xi, Y., et al. (2009). BSMAP: Whole Genome Bisulfite Sequence MAPping Program. BMC Bioinformatics, 10(1), 232. www.biomedcentral.com/1471-2105/10/232.Google Scholar
Zirkin, S., et al. (2014). Lighting Up Individual DNA Damage Sites by In Vitro Repair Synthesis. Journal of the American Chemical Society, 136(21), 7771–7776.Google Scholar
Zohar, H. and Muller, S. J. (2011). Labeling DNA for Single-Molecule Experiments: Methods of Labeling Internal Specific Sequences on Double-Stranded DNA. Nanoscale, 3(8), 3027–3039.Google Scholar

Save book to Kindle

To save this book to your Kindle, first ensure coreplatform@cambridge.org is added to your Approved Personal Document E-mail List under your Personal Document Settings on the Manage Your Content and Devices page of your Amazon account. Then enter the ‘name’ part of your Kindle email address below. Find out more about saving to your Kindle.

Note you can select to save to either the @free.kindle.com or @kindle.com variations. ‘@free.kindle.com’ emails are free but can only be saved to your device when it is connected to wi-fi. ‘@kindle.com’ emails can be delivered even when you are not connected to wi-fi, but note that service fees apply.

Find out more about the Kindle Personal Document Service.

Available formats
×

Save book to Dropbox

To save content items to your account, please confirm that you agree to abide by our usage policies. If this is the first time you use this feature, you will be asked to authorise Cambridge Core to connect with your account. Find out more about saving content to Dropbox.

Available formats
×

Save book to Google Drive

To save content items to your account, please confirm that you agree to abide by our usage policies. If this is the first time you use this feature, you will be asked to authorise Cambridge Core to connect with your account. Find out more about saving content to Google Drive.

Available formats
×