Faculty Research Page

Srigokul Upadhyayula (Gokul)

Srigokul Upadhyayula (Gokul)

Assistant Professor in Residence of Cell and Developmental Biology*
*Scientific Director, Advanced Bioimaging Center & Chan Zuckerberg Initiative Imaging Scientist

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Research Interests

Our research interests bridge applied engineering with basic science. We are interested in mechanistic questions addressed at a molecular level using optical imaging acquired with high temporal and spatial resolution.

We are setting up the Advanced BioImaging Center (ABC), a global initiative where we will house cutting-edge pre-commercial imaging technologies, such as the next-generation Adaptive Optical Multi-functional Lattice Light-Sheet Microscope. The ABC will enable imaging across scales spanning several orders of magnitude in space and time in specimens up to several millimeters in extent, or over sessions lasting up to multiple days. These instruments consequently output explosive quantities of immensely complex data and the greatest challenge researchers face is the ability to visualize, analyze and understand the data in order to extract biologically meaningful insights. The prime goal of the ABC is therefore to not only provide cutting-edge microscopy, but also the dedicated human and hardware resources capable of handling tera- to petabyte scale projects and developing robust, open source computational workflows that allow biologists to easily mine the data.  At the ABC, we are interested in leveraging the powerful combination of artificial intelligence tools with the cutting-edge multimodal imaging systems to accelerate the pace of discoveries in both fundamental and translational sciences. 

Selected Publications

  1. Gao, R*., Asano, S*., Upadhyayula, S*., Pisarev, I., Milkie, D., Liu, T., Singh, V., Graves, A., Huynh, G., Zhao, Y., Bogovic, J., Colonell, J., Ott, C., Zugates, C., Tappan, S., Rodriguez, A., Mosaliganti, K., Megason, S., Lippincott-Schwartz, J., Hantman, A., Rubin, G., Kirchhausen, T., Saalfeld, S., Aso, Y., Boyden, E+., Betzig, E+.; "Cortical Column and Whole Brain Imaging of Neural Circuits with Molecular Contrast and Nanoscale Resolution," Science, 2019, 363:6424, 245; (*) equal contribution; (+) co-corresponding authors; work featured on the cover of January 18, 2019 issue.
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  2. Liu, T*., Upadhyayula, S*., Milkie, D., Singh, V., Wang, K., Swinburne, I., Mosaliganti, K., Shea, J., Dambournet, D., Forster, R., Hockemeyer, D., Drubin, D., Martin, B., Matus, D., Koyama, M., Megason, S., Kirchhausen, T., Betzig, E.; "Observing the Cell in Its Native State: Imaging Subcellular Dynamics in Multicellular Organisms," Science, 2018, 360:6386, 284; (*) equal contribution; work featured on the cover of April 20, 2018 issue.
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  3. Swinburne, I., Mosaliganti, K., Upadhyayula, S., Liu, T., Grant, D., Hildebrand, C., Tsai, T., Chen, A., Al-Obeidi, E., Fass, A., Malhotra, S., Engret, F., Lichtman, J., Kirchhausen, T., Betzig, E., Megason, S.; "Lamellar junctions in the endolymphatic sac act as a relief valve to regulate inner ear pressure," eLife 2018, 7:e37131. DOI: 10.7554/eLife.37131.
  4. Adell, M*., Migliano, S*., Upadhyayula, S*., Bykov, Y., Sprenger, S., Pakdel, M., Vogel, G., Jih, G., Skillern, W., Behrouzi, R., Babst, M., Schmidt, O., Hess, M., Briggs, J., Teis, D+., Kirchhausen, T+.; "Recruitment dynamics of ESCRT-III and Vps4 to endosomes and implications for the mechanism of ESCRT-mediated intraluminal vesicle formation," eLife 2017, 6:e31652. (*) equal contribution; (+) co-corresponding authors
  5. He, K., Marsland, R., Upadhyayula, S., Song, E., Skillern, W., Gaudin, R., Ma, M., Kirchhausen, T., Shaw, J., Cunniff, B.; "Dynamics of Phosphoinositide Conversion in Clathrin-Mediated Endocytic Traffic," Nature 2017, 552, 410-414.
  6. Paulsen, B*., Mandal, P*., Frock, R., Boyraz, B., Yadav, R., Upadhyayula, S., Gutierrez-Martinez, P., Ebina, W., Fasth, A., Kirchhausen, T., Talkowski, M., Agarwal, S., Alt, F., Rossi, D.; "Ectopic Expression of RAD52 and dn53BP1 Improves Homology-directed Repair Using CRISPR/Cas9-mediated Genome Editing," Nature Biomedical Engineering, 2017, 1, 878-888; (*) equal contribution
  7. Salgado,E., Upadhyayula, S., Harrison, S.; "Single-particle detection of transcription following rotavirus entry," J Virology 2017, 91(18):e00651-17.
  8. Schuler, M., Lewandowska, A., Di Caprio, G., Skillern, W., Upadhyayula, S., Kirchhausen, T.; "Miro1-mediated mitochondrial positioning shapes intracellular energy gradients required for cell migration," MBoC 2017, 28(16) 2159-2169.
  9. Aguet, F.*, Upadhyayula, S.*, Gaudin, R.*, Chou, Y., Cocucci, E., He, K., Chen, B., Mosaliganti, K., Pasham, M., Skillern, W., Legant, W., Liu, T., Findlay, G., Marino, E., Danuser, G., Megason, S., Betzig, E., Kirchhausen, T.; "Membrane Dynamics of Dividing Cells Imaged by Lattice Light-Sheet Microscopy," MBoC 2016, 27(22), 3418-3435. (*) equal contribution
  10. Wang, H., Becuwe, M., Housden, B., Chitraju, C., Porras, A., Graham, M., Liu, X., Thian, A., Savage, D., Agrawal, A., Garg, A., Olarte, M., Lin, Q., Frohlich, F., Hannibal-Bach, H., Upadhyayula, S., Perrimon, N., Kirchhausen, T., Ejsing, C., Walther, T., Farese, R. ; "Seipin is required for converting nascent to mature lipid droplets," eLife 2016, 5:e16582.
  11. Upadhyayula, S.; Nuñez, V.; Larsen, J.; Espinoza, E. M.; Bao, D.; Xia, B.; Shi, D.; Anvari, B.; Vullev, V.;  "Photoinduced Dynamics of a Cyanine Dye: Parallel Pathways of Non-radiative Deactivation Involving Multiple Excited-State Twisted Transients," Chem. Sci. 2015, 6, 2237-2251.
  12. Bao, D.; Upadhyayula, S.; Larsen, J.; Xia, B.; Hartman, J.; Georgieva, B.; Nuñez, V.; Espinoza, E.; Wurch, M.; Chang, A.; Lin, T.; Larkin, J.; Vasquez, K.; Beran, G. J. O.; Vullev, V.;  "Rectifying intramolecular charge separation and charge recombination," J. Am. Chem. Soc. 2014, 136(37), 12966-12973.
  13. Lock, J. Y.; Wyatt, E.; Upadhyayula, S.; Whall, A.; Nuñez, V.; Vullev, V.; Liu, H. "Degradation and Antimicrobial Properties of Magnesium Alloys in Artificial Urine for Potential Resorbable Ureteral Stent Applications," Journal of Biomedical Materials Research: Part A 2013, 102(3) 781-792.
  14. Guo, S.; Bao, D.; Upadhyayula, S.; Wang, W.; Guvenc, A. B.; Kyle, J. R.; Bay, H.; Bozhilov, K.;Vullev, V.; Ozkan, C.; Ozkan, M. "Photoinduced Electron Transfer between Pyridine-Coated Cadmium Selenide Quantum Dots and Single-Sheet Graphene," Adv. Funct. Mat. 2013, 23(41) 5199-5211.
  15. Nuñez, V.; Upadhyayula, S.; Millare, B.; Hadian, Ali.; Shin, S.; Vandrangi, P.; Gupta, S.; Xu, H.; Lin, A.; Larsen, J.; Georgiev, G.; Vullev, V. I. "Microfluidic space-domain time-resolved emission spectroscopy of terbium (III) and europium (III) chelates with pyridine-2,6-dicarboxylate," Analytical Chemistry 2013, 85(9) 4567-4577.
  16. Xia, B.; Bao, D.; Upadhyayula, S.; Jones, G.; Vullev, V. I. "Anthranilamides as Bioinspired Molecular Electrets: Experimental Evidence for Permanent Ground-State Electric Dipole Moment," Journal of Organic Chemistry 2013, 78(5) 1994-2004.
  17. Lock, J. Y.; Dragonov, M.; Whall, A.; Dhillon, S.; Upadhyayula, S.; Vullev, V.; Liu, H. "Antimicrobial Properties of Biodegradable Magnesium for Next Generation Ureteral Stent Applications," Proc. IEEE-EMBS 2012, Paper WeC20.5.
  18. Upadhyayula, S.; Lam, S.; Ha, A.; Malik-Chaudhry, H. K.; Vullev, V. "Dynamic Staining of Bacilli Endospores with Thioflavin T," Proc. IEEE-EMBS 2012, 2012:499-502.
  19. Upadhyayula, S.; Quinata, T.; Bishop, S.; Gupta, S.; Johnson, N.; Bahmani, B.; Bozhilov, K.; Stubbs, J.; Jreij, P.; Nallagatla, P.; Vullev, V. "Coatings of Polyethylene Glycol for Suppressing Non-specific Interactions between Solid Microspheres and Flat Surfaces," Langmuir 2012, 28 (11), 5059-5069.
  20. Upadhyayula, S.; Bao, D.; Millare, B.; Sylvia, S.; Habib, K. M. M.; Ashraf, M.; Ferreira, A.; Bishop, S.; Bonderer, R.; Baqai, S.; Jing, X.; Penchev, M.; Ozkan, M.; Ozkan, C.; Lake, R.; Vullev, V. "Permanent Electric Dipole Moments of Carboxyamides in Condensed Media: What Are the Limitations of Theory and Experiment?," J. Phys. Chem. B 2011, 115(30), 9473-9490.
  21. Xia, B.; Upadhyayula, S.; Nunez, V.; Landsman, P.; Lam, S.; Malik, H.; Gupta, S; Sarshar, M.; Hu, J.; Anvari, B.; Jones, G.; Vullev, V. I. "Amyloid Histology Stain for Rapid Bacterial Endospore Imaging," Journal of Clinical Microbiology 2011, 49(8), 2966-2975.
  22. Nuñez, V.; Upadhyayula, S.; Lin, A.; Chau, K.; Vullev, V. "Dynamic staining of bacteria at a single-cell level," Proc. SPIE 8018, 80180A 2011; doi:10.1117/12.884186
  23. Bahmani, B.; Gupta, S.; Upadhyayula, S.; Vullev, V.; Anvari, B. "Effect of Polyethylene Glycol Coatings on Uptake of Indocyanine Green Loaded Nanocapsules by Human Spleen Macrophages In-Vitro," Journal of Biomedical Optics 2011, 16(5) 051303.
  24. Chau, K.; Millare, B.; Lin, A.; Upadhyayula, S.; Nunez, V.; Xu, H.; Vullev, V. I. "Dependence of the Quality of Adhesion between Poly(dimethylsiloxane) and Glass Surfaces on the Composition of the Oxidizing Plasma," Microfluidics and Nanofluidics 2011, 10(4), 907-917.
  25. Bao, D.; Ramu, S.; Contreras, A.; Upadhyayula, S.; Vasquez, J.M.; Beran, G. and Vullev, V. I. "Electrochemical Reduction of Quinones: Interfacing Experiment and Theory for Defining Effective Radii of Redox Moieties," J. Phys. Chem. B 2010, 114, 14467-14479.
  26. Thomas, M. S.; Nunez, V.; Upadhyayula, S.; Zielins, E.; Bao, D.; Vasquez, J.M.; Bahmani, B. and Vullev, V. I. "Kinetics of Bacterial Fluorescence Staining with 3,3'-Diethylthiacyanine," Langmuir 2010, 26 (12), 9756-9765.

Last Updated 2019-05-06