Paper Roundup – January 2014

  • An interesting method for image-based cell sorting where photopolymerization is used to trap unwanted cells, allowing the selected cells to be washed off and collected [1]
  • Best Practices for Scientific Computing. Only microscopy related insofar as you write software or macros to analyze images, but very good to bear in mind if you do [2]
  • Trimethoprim tagging for STORM imaging with Alexa 647 and Atto 655 [3]
  • MS2 fusions to SNAP-tags and DHFR for targeting small molecule dyes to RNAs in vivo[4]
  • Luminescence imaging using a short focal length tube lens [5]
  • An overview of the Vaa3D image analysis package [6]
  • X-ray microtomography of Xenopus development. [7]
  • Super-resolution imaging and quantitation of RNA polymerase using a mirror to perform light sheet imaging of the cell nucleus [8]
  • A fast-folding Dronpa variant, and a variant that is green-to-red photoconvertible (though tetrameric) [9]
  • New fluorophores to change the spectral properties of the Spinach / Spinach2 fluorescent RNA apatamers [10]
  • A blue light inducible degron [11]
  • A blue light inducible homodimerization system [12]
  • Using the CRISPR/Cas system for imaging of genomic loci in live cells [13]
  • A new ratiometric calcium senso [14]
  • A direct measure of photoactivation efficency for photoactivatible fluorescent proteins [15]
  • A real-time FISH assay for measurement of RNA transcription rates [16]
  • Metal-induced energy transfer for measuring distances between dyes and a metal film, used to map the height of the basal membrane of cells with one nanometer accuracy. [17]
  • A review of genetically encoded fluorescent biosensors for phosphorylation [18]
  • A clever trick using SNAP-tag labeling of a solvatochromic dye for no-wash imaging of plasma membrane proteins [19]


  1. T. Sun, J. Kovac, and J. Voldman, "Image-Based Single-Cell Sorting via Dual-Photopolymerized Microwell Arrays", Analytical Chemistry, vol. 86, pp. 977-981, 2014.
  2. G. Wilson, D.A. Aruliah, C.T. Brown, N.P. Chue Hong, M. Davis, R.T. Guy, S.H.D. Haddock, K.D. Huff, I.M. Mitchell, M.D. Plumbley, B. Waugh, E.P. White, and P. Wilson, "Best Practices for Scientific Computing", PLoS Biology, vol. 12, pp. e1001745, 2014.
  3. T. Wang, L. Friedman, J. Gelles, W. Min, A. Hoskins, and V. Cornish, "The Covalent Trimethoprim Chemical Tag Facilitates Single Molecule Imaging with Organic Fluorophores", Biophysical Journal, vol. 106, pp. 272-278, 2014.
  4. T.J. Carrocci, and A.A. Hoskins, "Imaging of RNAs in live cells with spectrally diverse small molecule fluorophores", The Analyst, vol. 139, pp. 44-47, 2014.
  5. K. OGOH, R. AKIYOSHI, . MAY‐MAW‐THET, T. SUGIYAMA, S. DOSAKA, Y. HATTA‐OHASHI, and H. SUZUKI, "Bioluminescence microscopy using a short focal‐length imaging lens", Journal of Microscopy, vol. 253, pp. 191-197, 2014.
  6. H. Peng, A. Bria, Z. Zhou, G. Iannello, and F. Long, "Extensible visualization and analysis for multidimensional images using Vaa3D", Nature Protocols, vol. 9, pp. 193-208, 2014.
  7. J. Moosmann, A. Ershov, V. Weinhardt, T. Baumbach, M.S. Prasad, C. LaBonne, X. Xiao, J. Kashef, and R. Hofmann, "Time-lapse X-ray phase-contrast microtomography for in vivo imaging and analysis of morphogenesis", Nature Protocols, vol. 9, pp. 294-304, 2014.
  8. Z.W. Zhao, R. Roy, J.C.M. Gebhardt, D.M. Suter, A.R. Chapman, and X.S. Xie, "Spatial organization of RNA polymerase II inside a mammalian cell nucleus revealed by reflected light-sheet superresolution microscopy", Proceedings of the National Academy of Sciences, vol. 111, pp. 681-686, 2013.
  9. B. Moeyaert, N. Nguyen Bich, E. De Zitter, S. Rocha, K. Clays, H. Mizuno, L. van Meervelt, J. Hofkens, and P. Dedecker, "Green-to-Red Photoconvertible Dronpa Mutant for Multimodal Super-resolution Fluorescence Microscopy", ACS Nano, vol. 8, pp. 1664-1673, 2014.
  10. W. Song, R.L. Strack, N. Svensen, and S.R. Jaffrey, "Plug-and-Play Fluorophores Extend the Spectral Properties of Spinach", Journal of the American Chemical Society, vol. 136, pp. 1198-1201, 2014.
  11. K.M. Bonger, R. Rakhit, A.Y. Payumo, J.K. Chen, and T.J. Wandless, "General Method for Regulating Protein Stability with Light", ACS Chemical Biology, vol. 9, pp. 111-115, 2013.
  12. Y. Nihongaki, H. Suzuki, F. Kawano, and M. Sato, "Genetically Engineered Photoinducible Homodimerization System with Improved Dimer-Forming Efficiency", ACS Chemical Biology, vol. 9, pp. 617-621, 2014.
  13. B. Chen, L. Gilbert, B. Cimini, J. Schnitzbauer, W. Zhang, G. Li, J. Park, E. Blackburn, J. Weissman, L. Qi, and B. Huang, "Dynamic Imaging of Genomic Loci in Living Human Cells by an Optimized CRISPR/Cas System", Cell, vol. 155, pp. 1479-1491, 2013.
  14. T. Thestrup, J. Litzlbauer, I. Bartholomäus, M. Mues, L. Russo, H. Dana, Y. Kovalchuk, Y. Liang, G. Kalamakis, Y. Laukat, S. Becker, G. Witte, A. Geiger, T. Allen, L.C. Rome, T. Chen, D.S. Kim, O. Garaschuk, C. Griesinger, and O. Griesbeck, "Optimized ratiometric calcium sensors for functional in vivo imaging of neurons and T lymphocytes", Nature Methods, vol. 11, pp. 175-182, 2014.
  15. N. Durisic, L. Laparra-Cuervo, . Sandoval-Álvarez, J.S. Borbely, and M. Lakadamyali, "Single-molecule evaluation of fluorescent protein photoactivation efficiency using an in vivo nanotemplate", Nature Methods, vol. 11, pp. 156-162, 2014.
  16. Z. Zhang, A. Revyakin, J.B. Grimm, L.D. Lavis, and R. Tjian, "Single-molecule tracking of the transcription cycle by sub-second RNA detection", eLife, vol. 3, 2014.
  17. A.I. Chizhik, J. Rother, I. Gregor, A. Janshoff, and J. Enderlein, "Metal-induced energy transfer for live cell nanoscopy", Nature Photonics, vol. 8, pp. 124-127, 2014.
  18. L. Oldach, and J. Zhang, "Genetically Encoded Fluorescent Biosensors for Live-Cell Visualization of Protein Phosphorylation", Chemistry & Biology, vol. 21, pp. 186-197, 2014.
  19. E. Prifti, L. Reymond, M. Umebayashi, R. Hovius, H. Riezman, and K. Johnsson, "A Fluorogenic Probe for SNAP-Tagged Plasma Membrane Proteins Based on the Solvatochromic Molecule Nile Red", ACS Chemical Biology, vol. 9, pp. 606-612, 2014.