Super Resolution Single Molecule (SRSM) Journal Club

First Tuesday of each month, 12:00-1:00pm, B30 Weill

Future schedule

2017

Mar 7 Presenter:

Marshall Coville

Wang, G., J. Hauver, Z. Thomas, S. A. Darst and A. Pertsinidis (2016). "Single-Molecule Real-Time 3D Imaging of the Transcription Cycle by Modulation Interferometry." Cell 167(7): 1839-1852 e1821.  (PMID: 27984731).

Feb 6 Presenter:

Rebecca Williams

Balzarotti, F., Y. Eilers, K. C. Gwosch, A. H. Gynna, V. Westphal, F. D. Stefani, J. Elf and S. W. Hell (2016). "Nanometer resolution imaging and tracking of fluorescent molecules with minimal photon fluxes." Science. (PMID: 28008086).

2016

May 2 Presenters:

Marshall Colville and Vivek Gupta

Stewart-Ornstein, J. and G. Lahav (2016). "Dynamics of CDKN1A in Single Cells Defined by an Endogenous Fluorescent Tagging Toolkit." Cell Rep 14(7): 1800-1811.  (PMID: 26876176).

Apr 4 Presenters:

Max Kushner and Rebecca Williams

Schmied, J. J., M. Raab, C. Forthmann, E. Pibiri, B. Wunsch, T. Dammeyer and P. Tinnefeld (2014). "DNA origami-based standards for quantitative fluorescence microscopy." Nat Protoc 9(6): 1367-1391.  (PMID: 24833175).

Raab, M., J. J. Schmied, I. Jusuk, C. Forthmann and P. Tinnefeld (2014). "Fluorescence microscopy with 6 nm resolution on DNA origami." Chemphyschem 15(12): 2431-2435.  (PMID: 24895173).

Mar 14 Presenters:

Hao Pan and Carolyn Shurer

Jiang, H., B. P. English, R. B. Hazan, P. Wu and B. Ovryn (2015). Tracking surface glycans on live cancer cells with single-molecule sensitivity. Angew Chem Int Ed Engl 54(6): 1765-1769.  (PMID: 25515330).

Feb 8 Presenters:

Alex Van Slyke and Eshan Mitra

Stabley, D. R., T. Oh, S. M. Simon, A. L. Mattheyses and K. Salaita (2015). Real-time fluorescence imaging with 20 nm axial resolution. Nat Commun 6: 8307. (PMID: 26392382).

Jan 11 Presenters:

Juan Wang and Avtar Singh

Sternberg, S. H., S. Redding, M. Jinek, E. C. Greene and J. A. Doudna (2014). DNA interrogation by the CRISPR RNA-guided endonuclease Cas9. Nature 507:(7490): 62-7. (PMID: 24476820).

Nov 23 Presenters:

Marshall Colville and Vivek Gupta

Li, D., L. Shao, et al. (2015). ADVANCED IMAGING. Extended-resolution structured illumination imaging of endocytic and cytoskeletal dynamics. Science 349:(6251): aab3500. (PMID: 26315442).

Nov 9 Presenter:

Max Kushner

Kiuchi, T., M. Higuchi, A. Takamura, M. Maruoka and N. Watanabe (2015). Multitarget super-resolution microscopy with high-density labeling by exchangeable probes. Nat Methods 12:(8): 743-6. (PMID: 26147917).

Oct 26 Presenters:

Carolyn Shurer and Hao Pan

Torreno-Pina, J. A., B. M. Castro, C. Manzo, S. I. Buschow, A. Cambi and M. F. Garcia-Parajo (2014). Enhanced receptor-clathrin interactions induced by N-glycan-mediated membrane micropatterning. Proc Natl Acad Sci U S A 111:(30): 11037-42. (PMID: 25030450).

Oct 12 Presenters:  

Alex Van Slyke and Eshan Mitra

Zhang, Z., S. J. Kenny, M. Hauser, W. Li and K. Xu (2015). Ultrahigh-throughput single-molecule spectroscopy and spectrally resolved super-resolution microscopy. Nat Methods 12:(10): 935-8. (PMID: 26280329).

Sept 28 Presenters:  

Avtar Singh and Juan Wang

Normanno, D., L. Boudarene, C. Dugast-Darzacq, J. Chen, C. Richter, F. Proux, O. Benichou, R. Voituriez, X. Darzacq and M. Dahan (2015). Probing the target search of DNA-binding proteins in mammalian cells using TetR as model searcher. Nat Commun 6: 7357. (PMID: 26151127).

Sept 14 Presenters:  

Vivek Gupta and Rebecca Williams

Nihongaki, Y., F. Kawano, T. Nakajima and M. Sato (2015). Photoactivatable CRISPR-Cas9 for optogenetic genome editing. Nat Biotechnol. (PMID: 26076431).

Aug 24 Presenters:  

Max Kushner and Eshan Mitra

York, A. G., P. Chandris, D. D. Nogare, J. Head, P. Wawrzusin, R. S. Fischer, A. Chitnis and H. Shroff (2013). Instant super-resolution imaging in live cells and embryos via analog image processing. Nat Methods 10:(11): 1122-6. (PMID: 24097271).

Aug 10 Presenters:  

Avtar Singh and Hao Pan

Chen, K. H., A. N. Boettiger, J. R. Moffitt, S. Wang and X. Zhuang (2015). RNA imaging. Spatially resolved, highly multiplexed RNA profiling in single cells. Science 348:(6233): aaa6090. (PMID: 25858977).

July 27 Presenters:  

Carolyn Shurer and Alex Van Slyke

Tanenbaum, M. E., L. A. Gilbert, L. S. Qi, J. S. Weissman and R. D. Vale (2014). A protein-tagging system for signal amplification in gene expression and fluorescence imaging. Cell 159:(3): 635-46. (PMID: 25307933).

July 13 Presenters:  

Juan Wang

Liu, Z., W. R. Legant, B. C. Chen, L. Li, J. B. Grimm, L. D. Lavis, E. Betzig and R. Tjian (2014). 3D imaging of Sox2 enhancer clusters in embryonic stem cells. Elife 3: e04236. (PMID: 25537195).

Marshall Colville

Winter, P. W., P. Chandris, R. S. Fischer, Y. Wu, C. M. Waterman and H. Shroff (2015). Incoherent structured illumination improves optical sectioning and contrast in multiphoton super-resolution microscopy. Optics Express 23:(4): 5327. (PMID: 25836564).

June 22 Presenter:

Rebecca Williams

Chen, B. C., W. R. Legant, et al. (2014). Lattice light-sheet microscopy: imaging molecules to embryos at high spatiotemporal resolution. Science 346:(6208): 1257998. (PMID: 25342811).

 

Recommended Papers

Balzarotti, F., Y. Eilers, K. C. Gwosch, A. H. Gynna, V. Westphal, F. D. Stefani, J. Elf and S. W. Hell (2016). "Nanometer resolution imaging and tracking of fluorescent molecules with minimal photon fluxes." Science. (PMID: 28008086).

Chen, B. C., W. R. Legant, et al. (2014). Lattice light-sheet microscopy: imaging molecules to embryos at high spatiotemporal resolution. Science 346:(6208): 1257998. (PMID: 25342811).

Chen, J., Z. Zhang, et al. (2014). Single-molecule dynamics of enhanceosome assembly in embryonic stem cells. Cell 156:(6): 1274-85. (PMID: 24630727).

Chen, K. H., A. N. Boettiger, J. R. Moffitt, S. Wang and X. Zhuang (2015). RNA imaging. Spatially resolved, highly multiplexed RNA profiling in single cells. Science 348:(6233): aaa6090. (PMID: 25858977).

Grimm, J. B., B. P. English, et al. (2015). A general method to improve fluorophores for live-cell and single-molecule microscopy. Nat Methods 12:(3): 244-50, 3 p following 250. (PMID: 25599551).

Jia, S., J. C. Vaughan and X. Zhuang (2014). Isotropic 3D Super-resolution Imaging with a Self-bending Point Spread Function. Nat Photonics 8: 302-306. (PMID: 25383090).

Jiang, H., B. P. English, R. B. Hazan, P. Wu and B. Ovryn (2015). Tracking surface glycans on live cancer cells with single-molecule sensitivity. Angew Chem Int Ed Engl 54(6): 1765-1769.  (PMID: 25515330).

Kiuchi, T., M. Higuchi, A. Takamura, M. Maruoka and N. Watanabe (2015). Multitarget super-resolution microscopy with high-density labeling by exchangeable probes. Nat Methods 12:(8): 743-6. (PMID: 26147917).

Li, D., L. Shao, et al. (2015). ADVANCED IMAGING. Extended-resolution structured illumination imaging of endocytic and cytoskeletal dynamics. Science 349:(6251): aab3500. (PMID: 26315442).

Liu, Z., W. R. Legant, B. C. Chen, L. Li, J. B. Grimm, L. D. Lavis, E. Betzig and R. Tjian (2014). 3D imaging of Sox2 enhancer clusters in embryonic stem cells. Elife 3: e04236. (PMID: 25537195).

Normanno, D., L. Boudarene, C. Dugast-Darzacq, J. Chen, C. Richter, F. Proux, O. Benichou, R. Voituriez, X. Darzacq and M. Dahan (2015). Probing the target search of DNA-binding proteins in mammalian cells using TetR as model searcher. Nat Commun 6: 7357. (PMID: 26151127).

Nihongaki, Y., F. Kawano, T. Nakajima and M. Sato (2015). Photoactivatable CRISPR-Cas9 for optogenetic genome editing. Nat Biotechnol. (PMID: 26076431).

Pan, D., Z. Hu, F. Qiu, Z. L. Huang, Y. Ma, Y. Wang, L. Qin, Z. Zhang, S. Zeng and Y. H. Zhang (2014). A general strategy for developing cell-permeable photo-modulatable organic fluorescent probes for live-cell super-resolution imaging. Nat Commun 5: 5573. (PMID: 25410769).

Raab, M., J. J. Schmied, I. Jusuk, C. Forthmann and P. Tinnefeld (2014). "Fluorescence microscopy with 6 nm resolution on DNA origami." Chemphyschem 15(12): 2431-2435.  (PMID: 24895173).

Schmied, J. J., M. Raab, C. Forthmann, E. Pibiri, B. Wunsch, T. Dammeyer and P. Tinnefeld (2014). "DNA origami-based standards for quantitative fluorescence microscopy." Nat Protoc 9(6): 1367-1391.  (PMID: 24833175).

Stabley, D. R., T. Oh, S. M. Simon, A. L. Mattheyses and K. Salaita (2015). Real-time fluorescence imaging with 20 nm axial resolution. Nat Commun 6: 8307. (PMID: 26392382).

Sternberg, S. H., S. Redding, M. Jinek, E. C. Greene and J. A. Doudna (2014). DNA interrogation by the CRISPR RNA-guided endonuclease Cas9. Nature 507:(7490): 62-7. (PMID: 24476820).

Stewart-Ornstein, J. and G. Lahav (2016). "Dynamics of CDKN1A in Single Cells Defined by an Endogenous Fluorescent Tagging Toolkit." Cell Rep 14(7): 1800-1811.  (PMID: 26876176).

Tanenbaum, M. E., L. A. Gilbert, L. S. Qi, J. S. Weissman and R. D. Vale (2014). A protein-tagging system for signal amplification in gene expression and fluorescence imaging. Cell 159:(3): 635-46. (PMID: 25307933).

Torreno-Pina, J. A., B. M. Castro, C. Manzo, S. I. Buschow, A. Cambi and M. F. Garcia-Parajo (2014). Enhanced receptor-clathrin interactions induced by N-glycan-mediated membrane micropatterning. Proc Natl Acad Sci U S A 111:(30): 11037-42. (PMID: 25030450).

Wang, G., J. Hauver, Z. Thomas, S. A. Darst and A. Pertsinidis (2016). "Single-Molecule Real-Time 3D Imaging of the Transcription Cycle by Modulation Interferometry." Cell 167(7): 1839-1852 e1821.  (PMID: 27984731).

Winter, P. W., P. Chandris, R. S. Fischer, Y. Wu, C. M. Waterman and H. Shroff (2015). Incoherent structured illumination improves optical sectioning and contrast in multiphoton super-resolution microscopy. Optics Express 23:(4): 5327. (PMID: 25836564).

Wu, Y., P. Wawrzusin, et al. (2013). Spatially isotropic four-dimensional imaging with dual-view plane illumination microscopy. Nat Biotechnol 31:(11): 1032-8. (PMID: 24108093).

York, A. G., P. Chandris, D. D. Nogare, J. Head, P. Wawrzusin, R. S. Fischer, A. Chitnis and H. Shroff (2013). Instant super-resolution imaging in live cells and embryos via analog image processing. Nat Methods 10:(11): 1122-6. (PMID: 24097271).

Zhang, Z., S. J. Kenny, M. Hauser, W. Li and K. Xu (2015). Ultrahigh-throughput single-molecule spectroscopy and spectrally resolved super-resolution microscopy. Nat Methods 12:(10): 935-8. (PMID: 26280329).

Zhao, Z. W., R. Roy, J. C. Gebhardt, D. M. Suter, A. R. Chapman and X. S. Xie (2014). Spatial organization of RNA polymerase II inside a mammalian cell nucleus revealed by reflected light-sheet superresolution microscopy. Proc Natl Acad Sci U S A 111:(2): 681-6. (PMID: 24379392).

And there are more ideas in Kurt's Microscopy Blog from UCSF.