Scholars@Duke

• Background
• 

  Education, Training, & Certifications

  • D.S.Sc., Israel Institute of Technology (Israel) 1996
• 

  Academic Positions Outside Duke

  • Principal Investigator and Cryo-EM Core Director, National Institute of Environmental Health Science. 2017 - 2030
• Recognition
• 

  In the News

  • APR 6, 2021

    Duke Team Makes Cryo-EM Microscope Even Better Than Before

  • MAY 15, 2019

    Duke Research

    A Giant Tool to See the Tiniest Things
• Research
• 

  Selected Grants

  • A Hybrid Computational Platform for High-resolution Structure Determination Using Cryo-EM awarded by National Institutes of Health 2021 - 2025
• Publications & Artistic Works
• 

  Selected Publications

  • Academic Articles

    • Kumar, Shivesh, Yan Wang, Ye Zhou, Lucas Dillard, Fay-Wei Li, Carly A. Sciandra, Ning Sui, et al. “Structure and dynamics of the Arabidopsis O-fucosyltransferase SPINDLY.” Nat Commun 14, no. 1 (March 20, 2023): 1538. https://doi.org/10.1038/s41467-023-37279-1.
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    • Gordon, Jacob, Fleur L. Chapus, Elizabeth G. Viverette, Jason G. Williams, Leesa J. Deterding, Juno M. Krahn, Mario J. Borgnia, Joseph Rodriguez, Alan J. Warren, and Robin E. Stanley. “Cryo-EM reveals the architecture of the PELP1-WDR18 molecular scaffold.” Nat Commun 13, no. 1 (November 9, 2022): 6783. https://doi.org/10.1038/s41467-022-34610-0.
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    • Yin, Ying, Feng Zhang, Shasha Feng, Kevin John Butay, Mario J. Borgnia, Wonpil Im, and Seok-Yong Lee. “Activation mechanism of the mouse cold-sensing TRPM8 channel by cooling agonist and PIP2.” Science 378, no. 6616 (October 14, 2022): eadd1268. https://doi.org/10.1126/science.add1268.
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    • Klemm, Bradley P., Deepa Singh, Cassandra E. Smith, Allen L. Hsu, Lucas B. Dillard, Juno M. Krahn, Robert E. London, Geoffrey A. Mueller, Mario J. Borgnia, and Roel M. Schaaper. “Mechanism by which T7 bacteriophage protein Gp1.2 inhibits Escherichia coli dGTPase.” Proc Natl Acad Sci U S A 119, no. 37 (September 13, 2022): e2123092119. https://doi.org/10.1073/pnas.2123092119.
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    • Dasari, Anvesh K. R., Lucas Dillard, Sujung Yi, Elizabeth Viverette, Alimohammad Hojjatian, Urmi Sengupta, Rakez Kayed, Kenneth A. Taylor, Mario Juan Borgnia, and Kwang Hun Lim. “Untwisted α-Synuclein Filaments Formed in the Presence of Lipid Vesicles.” Biochemistry 61, no. 17 (September 6, 2022): 1766–73. https://doi.org/10.1021/acs.biochem.2c00283.
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    • Riccio, Amanda A., Jonathan Bouvette, Matthew J. Longley, Juno M. Krahn, Mario J. Borgnia, and William C. Copeland. “Method for the structural analysis of Twinkle mitochondrial DNA helicase by cryo-EM.” Methods 205 (September 2022): 263–70. https://doi.org/10.1016/j.ymeth.2022.06.012.
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    • Bouvette, Jonathan, Qinwen Huang, Amanda A. Riccio, William C. Copeland, Alberto Bartesaghi, and Mario J. Borgnia. “Automated systematic evaluation of cryo-EM specimens with SmartScope.” Elife 11 (August 23, 2022). https://doi.org/10.7554/eLife.80047.
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    • Frazier, Meredith N., Isha M. Wilson, Juno M. Krahn, Kevin John Butay, Lucas B. Dillard, Mario J. Borgnia, and Robin E. Stanley. “Flipped over U: structural basis for dsRNA cleavage by the SARS-CoV-2 endoribonuclease.” Nucleic Acids Res 50, no. 14 (August 12, 2022): 8290–8301. https://doi.org/10.1093/nar/gkac589.
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    • Riccio, Amanda A., Jonathan Bouvette, Lalith Perera, Matthew J. Longley, Juno M. Krahn, Jason G. Williams, Robert Dutcher, Mario J. Borgnia, and William C. Copeland. “Structural insight and characterization of human Twinkle helicase in mitochondrial disease.” Proc Natl Acad Sci U S A 119, no. 32 (August 9, 2022): e2207459119. https://doi.org/10.1073/pnas.2207459119.
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    • Klemm, Bradley P., Andrew P. Sikkema, Allen L. Hsu, James C. Horng, Traci M Tanaka Hall, Mario J. Borgnia, and Roel M. Schaaper. “High-resolution structures of the SAMHD1 dGTPase homolog from Leeuwenhoekiella blandensis reveal a novel mechanism of allosteric activation by dATP.” J Biol Chem 298, no. 7 (July 2022): 102073. https://doi.org/10.1016/j.jbc.2022.102073.
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    • Simões, Vanessa, Blanche K. Cizubu, Lana Harley, Ye Zhou, Joshua Pajak, Nathan A. Snyder, Jonathan Bouvette, et al. “Redox-sensitive E2 Rad6 controls cellular response to oxidative stress via K63-linked ubiquitination of ribosomes.” Cell Rep 39, no. 8 (May 24, 2022): 110860. https://doi.org/10.1016/j.celrep.2022.110860.
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    • Hong, Jessica, Hyung Joon Kwon, Raul Cachau, Catherine Z. Chen, Kevin John Butay, Zhijian Duan, Dan Li, et al. “Dromedary camel nanobodies broadly neutralize SARS-CoV-2 variants.” Proc Natl Acad Sci U S A 119, no. 18 (May 3, 2022): e2201433119. https://doi.org/10.1073/pnas.2201433119.
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    • Kumar, Shivesh, Raul Zavaliev, Qinglin Wu, Ye Zhou, Jie Cheng, Lucas Dillard, Jordan Powers, et al. “Structural basis of NPR1 in activating plant immunity.” Nature 605, no. 7910 (May 2022): 561–66. https://doi.org/10.1038/s41586-022-04699-w.
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    • Fu, Ying, Juliana da Fonseca Rezende E Mello, Bryan D. Fleming, Alex Renn, Catherine Z. Chen, Xin Hu, Miao Xu, et al. “A humanized nanobody phage display library yields potent binders of SARS CoV-2 spike.” Plos One 17, no. 8 (2022): e0272364. https://doi.org/10.1371/journal.pone.0272364.
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    • Frazier, Meredith N., Lucas B. Dillard, Juno M. Krahn, Lalith Perera, Jason G. Williams, Isha M. Wilson, Zachary D. Stewart, et al. “Characterization of SARS2 Nsp15 nuclease activity reveals it's mad about U.” Nucleic Acids Res 49, no. 17 (September 27, 2021): 10136–49. https://doi.org/10.1093/nar/gkab719.
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    • Kwon, Do Hoon, Feng Zhang, Yang Suo, Jonathan Bouvette, Mario J. Borgnia, and Seok-Yong Lee. “Heat-dependent opening of TRPV1 in the presence of capsaicin.” Nat Struct Mol Biol 28, no. 7 (July 2021): 554–63. https://doi.org/10.1038/s41594-021-00616-3.
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    • Williams, Wilton B., R Ryan Meyerhoff, R. J. Edwards, Hui Li, Kartik Manne, Nathan I. Nicely, Rory Henderson, et al. “Fab-dimerized glycan-reactive antibodies are a structural category of natural antibodies.” Cell 184, no. 11 (May 27, 2021): 2955-2972.e25. https://doi.org/10.1016/j.cell.2021.04.042.
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    • Hojjatian, Alimohammad, Anvesh K. R. Dasari, Urmi Sengupta, Dianne Taylor, Nadia Daneshparvar, Fatemeh Abbasi Yeganeh, Lucas Dillard, et al. “Tau induces formation of α-synuclein filaments with distinct molecular conformations.” Biochem Biophys Res Commun 554 (May 21, 2021): 145–50. https://doi.org/10.1016/j.bbrc.2021.03.091.
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    • Bouvette, Jonathan, Hsuan-Fu Liu, Xiaochen Du, Ye Zhou, Andrew P. Sikkema, Juliana da Fonseca Rezende E Mello, Bradley P. Klemm, et al. “Beam image-shift accelerated data acquisition for near-atomic resolution single-particle cryo-electron tomography.” Nat Commun 12, no. 1 (March 30, 2021): 1957. https://doi.org/10.1038/s41467-021-22251-8.
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    • Pillon, Monica C., Meredith N. Frazier, Lucas B. Dillard, Jason G. Williams, Seda Kocaman, Juno M. Krahn, Lalith Perera, et al. “Cryo-EM structures of the SARS-CoV-2 endoribonuclease Nsp15 reveal insight into nuclease specificity and dynamics.” Nat Commun 12, no. 1 (January 27, 2021): 636. https://doi.org/10.1038/s41467-020-20608-z.
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    • Travis, Brady A., Kathryn M. Ramsey, Samantha M. Prezioso, Thomas Tallo, Jamie M. Wandzilak, Allen Hsu, Mario Borgnia, et al. “Structural Basis for Virulence Activation of Francisella tularensis.” Mol Cell 81, no. 1 (January 7, 2021): 139-152.e10. https://doi.org/10.1016/j.molcel.2020.10.035.
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    • Henderson, Rory, Robert J. Edwards, Katayoun Mansouri, Katarzyna Janowska, Victoria Stalls, Sophie M. C. Gobeil, Megan Kopp, et al. “Controlling the SARS-CoV-2 spike glycoprotein conformation.” Nat Struct Mol Biol 27, no. 10 (October 2020): 925–33. https://doi.org/10.1038/s41594-020-0479-4.
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    • Zhou, Ye, Panagiotis L. Kastritis, Shannon E. Dougherty, Jonathan Bouvette, Allen L. Hsu, Laura Burbaum, Shyamal Mosalaganti, et al. “Structural impact of K63 ubiquitin on yeast translocating ribosomes under oxidative stress.” Proc Natl Acad Sci U S A 117, no. 36 (September 8, 2020): 22157–66. https://doi.org/10.1073/pnas.2005301117.
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    • Gunn, Kathryn H., Benjamin S. Roberts, Fengbin Wang, Joshua D. Strauss, Mario J. Borgnia, Edward H. Egelman, and Saskia B. Neher. “The structure of helical lipoprotein lipase reveals an unexpected twist in lipase storage.” Proc Natl Acad Sci U S A 117, no. 19 (May 12, 2020): 10254–64. https://doi.org/10.1073/pnas.1916555117.
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    • Suo, Yang, Zilong Wang, Lejla Zubcevic, Allen L. Hsu, Qianru He, Mario J. Borgnia, Ru-Rong Ji, and Seok-Yong Lee. “Structural Insights into Electrophile Irritant Sensing by the Human TRPA1 Channel.” Neuron 105, no. 5 (March 4, 2020): 882-894.e5. https://doi.org/10.1016/j.neuron.2019.11.023.
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    • Tang, Wai Kwan, Mario J. Borgnia, Allen L. Hsu, Lothar Esser, Tara Fox, Natalia de Val, and Di Xia. “Structures of AAA protein translocase Bcs1 suggest translocation mechanism of a folded protein.” Nat Struct Mol Biol 27, no. 2 (February 2020): 202–9. https://doi.org/10.1038/s41594-020-0373-0.
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    • Henderson, Rory, Maolin Lu, Ye Zhou, Zekun Mu, Robert Parks, Qifeng Han, Allen L. Hsu, et al. “Disruption of the HIV-1 Envelope allosteric network blocks CD4-induced rearrangements.” Nat Commun 11, no. 1 (January 24, 2020): 520. https://doi.org/10.1038/s41467-019-14196-w.
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    • Saunders, Kevin O., Kevin Wiehe, Ming Tian, Priyamvada Acharya, Todd Bradley, S Munir Alam, Eden P. Go, et al. “Targeted selection of HIV-specific antibody mutations by engineering B cell maturation.” Science 366, no. 6470 (December 6, 2019). https://doi.org/10.1126/science.aay7199.
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    • LaBranche, Celia C., Rory Henderson, Allen Hsu, Shay Behrens, Xuejun Chen, Tongqing Zhou, Kevin Wiehe, et al. “Correction: Neutralization-guided design of HIV-1 envelope trimers with high affinity for the unmutated common ancestor of CH235 lineage CD4bs broadly neutralizing antibodies.” Plos Pathog 15, no. 12 (December 2019): e1008200. https://doi.org/10.1371/journal.ppat.1008200.
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    • Pillon, Monica C., Allen L. Hsu, Juno M. Krahn, Jason G. Williams, Kevin H. Goslen, Mack Sobhany, Mario J. Borgnia, and Robin E. Stanley. “Cryo-EM reveals active site coordination within a multienzyme pre-rRNA processing complex.” Nat Struct Mol Biol 26, no. 9 (September 2019): 830–39. https://doi.org/10.1038/s41594-019-0289-8.
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    • LaBranche, Celia C., Rory Henderson, Allen Hsu, Shay Behrens, Xuejun Chen, Tongqing Zhou, Kevin Wiehe, et al. “Neutralization-guided design of HIV-1 envelope trimers with high affinity for the unmutated common ancestor of CH235 lineage CD4bs broadly neutralizing antibodies.” Plos Pathog 15, no. 9 (September 2019): e1008026. https://doi.org/10.1371/journal.ppat.1008026.
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    • Yin, Ying, Mengyu Wu, Allen L. Hsu, William F. Borschel, Mario J. Borgnia, Gabriel C. Lander, and Seok-Yong Lee. “Visualizing structural transitions of ligand-dependent gating of the TRPM2 channel.” Nat Commun 10, no. 1 (August 20, 2019): 3740. https://doi.org/10.1038/s41467-019-11733-5.
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    • Zhou, Bing-Rui, KN Sathish Yadav, Mario Borgnia, Jingjun Hong, Baohua Cao, Ada L. Olins, Donald E. Olins, Yawen Bai, and Ping Zhang. “Atomic resolution cryo-EM structure of a native-like CENP-A nucleosome aided by an antibody fragment.” Nat Commun 10, no. 1 (May 24, 2019): 2301. https://doi.org/10.1038/s41467-019-10247-4.
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    • Zubcevic, Lejla, Allen L. Hsu, Mario J. Borgnia, and Seok-Yong Lee. “Symmetry transitions during gating of the TRPV2 ion channel in lipid membranes.” Elife 8 (May 15, 2019). https://doi.org/10.7554/eLife.45779.
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    • Zubcevic, Lejla, William F. Borschel, Allen L. Hsu, Mario J. Borgnia, and Seok-Yong Lee. “Regulatory switch at the cytoplasmic interface controls TRPV channel gating.” Elife 8 (May 9, 2019). https://doi.org/10.7554/eLife.47746.
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    • Yin, Ying, Son C. Le, Allen L. Hsu, Mario J. Borgnia, Huanghe Yang, and Seok-Yong Lee. “Structural basis of cooling agent and lipid sensing by the cold-activated TRPM8 channel.” Science 363, no. 6430 (March 1, 2019). https://doi.org/10.1126/science.aav9334.
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    • Anderson, Cathy J., Matthew R. Baird, Allen Hsu, Emily H. Barbour, Yuka Koyama, Mario J. Borgnia, and Robert K. McGinty. “Structural Basis for Recognition of Ubiquitylated Nucleosome by Dot1L Methyltransferase.” Cell Rep 26, no. 7 (February 12, 2019): 1681-1690.e5. https://doi.org/10.1016/j.celrep.2019.01.058.
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    • Lo, Yu-Hua, Mack Sobhany, Allen L. Hsu, Brittany L. Ford, Juno M. Krahn, Mario J. Borgnia, and Robin E. Stanley. “Cryo-EM structure of the essential ribosome assembly AAA-ATPase Rix7.” Nat Commun 10, no. 1 (January 31, 2019): 513. https://doi.org/10.1038/s41467-019-08373-0.
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    • Fiori, Mariana C., Yunjiang Jiang, Wan Zheng, Miguel Anzaldua, Mario J. Borgnia, Guillermo A. Altenberg, and Hongjun Liang. “Polymer Nanodiscs: Discoidal Amphiphilic Block Copolymer Membranes as a New Platform for Membrane Proteins.” Sci Rep 7, no. 1 (November 9, 2017): 15227. https://doi.org/10.1038/s41598-017-15151-9.
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    • Pillon, Monica C., Mack Sobhany, Mario J. Borgnia, Jason G. Williams, and Robin E. Stanley. “Grc3 programs the essential endoribonuclease Las1 for specific RNA cleavage.” Proc Natl Acad Sci U S A 114, no. 28 (July 11, 2017): E5530–38. https://doi.org/10.1073/pnas.1703133114.
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    • Frank, Gabriel A., Suneet Shukla, Prashant Rao, Mario J. Borgnia, Alberto Bartesaghi, Alan Merk, Aerfa Mobin, et al. “Cryo-EM Analysis of the Conformational Landscape of Human P-glycoprotein (ABCB1) During its Catalytic Cycle.” Mol Pharmacol 90, no. 1 (July 2016): 35–41. https://doi.org/10.1124/mol.116.104190.
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    • Borgnia, Mario J., Soojay Banerjee, Alan Merk, Doreen Matthies, Alberto Bartesaghi, Prashant Rao, Jason Pierson, et al. “Using Cryo-EM to Map Small Ligands on Dynamic Metabolic Enzymes: Studies with Glutamate Dehydrogenase.” Mol Pharmacol 89, no. 6 (June 2016): 645–51. https://doi.org/10.1124/mol.116.103382.
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    • Matthies, Doreen, Olivier Dalmas, Mario J. Borgnia, Pawel K. Dominik, Alan Merk, Prashant Rao, Bharat G. Reddy, et al. “Cryo-EM Structures of the Magnesium Channel CorA Reveal Symmetry Break upon Gating.” Cell 164, no. 4 (February 11, 2016): 747–56. https://doi.org/10.1016/j.cell.2015.12.055.
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    • Bartesaghi, Alberto, Alan Merk, Mario J. Borgnia, Jacqueline L. S. Milne, and Sriram Subramaniam. “Prefusion structure of trimeric HIV-1 envelope glycoprotein determined by cryo-electron microscopy.” Nat Struct Mol Biol 20, no. 12 (December 2013): 1352–57. https://doi.org/10.1038/nsmb.2711.
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    • Schauder, David M., Oleg Kuybeda, Jinjin Zhang, Katherine Klymko, Alberto Bartesaghi, Mario J. Borgnia, Mark L. Mayer, and Sriram Subramaniam. “Glutamate receptor desensitization is mediated by changes in quaternary structure of the ligand binding domain.” Proc Natl Acad Sci U S A 110, no. 15 (April 9, 2013): 5921–26. https://doi.org/10.1073/pnas.1217549110.
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    • Kuybeda, Oleg, Gabriel A. Frank, Alberto Bartesaghi, Mario Borgnia, Sriram Subramaniam, and Guillermo Sapiro. “A collaborative framework for 3D alignment and classification of heterogeneous subvolumes in cryo-electron tomography.” J Struct Biol 181, no. 2 (February 2013): 116–27. https://doi.org/10.1016/j.jsb.2012.10.010.
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    • Milne, Jacqueline L. S., Mario J. Borgnia, Alberto Bartesaghi, Erin E. H. Tran, Lesley A. Earl, David M. Schauder, Jeffrey Lengyel, Jason Pierson, Ardan Patwardhan, and Sriram Subramaniam. “Cryo-electron microscopy--a primer for the non-microscopist.” Febs J 280, no. 1 (January 2013): 28–45. https://doi.org/10.1111/febs.12078.
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    • Frank, Gabriel A., Alberto Bartesaghi, Oleg Kuybeda, Mario J. Borgnia, Tommi A. White, Guillermo Sapiro, and Sriram Subramaniam. “Computational separation of conformational heterogeneity using cryo-electron tomography and 3D sub-volume averaging.” J Struct Biol 178, no. 2 (May 2012): 165–76. https://doi.org/10.1016/j.jsb.2012.01.004.
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    • Tran, Erin E. H., Mario J. Borgnia, Oleg Kuybeda, David M. Schauder, Alberto Bartesaghi, Gabriel A. Frank, Guillermo Sapiro, Jacqueline L. S. Milne, and Sriram Subramaniam. “Structural mechanism of trimeric HIV-1 envelope glycoprotein activation.” Plos Pathog 8, no. 7 (2012): e1002797. https://doi.org/10.1371/journal.ppat.1002797.
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    • Meyerson, Joel R., Tommi A. White, Donald Bliss, Amy Moran, Alberto Bartesaghi, Mario J. Borgnia, M Jason V. de la Cruz, et al. “Determination of molecular structures of HIV envelope glycoproteins using cryo-electron tomography and automated sub-tomogram averaging.” J Vis Exp, no. 58 (December 1, 2011). https://doi.org/10.3791/2770.
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    • White, Tommi A., Alberto Bartesaghi, Mario J. Borgnia, M Jason V. de la Cruz, Rachna Nandwani, James A. Hoxie, Julian W. Bess, Jeffrey D. Lifson, Jacqueline L. S. Milne, and Sriram Subramaniam. “Three-dimensional structures of soluble CD4-bound states of trimeric simian immunodeficiency virus envelope glycoproteins determined by using cryo-electron tomography.” J Virol 85, no. 23 (December 2011): 12114–23. https://doi.org/10.1128/JVI.05297-11.
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    • Harris, Audray, Mario J. Borgnia, Dan Shi, Alberto Bartesaghi, Haifeng He, Robert Pejchal, Yun Kenneth Kang, et al. “Trimeric HIV-1 glycoprotein gp140 immunogens and native HIV-1 envelope glycoproteins display the same closed and open quaternary molecular architectures.” Proc Natl Acad Sci U S A 108, no. 28 (July 12, 2011): 11440–45. https://doi.org/10.1073/pnas.1101414108.
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    • Khursigara, Cezar M., Ganhui Lan, Silke Neumann, Xiongwu Wu, Suchie Ravindran, Mario J. Borgnia, Victor Sourjik, Jacqueline Milne, Yuhai Tu, and Sriram Subramaniam. “Lateral density of receptor arrays in the membrane plane influences sensitivity of the E. coli chemotaxis response.” Embo J 30, no. 9 (May 4, 2011): 1719–29. https://doi.org/10.1038/emboj.2011.77.
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    • White, Tommi A., Alberto Bartesaghi, Mario J. Borgnia, Joel R. Meyerson, M Jason V. de la Cruz, Julian W. Bess, Rachna Nandwani, et al. “Molecular architectures of trimeric SIV and HIV-1 envelope glycoproteins on intact viruses: strain-dependent variation in quaternary structure.” Plos Pathog 6, no. 12 (December 23, 2010): e1001249. https://doi.org/10.1371/journal.ppat.1001249.
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    • Narasimha, Rajesh, Iman Aganj, Adam E. Bennett, Mario J. Borgnia, Daniel Zabransky, Guillermo Sapiro, Steven W. McLaughlin, Jacqueline L. S. Milne, and Sriram Subramaniam. “Evaluation of denoising algorithms for biological electron tomography.” J Struct Biol 164, no. 1 (October 2008): 7–17. https://doi.org/10.1016/j.jsb.2008.04.006.
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    • Liu, Jun, Alberto Bartesaghi, Mario J. Borgnia, Guillermo Sapiro, and Sriram Subramaniam. “Molecular architecture of native HIV-1 gp120 trimers.” Nature 455, no. 7209 (September 4, 2008): 109–13. https://doi.org/10.1038/nature07159.
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    • Liu, J., A. Bartesaghi, M. J. Borgnia, G. Sapiro, and S. Subramaniam. “Molecular Architecture of Native HIV-1 gp 120 Trimers.” Chemtracts 21, no. 6 (June 1, 2008): 227–28.
    • Borgnia, Mario J., Sriram Subramaniam, and Jacqueline L. S. Milne. “Three-dimensional imaging of the highly bent architecture of Bdellovibrio bacteriovorus by using cryo-electron tomography.” J Bacteriol 190, no. 7 (April 2008): 2588–96. https://doi.org/10.1128/JB.01538-07.
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    • Narasimha, R., I. Aganj, M. Borgnia, G. Sapiro, S. McLaughlin, J. Milne, and S. Subramaniam. “From gigabytes to bytes: Automated denoising and feature identification in electron tomograms of intact bacterial cells.” 2007 4th Ieee International Symposium on Biomedical Imaging: From Nano to Macro  Proceedings, November 27, 2007, 304–7. https://doi.org/10.1109/ISBI.2007.356849.
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    • Aganj, I., A. Bartesaghi, M. Borgnia, H. Y. Liao, G. Sapiro, and S. Subramaniam. “Regularization for inverting the radon transform with wedge consideration.” 2007 4th Ieee International Symposium on Biomedical Imaging: From Nano to Macro  Proceedings, November 27, 2007, 217–20. https://doi.org/10.1109/ISBI.2007.356827.
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    • Milne, Jacqueline L. S., Xiongwu Wu, Mario J. Borgnia, Jeffrey S. Lengyel, Bernard R. Brooks, Dan Shi, Richard N. Perham, and Sriram Subramaniam. “Molecular structure of a 9-MDa icosahedral pyruvate dehydrogenase subcomplex containing the E2 and E3 enzymes using cryoelectron microscopy.” J Biol Chem 281, no. 7 (February 17, 2006): 4364–70. https://doi.org/10.1074/jbc.M504363200.
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    • Borgnia, Mario J., Dan Shi, Peijun Zhang, and Jacqueline L. S. Milne. “Visualization of alpha-helical features in a density map constructed using 9 molecular images of the 1.8 MDa icosahedral core of pyruvate dehydrogenase.” J Struct Biol 147, no. 2 (August 2004): 136–45. https://doi.org/10.1016/j.jsb.2004.02.007.
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    • Zhang, Peijun, Mario J. Borgnia, Paul Mooney, Dan Shi, Ming Pan, Philip O’Herron, Albert Mao, David Brogan, Jacqueline L. S. Milne, and Sriram Subramaniam. “Automated image acquisition and processing using a new generation of 4K x 4K CCD cameras for cryo electron microscopic studies of macromolecular assemblies.” J Struct Biol 143, no. 2 (August 2003): 135–44. https://doi.org/10.1016/s1047-8477(03)00124-2.
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    • Wu, Xiongwu, Jacqueline L. S. Milne, Mario J. Borgnia, Alexey V. Rostapshov, Sriram Subramaniam, and Bernard R. Brooks. “A core-weighted fitting method for docking atomic structures into low-resolution maps: application to cryo-electron microscopy.” J Struct Biol 141, no. 1 (January 2003): 63–76. https://doi.org/10.1016/s1047-8477(02)00570-1.
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    • Pohl, P., S. M. Saparov, M. J. Borgnia, and P. Agre. “Highly selective water channel activity measured by voltage clamp: analysis of planar lipid bilayers reconstituted with purified AqpZ.” Proc Natl Acad Sci U S A 98, no. 17 (August 14, 2001): 9624–29. https://doi.org/10.1073/pnas.161299398.
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    • Borgnia, M. J., and P. Agre. “Reconstitution and functional comparison of purified GlpF and AqpZ, the glycerol and water channels from Escherichia coli.” Proc Natl Acad Sci U S A 98, no. 5 (February 27, 2001): 2888–93. https://doi.org/10.1073/pnas.051628098.
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    • Agre, P., M. J. Borgnia, M. Yasui, J. D. Neely, J. Carbrey, D. Kozono, E. Beitz, J. Hoffert, V. Leitch, and L. S. King. “Chapter 1 discovery of the aquaporins and their impact on basic and clinical physiology.” Current Topics in Membranes 51 (January 1, 2001): 1–38. https://doi.org/10.1016/S1063-5823(01)51003-0.
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    • Stahlberg, H., T. Braun, B. de Groot, A. Philippsen, M. J. Borgnia, P. Agre, W. Kühlbrandt, and A. Engel. “The 6.9-A structure of GlpF: a basis for homology modeling of the glycerol channel from Escherichia coli.” J Struct Biol 132, no. 2 (November 2000): 133–41. https://doi.org/10.1006/jsbi.2000.4317.
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    • Braun, T., A. Philippsen, S. Wirtz, M. J. Borgnia, P. Agre, W. Kühlbrandt, A. Engel, and H. Stahlberg. “The 3.7 A projection map of the glycerol facilitator GlpF: a variant of the aquaporin tetramer.” Embo Rep 1, no. 2 (August 2000): 183–89. https://doi.org/10.1093/embo-reports/kvd022.
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    • Scheuring, S., P. Tittmann, H. Stahlberg, P. Ringler, M. Borgnia, P. Agre, H. Gross, and A. Engel. “The aquaporin sidedness revisited.” J Mol Biol 299, no. 5 (June 23, 2000): 1271–78. https://doi.org/10.1006/jmbi.2000.3811.
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    • Scheuring, S., P. Ringler, M. Borgnia, H. Stahlberg, D. J. Müller, P. Agre, and A. Engel. “High resolution AFM topographs of the Escherichia coli water channel aquaporin Z.” Embo J 18, no. 18 (September 15, 1999): 4981–87. https://doi.org/10.1093/emboj/18.18.4981.
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    • Borgnia, M. J., D. Kozono, G. Calamita, P. C. Maloney, and P. Agre. “Functional reconstitution and characterization of AqpZ, the E. coli water channel protein.” J Mol Biol 291, no. 5 (September 3, 1999): 1169–79. https://doi.org/10.1006/jmbi.1999.3032.
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    • Ringler, P., M. J. Borgnia, H. Stahlberg, P. C. Maloney, P. Agre, and A. Engel. “Structure of the water channel AqpZ from Escherichia coli revealed by electron crystallography.” J Mol Biol 291, no. 5 (September 3, 1999): 1181–90. https://doi.org/10.1006/jmbi.1999.3031.
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    • Borgnia, M., S. Nielsen, A. Engel, and P. Agre. “Cellular and molecular biology of the aquaporin water channels.” Annu Rev Biochem 68 (1999): 425–58. https://doi.org/10.1146/annurev.biochem.68.1.425.
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    • Agre, P., M. Bonhivers, and M. J. Borgnia. “The aquaporins, blueprints for cellular plumbing systems.” J Biol Chem 273, no. 24 (June 12, 1998): 14659–62. https://doi.org/10.1074/jbc.273.24.14659.
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    • Borgnia, M. J., G. D. Eytan, and Y. G. Assaraf. “Competition of hydrophobic peptides, cytotoxic drugs, and chemosensitizers on a common P-glycoprotein pharmacophore as revealed by its ATPase activity.” J Biol Chem 271, no. 6 (February 9, 1996): 3163–71. https://doi.org/10.1074/jbc.271.6.3163.
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    • Eytan, G. D., M. J. Borgnia, R. Regev, and Y. G. Assaraf. “Transport of polypeptide ionophores into proteoliposomes reconstituted with rat liver P-glycoprotein.” J Biol Chem 269, no. 42 (October 21, 1994): 26058–65.
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    • Assaraf, Y. G., and M. J. Borgnia. “Probing the interaction of the multidrug-resistance phenotype with the polypeptide ionophore gramicidin D via functional channel formation.” Eur J Biochem 222, no. 3 (June 15, 1994): 813–24. https://doi.org/10.1111/j.1432-1033.1994.tb18928.x.
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    • Parisi, M., R. Dorr, R. Bonnet, M. Borgnia, and J. P. Rossi. “Fura-2 transport in toad urinary bladder epithelium: effects of antidiuretic hormone, colchicine and osmotic gradients.” Biochim Biophys Acta 1151, no. 1 (September 5, 1993): 1–6. https://doi.org/10.1016/0005-2736(93)90063-6.
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    • Assaraf, Y. G., and M. J. Borgnia. “Differential reversal of lipophilic antifolate resistance in mammalian cells with modulators of the multidrug resistance phenotype.” Anticancer Drugs 4, no. 3 (June 1993): 395–406. https://doi.org/10.1097/00001813-199306000-00018.
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  • Journal Issues

    • Travis, Brady A., Jared V. Peck, Raul Salinas, Brandon Dopkins, Nicholas Lent, Viet D. Nguyen, Mario J. Borgnia, Richard G. Brennan, and Maria A. Schumacher. “Molecular dissection of the glutamine synthetase-GlnR nitrogen regulatory circuitry in Gram-positive bacteria.” Nat Commun, July 1, 2022. https://doi.org/10.1038/s41467-022-31573-0.
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  • Conference Papers

    • Bouvette, J., Q. Huang, A. Bartesaghi, and M. J. Borgnia. “Smartscope: AI-driven grid navigation for high-throughput cryo-EM.” In Proceedings  Applied Imagery Pattern Recognition Workshop, Vol. 2021-October, 2021. https://doi.org/10.1109/AIPR52630.2021.9762104.
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    • Reddy, Bharat, Allen Lu, Navid Bavi, Allen Hsu, Mario Borgnia, and Eduardo Perozo. “High-Resolution Structures of MscS in a Lipid Bilayer: Reinterpreting “Force from Lipids” Activation in Mechanosensitive Channels.” In Biophysical Journal, 116:459a-459a. Elsevier BV, 2019. https://doi.org/10.1016/j.bpj.2018.11.2479.
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    • Borgnia, Mario J., Soojay Banerjee, Alberto Bartesaghi, Doreen Matthies, Prashant Rao, Alan Merk, Jason Pierson, Jacqueline L. Milne, and Sriram Subramaniam. “Using cryo-EM to Untangle the Conformational Landscape of a Small Allosterically-Regulated Complex.” In Biophysical Journal, 110:22a-22a. Elsevier BV, 2016. https://doi.org/10.1016/j.bpj.2015.11.179.
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    • Matthies, Doreen, Olivier Dalmas, Mario Borgnia, Pawel Dominik, Alan Merk, Prashant Rao, Bharat Reddy, et al. “Structures of the Mg2+ Channel Cora in the Open State by Cryo Electron Microscopy.” In Biophysical Journal, 110:291a-291a. Elsevier BV, 2016. https://doi.org/10.1016/j.bpj.2015.11.1574.
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    • Matthies, Doreen, Olivier Dalmas, Mario J. Borgnia, Pawel K. Dominik, Alan Merk, Prashant Rao, Bharat G. Reddy, et al. “Single-Particle Cryo-EM Studies of a 200-kDa Magnesium Ion Channel Reveal Large Structural Changes Upon Gating.” In Biophysical Journal, 110:10a-10a. Elsevier BV, 2016. https://doi.org/10.1016/j.bpj.2015.11.109.
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    • Borgnia, Mario J., Soojay Banerjee, Prashant Rao, Alberto Bartesaghi, Allan Merk, Jason Pierson, Sriram Subramaniam, and Jacqueline Milne. “Localization of Small Ligands in a Metabolic Protein Complex using Cryo-Electron Microscopy.” In Biophysical Journal, 108:514a-514a. Elsevier BV, 2015. https://doi.org/10.1016/j.bpj.2014.11.2818.
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    • Yoo, T. S., B. C. Lowekamp, O. Kuybeda, K. Narayan, G. A. Frank, A. Bartesaghi, M. Borgnia, S. Subramaniam, G. Sapiro, and M. J. Ackerman. “Accelerating discovery in 3D microanalysis: Leveraging open source software and deskside high performance computing.” In Microscopy and Microanalysis, 20:774–75, 2014. https://doi.org/10.1017/S1431927614005595.
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    • Bartesaghi, Alberto, Jason Pierson, Prashant Rao, Soojay Banerjee, Mario Borgnia, Lingbo Yu, Lesley Earl, Michael Alink, Jacqueline Milne, and Sriram Subramaniam. “Structure Determination of Small Macromolecular Complexes by Cryo-Electron Microscopy.” In Biophysical Journal, 106:601a-601a. Elsevier BV, 2014. https://doi.org/10.1016/j.bpj.2013.11.3329.
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    • Bartesaghi, Alberto, Jason Pierson, David Schauder, Mario Borgnia, and Sriram Subramaniam. “Automated Workflows for Structure Determination by Single-Particle Cryo-EM at Sub-Nanometer Resolutions.” In Biophysical Journal, 104:352a-352a. Elsevier BV, 2013. https://doi.org/10.1016/j.bpj.2012.11.1955.
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    • Borgnia, Mario J., Alberto Bartesaghi, Erin Tran, Jacqueline L. S. Milne, and Sriram Subramaniam. “9 Å Structure of Trimeric HIV-1 Envelope Glycoprotein in an Activated State.” In Biophysical Journal, 104:350a-350a. Elsevier BV, 2013. https://doi.org/10.1016/j.bpj.2012.11.1946.
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    • Frank, Gabriel A., Oleg Kuybeda, Alberto Bartesaghi, Mario J. Borgnia, Guillermo Sapiro, and Sriram Subramaniam. “Computational Separation of Conformational Heterogeneity using Cryo-Electron Tomography and 3D Sub-Volume Averaging.” In Biophysical Journal, 104:350a-351a. Elsevier BV, 2013. https://doi.org/10.1016/j.bpj.2012.11.1947.
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    • Schauder, David M., Oleg Kuybeda, Jinjin Zhang, Katherine Klymko, Alberto Bartesaghi, Mario J. Borgnia, Mark L. Mayer, and Sriram Subramaniam. “Glutamate Receptor Desensitization Mediated by Changes in Quaternary Structure of the Ligand Binding Domain.” In Biophysical Journal, 104:352a-352a. Elsevier BV, 2013. https://doi.org/10.1016/j.bpj.2012.11.1953.
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    • Milne, J. L. S., X. Wu, M. J. Borgnia, J. S. Lengyel, D. Shi, R. N. Perham, and S. Subramaniam. “Structure and function of icosahedral pyruvate dehydrogenase complexes.” In Microscopy and Microanalysis, 12:26–27, 2006. https://doi.org/10.1017/S1431927606069145.
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