Paper Roundup – March 2015

  • A spinning-disk confocal based super-resolution system, giving a fast 2-fold improvement in resolution [1]
  • PALMsiever: a localization microscopy tool implementing a number of algorithms for drift correction, clustering, and rendering of localization microscopy data [2]
  • An image-based microfluidic screen for cell deformation [3]
  • Six-color imaging using narrow-band filter sets [4]
  • 3D particle tracking using phase-contrast holography [5]
  • A new super-resolution approach, analogous to STED, that uses a transiently activated quencher dye, whose absorption and quenching is light-dependent [6]
  • A protease reporter based on conversion of iFP from a non-fluorescent to a fluorescent state on protease cleavage [7]
  • Osmium tetroxide fixable mEos4 proteins for correlative super-resolution microscopy and EM [8]
  • A simple chemical modification of many common dyes dramatically improves their quantum yield [9]
  • Ratiometric biosensors by dimeric partner exchange [10]
  • A simplified CLARITY protocol for brain imaging [11]
  • Following translation of RNA by removal of a bound fluorescent protein by the translating ribosome [12]
  • Single molecule imaging of DNA-bound proteins by using energy transfer from a DNA intercalating dye to activate a fluorescent label on a protein bound to the DNA [13]
  • Multicolor CRISPR labeling of chromosomal loci [14]
  • Make your own gridded coverslips using electron beam deposition of metal [15]

References

  1. S. Hayashi, and Y. Okada, "Ultrafast superresolution fluorescence imaging with spinning disk confocal microscope optics", Molecular Biology of the Cell, vol. 26, pp. 1743-1751, 2015. http://dx.doi.org/10.1091/mbc.E14-08-1287
  2. T. Pengo, S.J. Holden, and S. Manley, "PALMsiever: a tool to turn raw data into results for single-molecule localization microscopy", Bioinformatics, vol. 31, pp. 797-798, 2014. http://dx.doi.org/10.1093/bioinformatics/btu720
  3. O. Otto, P. Rosendahl, A. Mietke, S. Golfier, C. Herold, D. Klaue, S. Girardo, S. Pagliara, A. Ekpenyong, A. Jacobi, M. Wobus, N. Töpfner, U.F. Keyser, J. Mansfeld, E. Fischer-Friedrich, and J. Guck, "Real-time deformability cytometry: on-the-fly cell mechanical phenotyping", Nature Methods, vol. 12, pp. 199-202, 2015. http://dx.doi.org/10.1038/nmeth.3281
  4. S. Kijani, U. Yrlid, M. Heyden, M. Levin, J. Borén, and P. Fogelstrand, "Filter-Dense Multicolor Microscopy", PLOS ONE, vol. 10, pp. e0119499, 2015. http://dx.doi.org/10.1371/journal.pone.0119499
  5. F. Cheong, C. Wong, Y. Gao, M. Nai, Y. Cui, S. Park, L. Kenney, and C. Lim, "Rapid, High-Throughput Tracking of Bacterial Motility in 3D via Phase-Contrast Holographic Video Microscopy", Biophysical Journal, vol. 108, pp. 1248-1256, 2015. http://dx.doi.org/10.1016/j.bpj.2015.01.018
  6. T. Rosales, D.L. Sackett, J. Xu, Z. Shi, B. Xu, H. Li, G. Kaur, E. Frohart, N. Shenoy, S.M. Cheal, H. Wu, A.E. Dulcey, Y. Hu, C. Li, K. Lane, G.L. Griffiths, and J.R. Knutson, "STAQ: A route toward low power, Multicolor nanoscopy", Microscopy Research and Technique, vol. 78, pp. 343-355, 2015. http://dx.doi.org/10.1002/jemt.22478
  7. T. To, B.J. Piggott, K. Makhijani, D. Yu, Y.N. Jan, and X. Shu, "Rationally designed fluorogenic protease reporter visualizes spatiotemporal dynamics of apoptosis in vivo", Proceedings of the National Academy of Sciences, vol. 112, pp. 3338-3343, 2015. http://dx.doi.org/10.1073/pnas.1502857112
  8. M.G. Paez-Segala, M.G. Sun, G. Shtengel, S. Viswanathan, M.A. Baird, J.J. Macklin, R. Patel, J.R. Allen, E.S. Howe, G. Piszczek, H.F. Hess, M.W. Davidson, Y. Wang, and L.L. Looger, "Fixation-resistant photoactivatable fluorescent proteins for CLEM", Nature Methods, vol. 12, pp. 215-218, 2015. http://dx.doi.org/10.1038/nmeth.3225
  9. J.B. Grimm, B.P. English, J. Chen, J.P. Slaughter, Z. Zhang, A. Revyakin, R. Patel, J.J. Macklin, D. Normanno, R.H. Singer, T. Lionnet, and L.D. Lavis, "A general method to improve fluorophores for live-cell and single-molecule microscopy", Nature Methods, vol. 12, pp. 244-250, 2015. http://dx.doi.org/10.1038/nmeth.3256
  10. Y. Ding, J. Li, J.R. Enterina, Y. Shen, I. Zhang, P.H. Tewson, G.C.H. Mo, J. Zhang, A.M. Quinn, T.E. Hughes, D. Maysinger, S.C. Alford, Y. Zhang, and R.E. Campbell, "Ratiometric biosensors based on dimerization-dependent fluorescent protein exchange", Nature Methods, vol. 12, pp. 195-198, 2015. http://dx.doi.org/10.1038/nmeth.3261
  11. H. Zheng, and L. Rinaman, "Simplified CLARITY for visualizing immunofluorescence labeling in the developing rat brain", Brain Structure and Function, vol. 221, pp. 2375-2383, 2015. http://dx.doi.org/10.1007/s00429-015-1020-0
  12. J.M. Halstead, T. Lionnet, J.H. Wilbertz, F. Wippich, A. Ephrussi, R.H. Singer, and J.A. Chao, "An RNA biosensor for imaging the first round of translation from single cells to living animals", Science, vol. 347, pp. 1367-1671, 2015. http://dx.doi.org/10.1126/science.aaa3380
  13. H. Geertsema, A. Schulte, L. Spenkelink, W. McGrath, S. Morrone, J. Sohn, W. Mangel, A. Robinson, and A. van Oijen, "Single-Molecule Imaging at High Fluorophore Concentrations by Local Activation of Dye", Biophysical Journal, vol. 108, pp. 949-956, 2015. http://dx.doi.org/10.1016/j.bpj.2014.12.019
  14. H. Ma, A. Naseri, P. Reyes-Gutierrez, S.A. Wolfe, S. Zhang, and T. Pederson, "Multicolor CRISPR labeling of chromosomal loci in human cells", Proceedings of the National Academy of Sciences, vol. 112, pp. 3002-3007, 2015. http://dx.doi.org/10.1073/pnas.1420024112
  15. L. Benedetti, E. Sogne, S. Rodighiero, D. Marchesi, P. Milani, and M. Francolini, "Customized patterned substrates for highly versatile correlative light-scanning electron microscopy", Scientific Reports, vol. 4, 2014. http://dx.doi.org/10.1038/srep07033