Paper Roundup: November 2013

  • A review on determining protein quaternary structure by FRET. I’m a little skeptical of their ability to extract as much information from (typically noisy) FRET data as they want to, but it’s an interesting review nonetheless. [1]
  • Using GFP-labeled TALEs to fluorescently label chromosomal regions [2]
  • Another compressed sensing algorithm for fast STORM/PALM imaging [3]
  • A review on Raman microscopy [4]
  • STED imaging of individual diamond nitrogen vacancies with ~10 nm resolution [5]
  • Ultra-high speed 3D imaging of second harmonic generation using holography [6]
  • Single molecule super-resolution imaging used to count molecules and measure the fraction of dimers [7]
  • High speed 3D holographic imaging of ciliary beating [8]
  • Temperature sensitive GFPs for measurement of the temperature inside cells [9]
  • An improved version of the spinach aptamer, spinach2, for fluorescent labeling of RNAs [10]
  • A new method for monovalent functionalization of quantum dots for single molecule labeling and imaging [11]
  • A new method for segmenting nuclei. It has a nice overview of current algorithms for nuclear segmentation in the introduction [12]
  • A microfluidic method for trapping cells in droplets and imaging them for long periods of time [13]
  • A review of superresolution localization methods, specifically on fitting algorithms [14]
  • An introduction to machine learning approaches for analyzing imaging data in cell biology [15]

References

  1. V. Raicu, and D. Singh, "FRET Spectrometry: A New Tool for the Determination of Protein Quaternary Structure in Living Cells", Biophysical Journal, vol. 105, pp. 1937-1945, 2013. http://dx.doi.org/10.1016/j.bpj.2013.09.015
  2. Y. Miyanari, C. Ziegler-Birling, and M. Torres-Padilla, "Live visualization of chromatin dynamics with fluorescent TALEs", Nature Structural & Molecular Biology, vol. 20, pp. 1321-1324, 2013. http://dx.doi.org/10.1038/nsmb.2680
  3. H.P. Babcock, J.R. Moffitt, Y. Cao, and X. Zhuang, "Fast compressed sensing analysis for super-resolution imaging using L1-homotopy", Optics Express, vol. 21, pp. 28583, 2013. http://dx.doi.org/10.1364/OE.21.028583
  4. K.A. Antonio, and Z.D. Schultz, "Advances in Biomedical Raman Microscopy", Analytical Chemistry, vol. 86, pp. 30-46, 2013. http://dx.doi.org/10.1021/ac403640f
  5. S. Arroyo-Camejo, M. Adam, M. Besbes, J. Hugonin, V. Jacques, J. Greffet, J. Roch, S.W. Hell, and F. Treussart, "Stimulated Emission Depletion Microscopy Resolves Individual Nitrogen Vacancy Centers in Diamond Nanocrystals", ACS Nano, vol. 7, pp. 10912-10919, 2013. http://dx.doi.org/10.1021/nn404421b
  6. D.R. Smith, D.G. Winters, and R.A. Bartels, "Submillisecond second harmonic holographic imaging of biological specimens in three dimensions", Proceedings of the National Academy of Sciences, vol. 110, pp. 18391-18396, 2013. http://dx.doi.org/10.1073/pnas.1306856110
  7. X. Nan, E.A. Collisson, S. Lewis, J. Huang, T.M. Tamguney, J.T. Liphardt, F. McCormick, J.W. Gray, and S. Chu, "Single-molecule superresolution imaging allows quantitative analysis of RAF multimer formation and signaling", Proceedings of the National Academy of Sciences, vol. 110, pp. 18519-18524, 2013. http://dx.doi.org/10.1073/pnas.1318188110
  8. L.G. Wilson, L.M. Carter, and S.E. Reece, "High-speed holographic microscopy of malaria parasites reveals ambidextrous flagellar waveforms", Proceedings of the National Academy of Sciences, vol. 110, pp. 18769-18774, 2013. http://dx.doi.org/10.1073/pnas.1309934110
  9. S. Kiyonaka, T. Kajimoto, R. Sakaguchi, D. Shinmi, M. Omatsu-Kanbe, H. Matsuura, H. Imamura, T. Yoshizaki, I. Hamachi, T. Morii, and Y. Mori, "Genetically encoded fluorescent thermosensors visualize subcellular thermoregulation in living cells", Nature Methods, vol. 10, pp. 1232-1238, 2013. http://dx.doi.org/10.1038/nmeth.2690
  10. R.L. Strack, M.D. Disney, and S.R. Jaffrey, "A superfolding Spinach2 reveals the dynamic nature of trinucleotide repeat–containing RNA", Nature Methods, vol. 10, pp. 1219-1224, 2013. http://dx.doi.org/10.1038/nmeth.2701
  11. J. Farlow, D. Seo, K.E. Broaders, M.J. Taylor, Z.J. Gartner, and Y. Jun, "Formation of targeted monovalent quantum dots by steric exclusion", Nature Methods, vol. 10, pp. 1203-1205, 2013. http://dx.doi.org/10.1038/nmeth.2682
  12. J. QI, "Dense nuclei segmentation based on graph cut and convexity-concavity analysis", Journal of Microscopy, vol. 253, pp. 42-53, 2013. http://dx.doi.org/10.1111/jmi.12096
  13. M.A. Khorshidi, P.K.P. Rajeswari, C. Wählby, H.N. Joensson, and H. Andersson Svahn, "Automated analysis of dynamic behavior of single cells in picoliter droplets", Lab on a Chip, vol. 14, pp. 931, 2014. http://dx.doi.org/10.1039/C3LC51136G
  14. A.R. Small, and R. Parthasarathy, "Superresolution Localization Methods", Annual Review of Physical Chemistry, vol. 65, pp. 107-125, 2014. http://dx.doi.org/10.1146/annurev-physchem-040513-103735
  15. C. Sommer, and D.W. Gerlich, "Machine learning in cell biology – teaching computers to recognize phenotypes", Journal of Cell Science, vol. 126, pp. 5529-5539, 2013. http://dx.doi.org/10.1242/jcs.123604