Oldenbourg Publications

Articles in reverse chronological order

  1. Tran, M. T. and Oldenbourg, R. (2018). Mapping birefringence in three dimensions using polarized light field microscopy: the case of the juvenile clamshell. J. Microsc., 271(3):315-324. http://dx.doi.org/10.1111/jmi.12721
  2. Yoshizawa, T., Ali, R., Jiou, J., Fung, H. Y. J., Burke, K. A., Kim, S. J., Lin, Y., Peeples, W. B., Saltzberg, D., Soniat, M., Baumhardt, J. M., Oldenbourg, R., Sali, A., Fawzi, N. L., Rosen, M. K. and Chook, Y. M. (2018). Nuclear Import Receptor Inhibits Phase Separation of FUS through Binding to Multiple Sites. Cell, 173(3):693-705 e22. http://dx.doi.org/10.1016/j.cell.2018.03.003
  3. Chandler, T., Mehta, S., Shroff, H., Oldenbourg, R., and La Riviere, P. J. (2017). Single-fluorophore orientation determination with multiview polarized illumination: modeling and microscope design. Opt Express, 25(25):31309-31325. http://dx.doi.org/10.1364/OE.25.031309
  4. Nordenfelt, P., Moore, T. I., Mehta, S. B., Kalappurakkal, J. M., Swaminathan, V., Koga, N., Lambert, T. J., Baker, D., Waters, J. C., Oldenbourg, R., Tani, T., Mayor, S., Waterman, C. M. and Springer, T. A. (2017). Direction of actin flow dictates integrin LFA-1 orientation during leukocyte migration. Nature communications, 8(1):2047. http://dx.doi.org/10.1038/s41467-017-01848-y
  5. Spira, F., Cuylen-Haering, S., Mehta, S., Samwer, M., Reversat, A., Verma, A., Oldenbourg, R., Sixt, M. and Gerlich, D. W. (2017). Cytokinesis in vertebrate cells initiates by contraction of an equatorial actomyosin network composed of randomly oriented filaments. Elife, 6. http://dx.doi.org/10.7554/eLife.30867
  6. Gibaud, T., Kaplan, C. N., Sharma, P., Zakhary, M. J., Ward, A., Oldenbourg, R., Meyer, R. B., Kamien, R. D., Powers, T. R. and Dogic, Z. (2017). Achiral symmetry breaking and positive Gaussian modulus lead to scalloped colloidal membranes. Proc Natl Acad Sci U S A, 114(17):E3376-E3384. http://dx.doi.org/10.1073/pnas.1617043114
  7. Keikhosravi, A., Liu, Y., Drifka, C., Woo, K. M., Verma, A., Oldenbourg, R. and Eliceiri, K. W. (2017). Quantification of collagen organization in histopathology samples using liquid crystal based polarization microscopy. Biomed Opt Express, 8(9):4243-4256. http://dx.doi.org/10.1364/BOE.8.004243
  8. Swaminathan, V., Kalappurakkal, J. M., Mehta, S. B., Nordenfelt, P., Moore, T. I., Koga, N., Baker, D. A., Oldenbourg, R., Tani, T., Mayor, S., Springer, T. A. and Waterman, C. M. (2017). Actin retrograde flow actively aligns and orients ligand-engaged integrins in focal adhesions. Proc Natl Acad Sci U S A, 114(40):10648-10653. http://dx.doi.org/10.1073/pnas.1701136114
  9. Tkacz, R., Abedin, M. J., Sheath, P., Mehta, S. B., Verma, A., Oldenbourg, R. and Majumder, M. (2017). Phase Transition and Liquid Crystalline Organization of Colloidal Graphene Oxide as a Function of pH. Particle & Particle Systems Characterization, 34(9):1600391. http://dx.doi.org/10.1002/ppsc.201600391
  10. McQuilken, M., Jentzsch, M. S., Verma, A., Mehta, S. B., Oldenbourg, R., and Gladfelter, A. S. (2017). Analysis of Septin Reorganization at Cytokinesis Using Polarized Fluorescence Microscopy. Front Cell Dev Biol, 5:42. http://dx.doi.org/10.3389/fcell.2017.00042
  11. Mehta, S. B., M. McQuilken, P. J. La Riviere, P. Occhipinti, A. Verma, R. Oldenbourg, A. S. Gladfelter and T. Tani. 2016. Dissection of molecular assembly dynamics by tracking orientation and position of single molecules in live cells. Proceedings of the National Academy of Sciences 113:E6352-E6361. http://dx.doi.org/10.1073/pnas.1607674113
  12. Valm, A. M., R. Oldenbourg and G. G. Borisy. 2016. Multiplexed Spectral Imaging of 120 Different Fluorescent Labels. PLoS One 11: e0158495. http://dx.doi.org/10.1371/journal.pone.0158495
  13. Tani, T., M. Shribak and R. Oldenbourg. 2016. Living Cells and Dynamic Molecules Observed with the Polarized Light Microscope: the Legacy of Shinya Inoue. Biological Bulletin 231: 85-95. http://dx.doi.org/10.1086/689593

  14. Thievessen, I., Fakhri, N., Steinwachs, J., Kraus, V., McIsaac, R. S., Gao, L., Chen, B. C., Baird, M. A., Davidson, M. W., Betzig, E., Oldenbourg, R., Waterman, C. M. and Fabry, B. (2015). Vinculin is required for cell polarization, migration, and extracellular matrix remodeling in 3D collagen. FASEB J., 29(11):4555-67. doi: 10.1096/fj.14-268235

  15. Min, K. A., Rajeswaran, W. G., Oldenbourg, R., Harris, G., Keswani, R. K., Chiang, M., Rzeczycki, P., Talattof, A., Hafeez, M., Horobin, R. W., Larsen, S. D., Stringer, K. A. and Rosania, G. R. (2015). Massive Bioaccumulation and Self-Assembly of Phenazine Compounds in Live Cells. Adv Sci (Weinh), 2(8). doi: 10.1002/advs.201500025
  16. McQuilken, M., Mehta, S. B., Verma, A., Harris, G., Oldenbourg, R. and Gladfelter, A. S. (2015). Polarized Fluorescence Microscopy to Study Cytoskeleton Assembly and Organization in Live Cells. Curr Protoc Cell Biol, 67:4 29 1-4 29 13. doi: 10.1002/0471143030.cb0429s67
  17. Koike-Tani, M., Tani, T., Mehta, S. B., Verma, A. and Oldenbourg, R. (2015). Polarized light microscopy in reproductive and developmental biology. Mol. Reprod. Dev., 82(7-8):548-62. doi: 10.1002/mrd.22221
  18. Henson, J. H., Yeterian, M., Weeks, R. M., Medrano, A. E., Brown, B. L., Geist, H. L., Pais, M. D., Oldenbourg, R. and Shuster, C. B. (2015). Arp2/3 Complex Inhibition Radically Alters Lamellipodial Actin Architecture, Suspended Cell Shape, and the Cell Spreading Process. Mol. Biol. Cell, 26(5):887-900. doi: 10.1091/mbc.E14-07-1244
  19. Abrahamsson, S., McQuilken, M., Mehta, S. B., Verma, A., Larsch, J., Ilic, R., Heintzmann, R., Bargmann, C. I., Gladfelter, A. S. and Oldenbourg, R. (2015). MultiFocus Polarization Microscope (MF-PolScope) for 3D polarization imaging of up to 25 focal planes simultaneously. Optics Express, 23(6):7734-7754. doi: 10.1364/OE.23.007734
  20. Zakhary, M. J., Gibaud, T., Kaplan, C. N., Barry, E., Oldenbourg, R., Meyer, R. B. and Dogic, Z. (2014). Imprintable membranes from incomplete chiral coalescence. Nat. Comm., 5:3063. doi: 10.1038/ncomms4063
  21. Tkacz, R., Oldenbourg, R., Mehta, S. B., Miansari, M., Verma, A. and Majumder, M. (2014). pH dependent isotropic to nematic phase transitions in graphene oxide dispersions reveal droplet liquid crystalline phases. Chem Commun, 50(50):6668-6671. doi: 10.1039/C4CC00970C
  22. Tkacz, R., Oldenbourg, R., Fulcher, A., Miansari, M. and Majumder, M. (2014). Capillary-Force-Assisted Self-Assembly (CAS) of Highly Ordered and Anisotropic Graphene-Based Thin Films. J Phys Chem C, 118(1):259-267. doi: 10.1021/jp4080114
  23. Mehta, S. B. and Oldenbourg, R. (2014). Image simulation for biological microscopy: microlith. Biomed. Opt. Express, 5(6):1822-1838. doi: 10.1364/BOE.5.001822
  24. LaFountain, J. R., Jr. and Oldenbourg, R. (2014). Kinetochore-driven outgrowth of microtubules is a central contributor to kinetochore fiber maturation in crane-fly spermatocytes. Mol. Biol. Cell, 25(9):1437-45. doi: 10.1091/mbc.E14-01-0008
  25. Henson, J. H., Gianakas, A. D., Henson, L. H., Lakin, C. L., Voss, M. K., Bewersdorf, J., Oldenbourg, R. and Morris, R. L. (2014). Broadening the spectrum of actin-based protrusive activity mediated by Arp2/3 complex-facilitated polymerization: motility of cytoplasmic ridges and tubular projections. Cytoskeleton (Hoboken), 71(8):484-500. doi: 10.1002/cm.21186.
  26. Oldenbourg, R. (2013) Polarization Microscopy. in N. T. Shaked Z. Zalevskey and L. Satterwhite (eds.) Biomedical Optical Phase Microscopy and Nanoscopy. Amsterdam: Elsevier.
  27. Mehta, S. B., Shribak, M. and Oldenbourg, R. (2013). Polarized light imaging of birefringence and diattenuation at high resolution and high sensitivity. Journal of Optics, 15:094007 (13pp). doi: 10.1088/2040-8978/15/9/094007.
  28. LaFountain, J. R., Jr., C. S. Cohan and R. Oldenbourg. 2012. Pac-man motility of kinetochores unleashed by laser microsurgery. Molecular Biology of the Cell 23: 3133-42.
  29. Gibaud, T., E. Barry, M. J. Zakhary, M. Henglin, A. Ward, Y. Yang, C. Berciu, R. Oldenbourg, M. F. Hagan, D. Nicastro, R. B. Meyer and Z. Dogic. 2012. Reconfigurable self-assembly through chiral control of interfacial tension. Nature 481: 348-51.
  30. LaFountain, J. R., Jr., C. S. Cohan and R. Oldenbourg. 2011. Functional states of kinetochores revealed by laser microsurgery and fluorescent speckle microscopy. Molecular Biology of the Cell 22: 4801-8.
  31. DeMay, B. S., N. Noda, A. S. Gladfelter and R. Oldenbourg. 2011. Rapid and quantitative imaging of excitation polarized fluorescence reveals ordered septin dynamics in live yeast. Biophys. J. 101: 985-94.
  32. DeMay, B. S., X. Bai, L. Howard, P. Occhipinti, R. A. Meseroll, E. T. Spiliotis, R. Oldenbourg and A. S. Gladfelter. 2011. Septin filaments exhibit a dynamic, paired organization that is conserved from yeast to mammals. J. Cell Biol. 193: 1065-81.
  33. Valm, A. M., J. L. Welch, C. W. Rieken, Y. Hasegawa, M. L. Sogin, R. Oldenbourg, F. E. Dewhirst and G. G. Borisy. 2011. Systems-level analysis of microbial community organization through combinatorial labeling and spectral imaging. Proc Natl Acad Sci U S A 108: 4152-7.
  34. Miyata, H., N. Noda, D. J. Fairbairn, R. Oldenbourg and R. A. Cardullo. 2011. Assembly of the fluorescent acrosomal matrix and its fate in fertilization in the water strider, Aquarius remigis. J. Cell. Physiol. 226: 999-1006.
  35. Henson, J. H., D. Cheung, C. A. Fried, C. B. Shuster, M. K. McClellan, M. K. Voss, J. T. Sheridan and R. Oldenbourg. 2009. Structure and dynamics of an Arp2/3 complex-independent component of the lamellipodial actin network. Cell Motil. Cytoskeleton 66: 679-92.
  36. Barry, E., Z. Dogic, R. B. Meyer, R. A. Pelcovits and R. Oldenbourg. 2009. Direct Measurement of the Twist Penetration Length in a Single Smectic A Layer of Colloidal Virus Particles. J Phys Chem B 113: 3910-3.
  37. Guo, Y., Y. Liu, R. Oldenbourg, J. X. Tang and J. M. Valles, Jr. 2008. Effects of osmotic force and torque on microtubule bundling and pattern formation. Physical Review E (Statistical, Nonlinear, and Soft Matter Physics) 78: 041910.
  38. Oldenbourg, R. 2008. Polarized light field microscopy: an analytical method using a microlens array to simultaneously capture both conoscopic and orthoscopic views of birefringent objects. J. Microsc. 231: 419-32.
  39. Henson, J. H., C. A. Fried, M. K. McClellan, J. Ader, J. E. Davis, R. Oldenbourg and C. R. Simerly. 2008. Bipolar, anastral spindle development in artificially activated sea urchin eggs. Dev. Dyn. 237: 1348-58.
  40. Oldenbourg, R. 2007. Analysis of microtubule dynamics by polarized light. Methods Mol Med, 137, 111-123.
  41. Janicke, M. A., L. Lasko, R. Oldenbourg and J. R. LaFountain, Jr. 2007. Chromosome malorientations after meiosis II arrest cause nondisjunction. Mol. Biol. Cell 18: 1645-56.
  42. Barry, E., Z. Hensel, Z. Dogic, M. Shribak and R. Oldenbourg. 2006. Entropy-driven formation of a chiral liquid-crystalline phase of helical filaments. Phys. Rev. Lett. 96: Art. No. 018305.
  43. LaFountain, J. R., Jr. and R. Oldenbourg. 2004. Maloriented bivalents have metaphase positions at the spindle equator with more kinetochore microtubules to one pole than to the other. Mol. Biol. Cell 15: 5346-55.
  44. Kagawa, Y., T. L. Megraw and R. Oldenbourg. 2004. Cell division dynamics of Drosophila kc cells without functional mitotic centrosomes. Biol. Bull. 207: 161.
  45. Shribak, M. and R. Oldenbourg. 2003. Techniques for fast and sensitive measurements of two-dimensional birefringence distributions. Appl. Opt. 42: 3009-17.
  46. Shribak, M. and R. Oldenbourg. 2003. Three-dimensional birefringence distribution in reconstituted asters of Spisula oocytes revealed by scanned aperture polarized light microscopy. Biol. Bull. 205: 194-5.
  47. Wang, W. H., L. Meng, R. J. Hackett, R. Oldenbourg and D. L. Keefe. 2002. Rigorous thermal control during intracytoplasmic sperm injection stabilizes the meiotic spindle and improves fertilization and pregnancy rates. Fertil. Steril. 77: 1274-7.
  48. Shribak, M., S. Inoué and R. Oldenbourg. 2002. Polarization aberrations caused by differential transmission and phase shift in high NA lenses: theory, measurement and rectification. Opt. Eng. 41: 943-954.
  49. LaFountain, J. R., Jr., R. Oldenbourg, R. W. Cole and C. L. Rieder. 2001. Microtubule flux mediates poleward motion of acentric chromosome fragments during meiosis in insect spermatocytes. Mol. Biol. Cell 12: 4054-65.
  50. Oldenbourg, R. and P. Török. 2000. Point spread functions of a polarizing microscope equipped with high numerical aperture lenses. Appl. Opt. 39: 6325-6331.
  51. Oldenbourg, R., K. Katoh and G. Danuser. 2000. Mechanism of lateral movement of filopodia and radial actin bundles across neuronal growth cones. Biophys. J. 78: 1176-82.
  52. Liu, L., J. R. Trimarchi, R. Oldenbourg and D. L. Keefe. 2000. Increased Birefringence in the Meiotic Spindle Provides a New Marker for the Onset of Activation in Living Oocytes. Biol. Reprod. 63: 251-258.
  53. Liu, L., R. Oldenbourg, J. R. Trimarchi and D. L. Keefe. 2000. A reliable, noninvasive technique for spindle imaging and enucleation of mammalian oocytes. Nat. Biotechnol. 18: 223-5.
  54. Danuser, G. and R. Oldenbourg. 2000. Probing f-actin flow by tracking shape fluctuations of radial bundles in lamellipodia of motile cells. Biophys. J. 79: 191-201.
  55. Silva, C. P., K. Kommineni, R. Oldenbourg and D. L. Keefe. 1999. The first polar body does not predict accurately the location of the metaphase II meiotic spindle in mammalian oocytes. Fertil. Steril. 71: 719-21.
  56. Oldenbourg, R. 1999. Polarized light microscopy of spindles. Methods Cell Biol. 61: 175-208.
  57. Katoh, K., K. Hammar, P. J. Smith and R. Oldenbourg. 1999. Arrangement of radial actin bundles in the growth cone of Aplysia bag cell neurons shows the immediate past history of filopodial behavior. Proc Natl Acad Sci U S A 96: 7928-31.
  58. Katoh, K., K. Hammar, P. J. Smith and R. Oldenbourg. 1999. Birefringence imaging directly reveals architectural dynamics of filamentous actin in living growth cones. Mol. Biol. Cell 10: 197-210.
  59. Oldenbourg, R., E. D. Salmon and P. T. Tran. 1998. Birefringence of single and bundled microtubules. Biophys. J. 74: 645-54.
  60. Inoue, S. and R. Oldenbourg. 1998. Microtubule dynamics in mitotic spindle displayed by polarized light microscopy. Mol. Biol. Cell 9: 1603-7.
  61. Tran, P. T., A. DePina, S. Inoue, R. Oldenbourg, S. J. Segal and M. H. Burgos. 1997. Effect of gossypol on Spisula sperm observed with real-time confocal microscopy, polarized light microscopy, and video microscopy. Biol. Bull. 193: 227-8.
  62. Keefe, D., P. Tran, C. Pellegrini and R. Oldenbourg. 1997. Polarized light microscopy and digital image processing identify a multilaminar structure of the hamster zona pellucida. Hum. Reprod. 12: 1250-2.
  63. Katoh, K., G. Langford, K. Hammar, P. J. Smith and R. Oldenbourg. 1997. Actin bundles in neuronal growth cone observed with the Pol-Scope. Biol. Bull. 193: 219-20.
  64. Tran, P., E. D. Salmon and R. Oldenbourg. 1996. Mitotic spindle fine structures observed with polarized light. Biol. Bull. 191: 271-272.
  65. Oldenbourg, R. 1996. A new view on polarization microscopy. Nature 381: 811-2.
  66. Katoh, K., K. Yamada, F. Oosawa and R. Oldenbourg. 1996. Birefringence Measurements of the actin bundle in acrosomal processes of Limulus sperm. Biol. Bull. 191: 271-272.
  67. Tran, P., E. D. Salmon and R. Oldenbourg. 1995. Quantifying single and bundled microtubules with the polarized light microscope. Biol. Bull. 189: 206.
  68. Oldenbourg, R. and G. Mei. 1995. New polarized light microscope with precision universal compensator. J. Microsc. 180 ( Pt 2): 140-7.
  69. Flamarique, I. N., R. Oldenbourg and F. I. Harosi. 1995. Transmission of polarized light through sunfish double cones reveals minute optical anisotropies. Biol. Bull. 189: 220-2.
  70. Tran, P. T., S. Inoue, E. D. Salmon and R. Oldenbourg. 1994. Muscle fine structure and microtubule birefringence measured with a new pol-scope. Biol. Bull. 187: 244-5.
  71. Oldenbourg, R., H. Terada, R. Tiberio and S. Inoue. 1993. Image sharpness and contrast transfer in coherent confocal microscopy. J. Microsc. 172 ( Pt 1): 31-9.
  72. Oldenbourg, R., G. Mei and R. E. Palazzo. 1993. Asters in lysates of Spisula oocytes observed with a new type of polarized light microscope. Biol. Bull. 185: 288.

Book Chapters:

  1. Oldenbourg, R. 2018. Observing the living cell: Shinya Inoué and the reemergence of light microscopy. in K. S. Matlin, Maienschein, J., Laubichler, M.D. (ed.) Visions of Cell Biology: Reflections inspired by Cowdry’s GENERAL CYTOLOGY. Chicago: The University of Chicago Press. http://dx.doi.org/10.7208/chicago/9780226520650.001.0001
  2. Oldenbourg, R. 2012. Polarization Microscopy. in N. T. Shaked, Z. Zalevskey, and L. Satterwhite (eds.) Biomedical Optical Phase Microscopy and Nanoscopy. Amsterdam: Elsevier.
  3. Oldenbourg, R. 2010. Polarized Light Microscopy: Principles and Practice. In: Rafael Yuste, editor. Optical Imaging Techniques: A Laboratory Manual. Cold Spring Harbor, NY: Cold Spring Harbor Laboratory Press.
  4. Oldenbourg, R. and M. Shribak. 2010. Microscopes. In: Michael Bass, Jay M. Enoch, Vasudevan Lakshminarayanan, Guifang Li, Carolyn Macdonald, Virendra N. Mahajan, Eric Van Stryland, editors. Handbook of Optics. 3rd ed. New York: McGraw-Hill, Inc. p 28.1 – 28.62.
  5. Oldenbourg, R. 2005. Polarization microscopy with the LC-PolScope. In: R. D. Goldman and D. L. Spector, editors. Live Cell Imaging: A Laboratory Manual. Cold Spring Harbor, NY: Cold Spring Harbor Laboratory Press. p 205-37.
  6. Oldenbourg, R., S. Inoué, R. Tiberio, A. Stemmer, G. Mei and M. Skvarla. 1996. Standard test targets for high resolution light microscopy. In: H. C. Hoch, L. W. Jelinsky and H. Craighead, editors. Nanofabrication and Biosystems: Integrating Material Science, Engineering and Biology. Cambridge, England: Cambridge University Press. p 123-138.
  7. Inoué, S. and R. Oldenbourg. 1995. Microscopes. In: M. Bass, editor. Handbook of Optics. 2nd ed. New York: McGraw-Hill, Inc. p 17.1-17.52.

Patents:

  1. Shribak, M. and R. Oldenbourg. 2008. Retardance Measurement System and Method. US Patent, Number 7,372,567. USA, Marine Biological Laboratory (Woods Hole, MA).
  2. Shribak, M. and R. Oldenbourg. 2007. Retardance Measurement System and Method. US Patent, Number 7,239,388. USA, Marine Biological Laboratory (Woods Hole, MA).
  3. Shribak, M. and R. Oldenbourg. 2007. Retardance Measurement System and Method. US Patent, Number 7,202,950. USA, Marine Biological Laboratory (Woods Hole, MA).
  4. Shribak, M., R. Oldenbourg, P. J. Cronin, C. C. Hoyt and P. J. Miller. 2006. Instantaneous Polarization Measurement System and Method. US Patent, Number 7,079,247. USA, Marine Biological Laboratory (Woods Hole, MA).
  5. Oldenbourg, R., M. Shribak, C. C. Hoyt and P. Török. 2005. Enhancing Polarized Light Microscopy. US Patent, Number 6,924,893 B2. USA, Marine Biological Laboratory (Woods Hole, MA).
  6. Oldenbourg, R. 2002. Retardance measurement method. US Patent, Number 6,501,548. USA, Cambridge Research & Instrumentation Inc. (Woburn, MA).
  7. Oldenbourg, R. and G. Mei. 1996. Polarized Light Microscopy. US Patent, Number 5,521,705. USA, Marine Biological Laboratory (Woods Hole, MA).