Acknowledgement

Please provide the following statement in any publications that used center resources:

“(Cryo) Electron microscopy was performed in the Beckman Institute Resource Center for Transmission Electron Microscopy at Caltech. “

Publications

“*” Denotes equal contribution

2020

    1. Barnes CO, Jette CA, Abernathy MA, Dam K-M A, Esswein SR, Gristick HB, Malyutin AG, Sharaf NG, Huey-Tubman KE, Lee YE, Robbiani DF, Nussenzweig MC, West AP, Bjorkman PJ. SARS-CoV-2 neutralizing antibody structures inform therapeutic strategies. Nature, in press, 2020. DOI:10.1038/s41586-020-2852-1.
    2. Jette CA, Barnes CO, Kirk SM, Melillo B, Smith III AB, Bjorkman PJ. Cryo-EM Structures of HIV-1 trimer bound to CD4-mimetics M48U1 and BNM-III-170 adopt a CD4-bound open conformation. bioRxiv, 2020. DOI:10.1101/2020.08.21.261974
    3. Bain W, Penaloza HF, Ladinsky MS, van der Geest R, Sullivan M, Ross M, Kitsios GD, Methe B, McVerry BJ, Morris A, Watson AM, Watkins SC, St. Croix CM, Stolz DB, Bjorkman PJ, Lee JS. Lower respiratory tract myeloid cells harbor SARS-CoV-2 and display an inflammatory phenotype. medRxiv, 2020. DOI:10.1101/2020.08.11.20171967
    4. Ladinsky MS, Gnanapragasam PNP, Yang Z, West Jr. AP, Kay MS, Bjorkman PJ. Electron tomography visualization of HIV-1 fusion with target cells using fusion inhibitors to trap the pre-hairpin intermediate. eLife, 9,e58411, 2020. DOI: 10.7554/eLife.58411
    5. Hoffmann MAG, Bar-On Y, Yang Z, Gristick HB, Gnanapragasam PNP, Vielmetter J, Nussenzweig MC, Bjorkman PJ. Nanoparticles presenting clusters of CD4 expose a universal vulnerability of HIV-1 by mimicking target cells. Proc Natl Acad Sci USA., 117, 18719-18728, 2020. DOI: 10.1073/pnas.2010320117
    6. Wang Z, Barnes CO, Gautam R, Cetrulo Lorenzi JC, Mayer CT, Oliveira TY, Ramos V, Cipolla M, Gordon KM, Gristick HB, West AP, Nishimura Y, Raina H, Seaman MS, Gazumyan A, Martin M, Bjorkman PJ, Nussenzweig MC, Escolano A. A broadly neutralizing macaque monoclonal antibody against the HIV-1 V3-Glycan patch. eLife, 9:e61991, 2020. DOI: 10.7554/eLife.61991
    7. Chreifi G, Chen S, Jensen GJ. Rapid tilt-series method for cryo-electron tomography: characterizing stage behavior during FISE acquisition. bioRxiv, 2020. DOI: 101101/20200519104828
    8. Gorasia DG*, Chreifi G*, Seers CA, Butler CA, Heath JE, Glew MD, McBride MJ, Subramanian P, Kjaer A, Jensen GJ+, Veith PD+, Reynolds EC+. In situ structure and organization of the type IX secretion system. bioRxiv, 2020. DOI: 101101/20200513094771
    9. Nicolas WJ, Ghosal D, Tocheva EI, Meyerowitz EM, Jensen GJ. Structure of the bacterial cellulose ribbon and its assembly-guiding cytoskeleton by electron cryotomography. bioRxiv, 2020. DOI: 101101/20200416045534
    10. Kaplan M, Sweredoski MJ, Rodrigues JPGLM, Tocheva EI, Chang Y-W, Ortega DR, Beeby M, Jensen GJ. Bacterial flagellar motor PL-ring disassembly subcomplexes are widespread and ancient. Proc. Natl. Acad. Sci. USA, 117(16), 8941 – 8947, 2020. DOI: 10.1073/pnas.1916935117
    11. Carter SD*, Hampton CM*, Langlois R*, Melero R, Farino ZJ, Calderon MJ, Li W, Wallace CT, Tran NH, Grassucci RA, Siegmund S, Pemberton J, Morgenstern TJ, Eisenmann L, Aguilar JI, Greenberg NL, Levy ES, Yi E, Mitchell WG, Rice WJ, Wigge C, Pilli J, George EW, Aslanoglou D, Courel M, Freyberg RJ, Javitch JA, Wills ZP, Area-Gomez E, Shiva S, Bartolini F, Volchuk A, Murray SA, Aridor M, Fish KN, Walter P, Balla T, Fass D, Wolf SG, Watkins SC, Carazo JM, Jensen GJ+, Frank J+,Freyberg Z+. Ribosome-associated vesicles: a dynamic vesicular endoplasmic reticulum in secretory cells. Sci. Adv. 6(14), eaay9572, 2020. DOI: 10.1126/sciadv.aay9572
    12. Pleiner T, Tomaleri PG, Januszyk K, Inglis AJ, Hazu M, Voorhees R. Structural Basis for membrane insertion by the human ER membrane protein complex. Science, 2020. DOI: 10.1126/science.abb5008
    13. Weaver S, Sazinsky M, Dalia T, Dalia A, Jensen G. CryoEM structure of the Vibrio cholerae Type IV competence pilus secretin PilQ.  bioRxiv, 2020. DOI: 10.1101/2020.03.03.975896
    14. Schommers P*, Gruell H*, Abernathy ME*, Tran M-K, Dingens AS, Gristick HB, Barnes C.O, Schoofs T, Schlotz M, Vanshylla K, Kreer C, Weiland D, Holtick U, Schei C, Valter MM, van Gils MJ, Sanders RW, Vehreschild JJ, Cornely OA, Lehmann C, Fatkenheuer G, Seaman MS, Bloom JD, Bjorkman PJ, and Klein F. (2020). Restriction of HIV-1 Escape by a Highly Broad and Potent Neutralizing Antibody. Cell 180, 1-19. https://doi.org/10.1016/j.cell.2020.01.010
    15. Barnes CO, West Jr AP, Huey-Tubman KE, Hoffmann MAG, Sharaf NG, Hoffman PR, Koranda N, Gristick HB, Gaebler C, Muecksch F, Cetrulo Lorenzi JC, Finkin S, Hägglöf T, Hurley A, Millard KG, Weisblum Y, Schmidt F, Hatziioannou T, Bieniasz PD, Caskey M, Robbiani DF, Nussenzweig MC, Bjorkman PJ. Structures of human antibodies bound to SARS-CoV-2 spike reveal common epitopes and recurrent features of antibodies. Cell, 2020. DOI: 10.1016/j.cell.2020.06.025.
    16. Robbiani DF, Gaebler C, Muecksch F, Lorenzi JCC, Wang Z, Cho A, Agudelo M, Barnes CO, Gazumyan A, Finkin S, Hägglöf T, Oliveira TY, Viant C, Hurley A, Hoffmann HH, Millard KG, Kost RG, Cipolla M, Gordon K, Bianchini F, Chen ST, Ramos V, Patel R, Dizon J, Shimeliovich I, Mendoza P, Hartweger H, Nogueira L, Pack M, Horowitz J, Schmidt F, Weisblum Y, Michailidis E, Ashbrook AW, Waltari E, Pak JE, Huey-Tubman KE, Koranda N, Hoffman PR, West Jr AP, Rice CM, Hatziioannou T, Bjorkman PJ, Bieniasz PD, Caskey M, Nussenzweig MC. Convergent antibody responses to SARS-CoV-2 in convalescent individuals. Nature, 2020. DOI: 10.1038/s41586-020-2456-9.
    17. Ladinsky MS, Gnanapragasam PNP, Yang Z, West Jr AP, Kay MS, Bjorkman PJ. Electron tomography visualization of HIV-1 fusion with target cells using fusion inhibitors to trap the pre-hairpin intermediate. bioRxiv, 2020. DOI: 10.1101/2020.04.29.068775
    18. Cohen AA, Yang Z, Gnanapragasam P, Ou S, Dam K-M, Wang H, Bjorkman PJ. Construction, characterization, and immunization of nanoparticles that display a diverse array of influenza HA trimers. bioRxiv, 2020.  DOI: 10.1101/2020.01.18.911388

2019

    1. Varuzhanyan G, Rojansky R, Sweredoski MJ, Graham RLJ, Hess S, Ladinsky MS, Chan DC. Mitochondrial fusion is required for spermatogonial differentiation and meiosis. eLife, e51601, 2019. DOI: 10.7554/eLife.51601
    2. Bublitz DC, Chadwick GL, Magyar JS, Sandoz KM, Brooks DM, Mesnage S, Ladinsky MS, Garber AI, Bjorkman PJ, Orphan VJ, McCutcheon JP. Peptidoglycan Production by an Insect-Bacterial Mosaic. Cell 179, 1-10, 2019. DOI:10.1016/j.cell.2019.08.054
    3. Ladinsky MS, Khamaikawin W, Jung Y, Lin S, Lam J, An DS, Bjorkman PJ, Kieffer C. Mechanisms of virus dissemination in bone marrow of HIV-1–infected humanized BLT mice. eLife 8, e46916, 2019. DOI:10.7554/eLife.46916
    4. Yang Z, Wang H, Liu AZ, Gristick HB, Bjorkman PJ. Asymmetric opening of HIV-1 Env bound to CD4 and a coreceptor-mimicking antibody reveals intermediate states induced by CD4 binding. Nature Struct Mol Biol, 2019. DOI:10.1038/s41594-019-0344-5. [Epub ahead of print]
    5. Escolano A*, Gristick HB*, Abernathy ME, Merkenschlager J, Gautam R, Oliveira TY, Pai J, West AP Jr, Barnes CO, Cohen AA, Wang H, Golijanin J, Yost D, Keeffe JR, Wang Z, Zhao P, Yao KH, Bauer J, Nogueira L, Gao H, Voll AV, Montefiori DC, Seaman MS, Gazumyan A, Silva M, McGuire AT, Stamatatos L, Irvine DJ, Wells L, Martin MA, Bjorkman PJ, Nussenzweig MC. Immunization expands B cells specific to HIV-1 V3 glycan in mice and macaques. Nature 570, 468-73, 2019. DOI: 10.1038/s41586-019-1250-z
    6. Schoofs T*, Barnes CO*, Suh-Toma N, Golijanin J, Schommers P, Gruell H, West AP Jr, Bach F, Lee YE, Nogueira L, Georgiev IS, Bailer RT, Czartoski J, Mascola JR, Seaman MS, McElrath MJ, Doria-Rose NA, Klein F, Nussenzweig MC, Bjorkman PJ. Broad and Potent Neutralizing Antibodies Recognize the Silent Face of the HIV Envelope. Immunity 50 (6), 2019. DOI: 10.1016/j.immuni.2019.04.014
    7. Jones C, Asay M, Kim L J, Kleinsasser J, Saha A, Fulton T, Berkley K, Cascio D, Malyutin A, Conley M, Stoltz B, Jose V, Nelson R H. Characterization of reactive organometallic species via MicroED. ChemRxiv 2019. DOI: 10.26434/chemrxiv.7940525.v2.
    8. Kaplan M, Subramanian P, Ghosal D, Oikonomou CM, Pirbadian S, Starwalt-Lee R, Mageswaran SK, Ortega DR, Gralnick JA, El-Naggar MY, Jensen G. In situ imaging of the bacterial flagellar motor disassembly and assembly processes. EMBO 38, 2019. DOI: 10.15252/embj.2018100957
    9. Farhadi A, Ho GH, Sawyer DP, Bourdeau RW, Shapiro MG. Ultrasound imaging of gene expression in mammalian cells. Submitted. bioRxiv 2019. DOI: 10.1101/580647
    10. Ghosal D*, Jeong KC*, Chang Y-W, Gyore J, Teng L, Gardner A, Vogel JP, Jensen G. Molecular architecture, polar targeting and biogenesis of the Legionella Dot/Icm T4SS. Nature Microbiology 2019. DOI: 10.1038/s41564-019-0427-4
    11. Yao Q*, Weaver SJ*, Mock J-Y, Jensen G.J. Fusion of DARPin to Aldolase Enables Visualization of Small Protein by Cryo-EM. Structure 27, 1–8, 2019. DOI: 10.1016/j.str.2019.04.003
    12. Ladinsky MS, Araujo LP, Zhang X, Veltri J, Galan-Diez M, Soualhi S, Lee C, Irie K, Pinker EY, Narushima S, Bandyopadhyay S, Nagayama M, Elhenawy W, Coombes BK, Ferraris RP, Honda K, Iliev ID, Gao N, Bjorkman PJ, Ivanov II. Endocytosis of commensal antigens by intestinal epithelial cells regulates mucosal T cell homeostasis. Science 363, 2019. DOI: 10.1126/eaat4042
    13. Uchil PD, Pi R, Haugh KA, Ladinsky MS, Ventura JD, Barrett BS, Santiago ML, Bjorkman PJ, Kassiotis G, Sewald X, Mothes W. A protective role for the Lectin CD169/Siglec-1 against a pathogenic murine retrovirus. Cell Host and Microbe 25, 87-100, 2019. DOI: 10.1016/j.chom.2018.11.011
    14. Azubel M, Carter SD, Weiszmann J, Zhang J, Jensen GJ, Li Y, Kornberg RD. FGF21 trafficking in intact human cells revealed by cryo-electron tomography with gold nanoparticles. eLife 2019. DOI: 10.7554/eLife.43146
    15. Ghosal D, Kim KW, Zheng H, Kaplan M, Vogel JP, Cianciotto NP, Jensen G. In vivo structure of the Legionella type II secretion system by electron cryotomography. bioRxiv 2019. DOI: 10.1101/525063
    16. Martynowycz MW, Zhao W, Hattne J, Jensen G, Gonen T. Collection of continuous rotation MicroED data from ion beam-milled crystals of any size. Structure 27 (3), 545-548, 2019. DOI: 10.1016/j.str.2018.12.003
    17. Kaplan M, Ghosal D, Subramanian P, Oikonomou CM, Kjaer A, Pirbadian S, Ortega DR, Briegel A, El-Naggar MY, Jensen G. The presence and absence of periplasmic rings in bacterial flagellar motors correlates with stator type. eLife 2019. DOI: 10.7554/eLife.43487
    18. Chreifi G, Chen S, Metskas LA, Kaplan M, Jensen G. Rapid tilt-series acquisition for electron cryotomography. J Struct Bio 205 (2), 163-169, 2019. DOI: 10.1016/j.jsb.2018.12.008

2018

    1. Bourdeau RW, Lee-Gosselin A, Lakshmanan A, Farhadi A, Ravindra Kumar S, Nety ST, Shapiro MG. Acoustic reporter genes for noninvasive imaging of microorganisms in mammalian hosts. Nature 553, 86-90, 2018. Cover article. DOI: 10.1038/nature25021
    2. Wang H*, Barnes CO*, Yang Z, Nussenzweig MC, Bjorkman PJ. Partially-open HIV-1 envelope structures exhibit conformational changes relevant for coreceptor binding and fusion. Cell Host and Microbe 24, 579-592, 2018. DOI: 10.1016/j.chom.2018.09.003
    3. Donaldson GP, Ladinsky MS, Yu KB, Sanders JG, Yoo BB, Chou WC, Conner ME, Earl AM, Knight R, Bjorkman PJ, Mazmanian SK. Gut microbiota utilize immunoglobulin A for mucosal colonization. Science 360, 795-800, 2018. DOI: 10.1126/science.aaq0926
    4. Yao Q*, Weaver SJ*, Mock J-Y, Jensen G. Fusion of DARPin to aldolase enables visualization of small protein by cryoEM. bioRxiv 2018. DOI: 10.1101/455063
    5. Kaplan M, Subramanian P, Ghosal D, Oikonomou CM, Pirbadian S, Starwalt-Lee R, Gralnick JA, El-Naggar MY, Jensen G. Stable sub-complexes observed in situ suggest a modular assembly pathway of the bacterial flagellar motor. bioRxiv 2018. DOI: 10.1101/369405
    6. Ghosal D, Chang Y-W, Jeong KC, Vogel JP, Jensen G. Molecular architecture of the Legionella Dot/Icm type IV secretion system. bioRxiv 2018. DOI: 10.1101/312009, 2018.
    7. Chang Y-W, Shaffer C, Rettberg L, Ghosal D, Jensen G. In vivo structures of the Helicobacter pylori cag type IV secretion system. Cell Reports 23 (3), 673-681, 2018. DOI: 10.1016/j.celrep.2018.03.085
    8. Subramanian P, Pirbadian S, El-Naggar M, Jensen G. Ultrastructure of Shewanella oneidensis MR-1 nanowires revealed by electron cryotomography. PNAS 115 (14), E3246-E3255, 2018. DOI: 10.1073/pnas.1718810115
    9. Auer G, Oliver P, Rajendram M, Yao Q, Jensen G, Weibel D. Bacterial swarming reduces Proteus mirabilis and Vibrio parahaemolyticus cell stiffness and increases β-lactam susceptibility. bioRxiv 2018. DOI: 10.1101/275941
    10. Krause D, Chen S, Shi J, Jensen A, Sheppard E, Jensen G. Electron cryotomography of Mycoplasma pneumoniae mutants correlates terminal organelle architectural features and function. Molecular Microbiology 108 (3), 306-318, 2018. DOI: 10.1111/mmi.13937
    11. Swulius M, Mguyen L, Ladisnky M, Ortega D, Aich S, Mishra M, Jensen G. Structure of the fission yeast actomyosin ring during constriction. PNAS 201711218, 2018. DOI: 10.1073/pnas.1711218115

2017

    1. Lakshmanan A, Lu GJ, Farhadi A, Nety SP, Kunth M, Lee-Gosselin A, Maresca D, Bourdeau RW, Yin M, Yan J, Witte C, Foster FS, Schroder L, Shapiro MG*. Preparation of biogenic gas vesicle nanostructures for use as contrast agents for ultrasound and MRI. Nature Protocols 12, 2050-2080, 2017. DOI: 10.1038/nprot.2017.081
    2. Carter S, Mageswaran S, Farino Z, Mamede J, Oikonomou C, Hope T, Freyberg Z, Jensen G. Distinguishing signal from autofluorescence in cryogenic correlated light and electron microscopy of mammalian cells. Journal of Structural Biology 201 (1), 15-25, 2017. DOI: 10.1016/j.jsb.2017.10.009
    3. Gristick, HB, Wang, H, Bjorkman, PJ. X-ray and EM structures of a natively glycosylated HIV-1 envelope trimer. Acta Cryst. D 73: 822–828, 2017. DOI: 10.1107/S2059798317013353
    4. Kieffer, C, Ladinsky MS, Bjorkman, PJ. Multiscale imaging of HIV-1 transmission in humanized mice. AIDS Res. Hum. Retroviruses 33(S1):S6-S7, 2017. DOI: 10.1089/AID.2017.0142
    5. Wang, H, Gristick, HB, Scharf, L, West, AP, Jr, Galimidi, RP, Seaman, MS, Freund, NT, Nussenzweig, MC, Bjorkman, PJ. Asymmetric recognition of HIV-1 Env trimer by V1V2 loop-targeting antibodies. eLife 6, e27389, 2017. DOI: 10.7554/eLife.27389.001
    6. Gu M, LaJoie D, Chen OS, von Appen A, Ladinsky MS, Redd MJ, Nikolova L, Bjorkman PJ, Sundquist WI, Ullman KS, Frost A. LEM2 recruits CHMP7 for ESCRT-mediated nuclear envelope closure in fission yeast and human cells. PNAS USA 114, E2166-E2175, 2017. DOI: 10.1073/pnas.1613916114
    7. Meier E, Daitch A, Yao Q, Bhargava A, Jensen G, Goley E. FtsEX-mediated regulation of the final stages of cell division reveals morphogenetic plasticity in Caulobacter crescentus. PLoS Genetics 13(9), e1006999. DOI: 10.1371/journal.pgen.1006999
    8. Kieffer C, Ladinsky MS, Ninh A, Galimidi RP, Bjorkman PJ. Longitudinal imaging of HIV-1 spread in humanized mice with parallel 3D immunofluorescence and electron tomography. eLife 6, e23282, 2017. DOI: 10.7554/eLife.23282.001
    9. Freund, NT, Wang, H, Scharf, L, Nogueira, L, Horwitz, JA, Bar-On, Y, Golijanin, J, Sievers, SA, Sok, D, Cai, H, Cesar Lorenzi, JC, Halper-Stromberg, A, Toth, I, Piechocka-Trocha, A, Gristick, HB, van Gils, MJ, Sanders, RW, Wang, L-X, Seaman, MS, Burton, DR, Gazumyan, A, Walker, BD, West, AP, Bjorkman, PJ, Nussenzweig, MC. Coexistence of potent HIV-1 broadly neutralizing antibodies and antibody-sensitive viruses in a viremic controller. Sci Transl Med 9, eaal2144, 2017. DOI: 10.1126/scitranslmed.aal2144
    10. Zielinska A, Billini M, Moll A, Kremer K, Briegel A, Martinez A, Jensen G, Thanbichler M. LytM factors affect the recruitment of autolysins to the cell division site in Caulobacter crescentus. Molecular Microbiology 106 (3), 419-438, 2017. DOI: 10.1111/mmi.13775
    11. Kaplan M, Yoo B, Tang J, Karam T, Liao B, Majumdar B, Baltimore D, Jensen G, Zewail A. Photon-induced near-field electron microscopy (PINEM) of eukaryotic cells. Angewandte Chemie International Edition 56 (38), 11498-11501, 2017. DOI: 10.1002/anie.201706120
    12. Briegel A, Oikonomou C, Chang Y-W, Kjaer A, Huang A, Kim K, Ghosal D, Nguyen H, Kenny D, Ogorzalek Loo R, Gunsalus R, Jensen G. Morphology of the archaellar motor and associated cytoplasmic cone in Thermococcus kodakaraensis. EMBO Reports e201744070, 2017. DOI: 10.15252/embr.201744070
    13. Jeong K, Ghosal D, Chang Y-W, Jensen G, Vogel J. Polar delivery of Legionella type IV secretion system substrates is essential for virulence. PNAS 201621438, 2017. DOI: 10.1073/pnas.1621438114
    14. Dobro MJ, Oikonomou CM, Piper A, Cohen J, Guo K, Jensen T, Tadayon J, Donermeyer J, Park Y, Solis BA, Kjaer A, Jewett AI, McDowall AW, Chen S, Chang Y-W, Shi J, Subramanian P, Iancu CV, Li Z, Briegel A, Tocheva EI, Pilhofer M, Jensen GJ. Uncharacterized bacterial structures revealed by electron cryotomography. J.Bacteriology 2017.  DOI: 10.1128/JB.00100-17