Upadhyaya Lab

laboratory for cellular biophysics :: department of physics :: university of maryland
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publications

  1. D.A. Garcia, G.J. Fettweis, D.M. Presman, V. Paakinaho, C. Jarzynski, A. Upadhyaya and G.L. Hager, "Power-law behavior of transcription factor dynamics at the single-molecule level implies a continuum affinity model", Nucleic Acids Research. (2021).

  2. D.A. Garcia, T.A. Johnson, D.M. Presman, G.J. Fettweis, K.S. Wagh, L. Rinaldi, D.A. Stavreva, V. Paakinaho, R.A.M. Jensen, S. Mandrup, A. Upadhyaya and G.L. Hager, "An intrinsically disordered region-mediated confinement state contributes to the dynamics and function of transcription factors", Molecular Cell. (2021).

  3. K.S. Wagh, B.A. Wheatley, M.K Traver, I. Hussain, B.C. Schaefer and A. Upadhyaya, "Bcl10 is associated with actin dynamics at the T cell immune synapse", Cell. Immunol. 356: 104161 (2020).

  4. I. Rey-Suarez, B. Wheatley, P. Koo, A. Bhanja, Z. Shu, S. Mochrie, W. Song, H. Shroff and A. Upadhyaya, "WASP family proteins regulate the mobility of the B cell receptor during signaling activation", Nat. Commun. 11:439 (2020).

  5. A. Chandrasekharan, A. Upadhyaya and G. A. Papoian, "Remarkable structural transformations of actin bundles are driven by their initial polarity, motor activity, crosslinking, and filament treadmilling", PLoS Comp. Bio., 15:e1007156 (2019).

  6. D. Stavreva, D.A. Garcia, ..., A. Upadhyaya, G.L. Hager, "Transcriptional Bursting and Co-bursting Regulation by Steroid Hormone Release Pattern and Transcription Factor Mobility", Mol. Cell, 75:1161-1171 (2019).

  7. C. M. Ketchum, X. Sun, J. T. Fourkas, W. Song and A. Upadhyaya*, "Substrate topography modulates actin dynamics and signaling in B cells", Mol. Biol. Cell, 29:1732-1742 (2018).

  8. M. Guo, P. Chandris, J. P. Giannini, A. J. Trexler, R. Fischer, J. Chen, H. D. Vishwasrao, I. Rey-Suarez, Y. Wu, X. Wu, C. M. Waterman, G. H. Patterson, A. Upadhyaya, J. Taraska, H. Shroff, "Single-shot super-resolution total internal reflection fluorescence microscopy", Nat. Meth., doi: 10.1038/s41592-018-0004-4, (2018).

  9. I. Rey, D. A. Garcia, B. W. Wheatley, W. Song and A. Upadhyaya, "Biophysical techniques to study B cell activation: single molecule imaging and force measurements", Methods in Molecular Biology, Methods Mol Biol., 1707, 51, (2018).

  10. Y. Wu, A. Kumar, C. Smith, E. Ardiel, P. Chandris, R. Christensen, I. Rey-Suarez, M. Guo, H.D. Vishwasrao, J. Chen, J. Tang, A. Upadhyaya, P.J. La Riviere, H. Shroff, "Reflective imaging improves resolution, speed, and collection efficiency in light sheet microscopy", Nat. Comm., 8, 1452, (2017).

  11. A. Upadhyaya, "Mechanosensing in the immune response", Semin. Cell Dev. Biol., 71,137, (2017).

  12. K.L. Hui and A. Upadhyaya*, “Dynamic microtubules regulate cellular contractility during T-cell activation”, Proc. Natl. Acad. Sci., 114:E4175 (2017).

  13. M. Azatov, S.M. Goicoechea, C.A. Otey and A. Upadhyaya*, “The actin crosslinking protein palladin modulates force generation and mechanosensitivity of tumor associated fibroblasts”, Sci. Rep., 29:28805 (2016).

  14. K.L. Hui†, L. Balagopalan, L.E. Samelson, and A. Upadhyaya*, “Cytoskeletal forces during signaling activation in Jurkat T cells”, Mol. Biol. Cell, 26:685 (2015).

  15. C. Ketchum†, C. Liu, H. Miller, W. Song and A. Upadhyaya*, “Ligand mobility regulates B cell receptor clustering and signaling activation”, Biophys. J., 106:26-36 (2014).

  16. M. Seeley-Fallen, L.J. Liu, M. Shapiro, O. Onabajo, S. Palaniyandi, X. Zhu, T.H. Tan, A. Upadhyaya and W. Song*, "Actin-binding protein 1 links B-cell antigen receptors to negative signaling pathways.", Proc. Natl. Acad. Sci., 111:9881-9886 (2014).

  17. K. L. Hui†, S. Kwak‡ and A. Upadhyaya*, “Adhesion dependent modulation of actin dynamics in Jurkat T cells”, Cytoskeleton, 71:119-135 (2014).

  18. W. Song*, C. Liu and A. Upadhyaya*, “The pivotal position of the actin cytoskeleton in the initiation and regulation of B cell receptor activation”, Biophysica Biochimica Acta Biomembranes, 1838:569 (2014).

  19. W. Song*, C. Liu, M. K. Seeley-Fallen, H. Miller, C. Ketchum and A. Upadhyaya*, “Actin-mediated feedback loops in B cell receptor signaling”, Immunological Reviews, 256:177-189 (2013).

  20. C. Liu, X. Bai, J. Wu, S. Sharma, A. Upadhyaya, C. Dahlberg, L. S. Westerberg, S. B. Snapper, X. Zhao, and W. Song*, “N-WASP is essential for the negative regulation of B cell antigen receptor signaling”, PLoS Biol., 11:e1001704 (2013).

  21. C. Liu, M. K. Fallen, H. Miller, A. Upadhyaya, and W. Song*, “The actin cytoskeleton coordinates the signal transduction and antigen processing functions of the B cell antigen receptor”, Frontiers in Biology, 8:475-485 (2013).

  22. C. Liu, H. Miller, S. Sharma, A. Beavan, K. Richard, A. Upadhyaya*, and W. Song*, “Analyzing actin dynamics during the activation of the B cell receptor in live B cells”, Biochem. Biophys. Res. Commun. 427: 202 (2012).

  23. B. Grooman†, I. Fujiwara, C. A. Otey and A. Upadhyaya*, “Morphology and viscoelasticity of actin networks crosslinked with the mutually interacting crosslinkers: palladin and alpha-actinin”, PLoS One, 7:e42773 (2012).

  24. C. Liu, H. Miller, G. Orlowsky, H. Hong, A. Upadhyaya, and W. Song*, “Actin reorganization is required for the formation of polarized B cell receptor signalosomes in response to both soluble and membrane-associated antigens”, J. Immunology, 188: 3237, (2012).

  25. K. L. Hui†, J. Wayt‡, B. Grooman and A. Upadhyaya*, “Membrane dynamics correlate with formation of signaling clusters during cell spreading”, Biophys. J., 102: 1524 (2012).

  26. C. Liu, H. Miller, G. Orlowsky, , S. Sharma, K. L. Hui, B. Grooman, A. Upadhyaya*, and W. Song*, “A balance of Bruton's tyrosine kinase and SHIP activation regulates B cell receptor cluster formation by controlling actin remodeling”, J. Immunology, 187: 230 (2011).

  27. A. Upadhyaya*, J. Wong, M. Daniels, A. van Oudenaarden and L. Mahadevan* Power-limited contraction dynamics of Vorticella convallaria: an ultra-fast biological spring, Biophys. J. 94: 265 (2008).

  28. W. G. Tharp, R. Yadav, D. Irimia, A. Upadhyaya et al. Neutrophil chemorepulsion in defined interleukin-8 gradients in vitro and in vivo, J. Leukocyt. Biol. 79: 539-554 (2006).

  29. A. Upadhyaya* and A. van Oudenaarden*, Actin polymerization: forcing flat faces forward, Curr. Biol. 14: R467 (2004).

  30. B. T. Nguyen, A. Upadhyaya, A. van Oudenaarden and M.P. Brenner* Elastic instability in a growing yeast droplet, Biophys. J., 86, 2720 (2004).

  31. A. Upadhyaya* and M. P. Sheetz*, Measurement of membrane tension in tubulovesicular networks of ER and Golgi using optical tweezers, Biophys. J. 86, 2923 (2004).

  32. N. B. Ouchi, J. A. Glazier, J. P. Rieu, A. Upadhyaya, and Y. Sawada, Improving the realism of the cellular Potts model in simulations of biological cells, Physica A, 329, 451 (2003).

  33. A. Upadhyaya* and A. van Oudenaarden*, Biomimetic systems for studying actin-based motility, Curr. Biol. 13, R734 (2003).

  34. A. Upadhyaya*, J. C. Chabot, A. Andreeva A. Samadani and A. van Oudenaarden*, Probing polymerization forces using actin propelled lipid vesicles, Proc. Nat. Acad. Sci. 100, 4521 (2003).

  35. M. J. Powers, K. Domansky, M. R. Kaazempur-Mofrad, A. Kalezi, A. Capitano, A. Upadhyaya, P. Kurzawski, K. E. Wack, D. B. Stolz, R. Kamm, and L. G. Griffith, A microfabricated array bioreactor for perfused 3D liver culture, Biotechnol. Bioeng. 78, 257 (2002).

  36. J. C. M. Mombach, R. M. C. de Almeida, G. L. Thomas, A. Upadhyaya, and J. A. Glazier*, Bursts and cavity formation in Hydra cell aggregates: Experiments and simulations, Physica A, 297, 495 (2001).

  37. A. Upadhyaya, J. P. Rieu, Y. Sawada*, J. A. Glazier*, Anomalous diffusion and non-Gaussian velocity distribution of Hydra cells in cellular aggregates, Physica A, 293, 549 (2001). Elemental discoveries

  38. J. P. Rieu, A. Upadhyaya, Y. Sawada, N.B. Ouchi and J. A. Glazier*, Diffusion and deformations of single Hydra cells in cellular aggregates, Biophys. J., 79, 1903 (2000).

  39. "First steps towards acomprehensive model of tissues" J. A. Glazier and A. Upadhyaya, Dynamical Networks in Physics and Biology, (D. Beysens and G. Forgacs eds. Springer Berlin, 1998).