Fluorescence and SEM correlative microscopy for nanomanipulation of subcellular structures

Zheng Gong; Brandon K Chen; Jun Liu; Chao Zhou; Dave Anchel; Xiao Li; Ji Ge; David P Bazett-Jones; Yu Sun

doi:10.1038/lsa.2014.105

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Fluorescence and SEM correlative microscopy for nanomanipulation of subcellular structures

Original Articles

- Fluorescence and SEM correlative microscopy for nanomanipulation of subcellular structures
- Light: Science & Applications Vol. 3, Issue 4, (2014)
- Affiliations：
  
  1.Advanced Micro and Nanosystems Laboratory, University of Toronto, Toronto, ON M5S 3G8, Canada
  2.State Key Laboratory of Intelligent Control and Management of Complex Systems, Institute of Automation, Chinese Academy of Sciences, Beijing 100190, China
  3.The Genetics and Genome Biology Program, the Hospital for Sick Children, Toronto, ON M5G 1X8, Canada
- Author bio：
  
  Professor DP Bazett-Jones, the Genetics and Genome Biology Program, the Hospital for Sick Children, 555 University Avenue, Toronto, ON M5G 1X8, Canad Email: david.bazett-jones@sickkids.ca
  Professor Y Sun, Advanced Micro and Nanosystems Laboratory, University of Toronto, 5 King's College Road, Toronto, ON M5S 3G8, Canada Email: sun@mie.utoronto.ca
- Funds：
- DOI：10.1038/lsa.2014.105
  CLC：
- Published：2014-12，
  
  Published Online：21 November 2014，
  
  Received：30 April 2014，
  
  Revised：15 September 2014，
  
  Accepted：16 September 2014
- Accepted：
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Gong, Z. et al. Fluorescence and SEM correlative microscopy for nanomanipulation of subcellular structures. Light: Science & Applications, 3, e224 (2014).
DOI：

Gong, Z. et al. Fluorescence and SEM correlative microscopy for nanomanipulation of subcellular structures. Light: Science & Applications, 3, e224 (2014). DOI： 10.1038/lsa.2014.105.

摘要

Abstract

Nanomanipulation under scanning electron microscopy (SEM) enables direct interactions of a tool with a sample. We recently developed a nanomanipulation technique for the extraction and identification of DNA contained within sub-nuclear locations of a single cell nucleus. In nanomanipulation of sub-cellular structures

key step is to identify targets of interest through correlating fluorescence and SEM images. The DNA extraction task must be conducted with low accelerating voltages resulting in low imaging resolutions. This is imposed by the necessity of preserving the biochemical integrity of the sample. Such poor imaging conditions make the identification of nanometer-sized fiducial marks difficult. This paper presents an affine scale-invariant feature transform (ASIFT) based method for correlating SEM images and fluorescence microscopy images. The performance of the image correlation approach under different noise levels and imaging magnifications was quantitatively evaluated. The optimal mean absolute error (MAE) of correlation results is 68±34 nm under standard conditions. Compared with manual correlation by skilled operators

the automated correlation approach demonstrates a speed that is higher by an order of magnitude. With the SEM-fluorescence image correlation approach

targeted DNA was successfully extracted

via

nanomanipulation under SEM conditions.

关键词

Keywords

correlative microscopyfluorescenceimage correlationnanomanipulationSEMsubcellular structures

references

Hübner MR, Eckersley-Maslin MA, Spector DL. Chromatin organization and transcriptional regulation.Curr Opin Genet Dev2013;23: 89–95..

Mercer TR, Mattick JS. Understanding the regulatory and transcriptional complexity of the genome through structure.Genome Res2013;23: 1081–1088..

Dundr M. Nuclear bodies: multifunctional companions of the genome.Curr Opin Cell Biol2012;24: 415–522..

Papantonis A, Cook PR. Transcription factories: genome organization and gene regulation.Chem Rev2013;113: 8683–8705..

Schneider R, Grosschedl R. Dynamics and interplay of nuclear architecture, genome organization, and gene expression.Genes Dev2007;21: 3027–3043..

de Thé H, Le Bras M, Lallemand-Breitenbach V. The cell biology of disease: acute promyelocytic leukemia, arsenic, and PML bodies.J Cell Biol2012;198: 11–21..

Luciani JJ, Depetris D, Usson Y, Metzler-Guillemain C, Mignon-Ravix Cet al. PML nuclear bodies are highly organised DNA-protein structures with a function in heterochromatin remodelling at the G2 phase.J Cell Sci2006;119: 2518–2531..

Slusarczyk A, Kamath R, Wang C, Anchel D, Pollock Cet al. Structure and function of the perinucleolar compartment in cancer cells.Cold Spring Harbor Symp Quant Biol2010;75: 599–605..

Schreiber KH, Kennedy BK. When lamins go bad: nuclear structure and disease.Cell2013;152: 1365–1375..

Sleeman JE, Trinkle-Mulcahy L. Nuclear bodies: new insights into assembly/dynamics and disease relevance.Curr Opin Cell Biol2014;28: 76–83..

Chen BK, Anchel D, Gong Z, Cotton R, Li Ret al. Nano-dissection and sequencing of DNA at single sub-nuclear structures.Small2014;12: 3267–3274..

Hansma HG, Vesenka J, Siegerist C, Kelderman G, Morrett Het al. Reproducible imaging and dissection of plasmid DNA under liquid with the atomic force microscope.Science1992;256: 1180–1184..

Hu J, Zhang Y, Gao H, Li M, Hartmann U. Artificial DNA patterns by mechanical nanomanipulation.Nano Lett2002;2: 55–57..

Lü J, An H, Li H, Li X, Wang Yet al. Nanodissection, isolation, and PCR amplification of single DNA molecules.Surf Interface Anal2006;38: 1010–1013..

Emmert-Buck MR, Bonner RF, Smith PD, Chuaqui RF, Zhuang Zet al. Laser capture microdissection.Science1996;274: 998–1001..

Sugioka K, Cheng Y. Ultrafast lasers-reliable tools for advanced materials processing.Light Sci Appl2014;3: e149, doi: 10.1038/lsa.2014.30..

Hao X, Kuang C, Gu Z, Wang Y, Li Set al. From microscopy to nanoscopyviavisible light.Light Sci Appl2013;2: e108, doi: 10.1038/lsa.2013.64..

Kopek BG, Shtengel G, Xu CS, Clayton DA, Hess HF. Correlative 3d super resolution fluorescence and electron microscopy reveal the relationship of mitochondrial nucleoids to membranes.Proc Natl Acad Sci2012;109: 6136–6141..

Kukulski W, Schorb M, Welsch S, Picco A, Kaksonen Met al. Correlated fluorescence and 3D electron microscopy with high sensitivity and spatial precision.J Cell Biol2011;192: 111–119..

Watanabe S, Punge A, Hollopeter G, Willig KI, Hobson RJet al. Protein localization in electron micrographs using fluorescence nanoscopy.Nat Methods2010;8: 80–84..

Fronczek DN, Quammen C, Wang H, Kisker C, Superfine Ret al. High accuracy FIONA-AFM hybrid imaging.Ultramicroscopy2011;111: 350–355..

Cao T, Zach C, Modla S, Powell D, Czymmek Ket al. Registration for correlative microscopy using image analogies. In: Proceedings of the 5th international conference on Biomedical Image Registration 2012; 7–8 July 2012; Nashville, TN, USA. IEEE: Piscataway, NJ, USA, 2012, pp296–306.

Halary S, Duperron S, Boudier T. Direct image-based correlative microscopy technique for coupling identification and structural investigation of bacterial symbionts associated with metazoans.Appl Environ Microbiol2011;77: 4172–4179..

Lowe DG. Distinctive image features from scale-invariant key-points.Int J Comput Vis2004;60: 91–110..

Mikolajczyk K, Schmid C. A performance evaluation of local descriptors.IEEE Trans Pattern Anal Mach Intell2005;27: 1615–1630..

Morel JM, Yu G. ASIFT: a new framework for fully affine invariant image comparison.SIAM J Imaging Sci2009;2: 438–469..

Gong Z, Chen BK, Liu J, Zhou C, Anchel Det al. Correlative microscopy for nanomanipulation of sub-cellular structures.Proc IEEE Int Conf Robot Autom2014;2014: 5209–5214..

Zhang YL, Zhang Y, Ru C, Chen BK, Sun Y. A load-lock-compatible nanomanipulation system for scanning electron microscope.IEEE/ASME Trans Mechatron2011;18: 230–237..

Gong Z, Chen BK, Liu J, Sun Y. Robotic probing of nanostructures inside scanning electron microscopy.IEEE Trans Robot2014;30: 758–765..

Schönherr E, Winckler E. A sample holder for measuring the interfacial angles of small crystals using a scanning electron microscope.J Cryst Growth1976;36: 353–354..

Buades A, Coll B, Morel JM. A non-local algorithm for image denoising.Comput Vis Pattern Recogn2005;2: 60–65..

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