Publications

“We render a tribute of respect to those that add original work to a library, and withhold it from those who carry a library around in their head. Our neurons should be used for more substantial things. Not only to know but also to transform knowledge; not only to experience but also to construct”. Ramon y Cajal.

IMG_0450.JPG

85. Seffouh A, Trahan C, Wasi T, Jain N, Basu K, Britton RA, Oeffinger M and Ortega J. RbgA Ensures the Correct Timing in the Maturation of the Functional Sites in the 50S Ribosomal Subunit. (2022). Nucleic Acids Research. In press.

84. Sun B, Ghosh S, Quinn B, He X, Tian M, Jahagirdar D, Mabrouk M, Ortega J, Shao S, Lovell J. Anti-cancer liposomal chemophototherapy using bilayer-localized photosensitizer and cabazitxel. (2022). Nano Research. In press.

83. He X, Zhou S, Quinn B, Jahagirdar D, Ortega J, Abrams SC and Lovell JF. An In Vivo Screen to Identify Short Peptide Mimotopes with Enhanced Anti-Tumor Immunogenicity. (2022). Cancer Immunology Research. In press.

82. He X, Zhou S, Dolan M, Shi Y, Wang J, Quinn B, Jahagirdar D, Huang WC, Tsuji M, Pili R, Ito F, Ortega J, Abrams SI, Ebos JML, Lovell J. Immunization with Short Peptide Particles Reveals a Functional CD8+ Neoepitope in a Murine Renal Carcinoma Model. (2021). Journal of Immunotherapy of Cancer. 9: e003101.

81. Mabrouk MT, Chiem K, Rujas E, Huang WC, Jahagirdar D, Nissly RH, Kuchipudi SV, Ortega J, Julien JP, Martinez-Sobrido L, Lovell J. Lyophilized, Thermostable Spike or RBD Immunogenic Liposomes Induce Protective Immunity Against SARS-CoV-2 in Mice. (2021). Science Advances. 7: eabj1476.

80. Shen Y, Gomez-Blanco J, Peters JE, Ortega J, Guarne A. TnsC determines the strict spacing between the target and insertion sites in Tn7 transposition. (2021). Nature Structural and Molecular Biology. In press.

79. He X, Zhou S, Quinn B, Jahagirdar D, Vega M, Ortega J, Abrams SC and Lovell JF. Position-Scanning Peptide Libraries as Particle Immunogens for Improving CD8+ T Cell Responses. (2021). Advanced Science. In press.

78. Kilian H, Pradhan AJ, Jahagirdar D, Ortega J, Atilla-Gokcumen GE and Lovell J. Light-triggered Release of Large Biomacromolecules from Porphyrin-phospholipid Liposomes. (2021). Langmuir. 37: 10859-10865.

77. Mabrouk M, Zhang H, Zidan A, Kilian H, Huang WC, Jahagirdar D, Ortega J, Xia J, Lovell J. Crosslinked Histone as a Nanocarrier for Gut Delivery of Hydrophobic Cargos. (2021). ACS Applied Materials & Interfaces. 13: 26712-26720.

76. Sia ZR, He X, Ang JC, Shao S, Seffouh A, Huang WC, D'Agostino M, Dereshgi AT, Suryaprakash S, Ortega J, Andersen H, Miller MS, Davidson B, Lovell JF. A liposome-displayed hemagglutinin vaccine platform protects mice and ferrets from heterologous influenza virus challenge. (2021). PNAS. 118 (22) e2025759118.

75. He X, Zhou S, Huang W, Seffouh A, Mabrouk MT, Morgan MT, Ortega J, Abrams S, Lovell JF. A Potent Cancer Vaccine Adjuvant for Particleization of Short, Synthetic CD8+ Epitopes. (2021). ACS Nano. 15: 4357-4371.

74. Federizon JF, Giresse C, Feugmo CGT, Huang WC, He X, Miura K, Razi A, Ortega J, Karttune M, Lovell JF. Experimental and Computational Observations of Immunogenic Cobalt Porphyrin Lipid Bilayers: Nanodomain-enhanced Antigen Association (2021). Pharmaceutics. 13: 98.
 
73. He X, Zhou S, Quinn B, Jahagirdar D, Ortega J, Abrams SI, Lovell JF. HPV-Associated Tumor Eradication by Vaccination with Synthetic Short Peptides and Particle-Forming Liposomes. (2021). Small. 17: e2007165.

72. Vikash J, Roy B, Jahagirdar D, McNutt Z, Shatoff E, Boleratz B, Watkins DE, Bundschuh R, Basu K, Fredrick K, Ortega J. Structural basis of sequestration of the Anti-Shine-Dalgarno sequence in the Bacteroidetes ribosome. (2020). NAR. 49: 547-567.

71. Huang WC, Zhou S, Mabrouk MT, Nissly RH, Strauss M, Sambhara S, Ortega J, Wohlfert EA, Kuchipudi SV, Davidson BA, Lovell JF. The SARS-CoV-2 RBD Neutralizing Antibody Response is Enhanced by Particulate Presentation. (2020). Advanced Materials. . 589: 119843
 
70. Jahagirdar D, Jha V, Basu K, Gomez-Blanco J, Vargas J, and Ortega J. Alternative Conformations and Motions Adopted by 30S Ribosomal Subunits Visualized by Cryo-Electron Microscopy. (2020). RNA. 26: 2017-2030.

69. Mabrouk MT, Huang WC, Deng B, Li-Purcell N, Seffouh A, Ortega J, Atilla-Gokcumen GE, Long C, Miura K and Lovell JF. Lyophilized, antigen-bound liposomes with reduced MPLA and enhanced thermostability. (2020). International Journal of Pharmaceutics. 589: 119843.

68. Huang WC, Deng B, Mabrouk M, Seffouh A, Ortega J, Long C, Miura K, Wu Y, Lovell JF. Particle-based, Pfs230 and Pfs25 immunization is effective, but not improved by duplexing at fixed total antigen dose. (2020). Malaria Journal. 19:309. 

67. Huang WC, Deng B, Seffouh A, Ortega J, Long C, Miura K, Wu Y, Lovell JF. Antibody Response of a Particle-Inducing, Liposome Vaccine Adjuvant Admixed with a Pfs230 Fragment. (2020). Nature Partner Journals-vaccines. 18 (5): 23. 

66. Sun B, Chitgupi U, Li C, Federizon JF, Zhang C, Ruszaj DM, Razi A, Ortega J, Neelamegham S, Zhang Y, Lovell JF. Surfactant-stripped Cabazitaxel Micelles Stabilized by Clotrimazole or Mifepristone. (2019). Advance therapeutics. 3:1900161. 

65. Gomez-Blanco J, Kaur S, Ortega J, Vargas J. A robust approach to ab initio cryo-electron microscopy initial volume determination. (2019). JSB. S1047-8477: 30208-4.

64. Seffouh A, Jain N, Jahagirdar D, Basu K, Razi A, Ni X, Guarne A, Britton RA and Ortega J.RbgA Triggers Folding of the 50S Subunit Functional Sites. (2019). NAR. 47: 10414–10425.

63.Nanji T, Gehrke E, Shen Y, Gloyd M, Zhang X, Firby C, Huynh A, Razi A, Ortega J, Elliot M, and Guarne A.  Streptomyces IHF uses multiple interfaces to bind DNA. (2019). BBA General Subjects. 1863: 129405. 

62. Razi A, Davis JH, Hao Y, Jahagirdar D, Thurlow B, Basu K, Jain N, Gomez-Blanco J, Britton RA, Vargas J, Woodson S, Guarné A, Williamson JR and Ortega J. Role of Era in Assembly and Homeostasis of the Ribosomal Small Subunit (2019). Nucleic Acids Research. 47:8301-8317.

61. Miranda D, Huang H, Kang H, Zhan Y, Wang D, Zhou Y, Geng J, Kilian H, Stiles W, Razi A,Ortega J, Xia J, Choi HS, Lovell JF.Highly-Soluble Cyanine J-aggregates Entrapped by Liposomes for In Vivo Optical Imaging around 930 nm. (2018). Theranostics. 9:381-390. 

60. Macháčeka M, Carter KA, Kostelanský F, Miranda D, Seffouh A, Ortega J, Šimůnek T, Zimčík P and Lovell JF. Binding of an amphiphilic phthalocyanine to pre-formed liposomes confers light-triggered cargo release. (2018). Journal of Materials Chemistry B. 6:7298-7305.

59. Huang W, Deng B, Lin C, Carter KA, Geng J, Razi A, He X, Chitgupi U, Federion, Sun JB, Long CA, Ortega J, Dutta S, King CR, Miura K, Lee SM and Lovell JF. A Potent Malaria Vaccine Adjuvant Based on Spontaneous Nanoliposome-Antigen Particleization. (2018). Nature Nanotechnology. 13:1174-1181.

58. Fu Y, Long M, Wisitpitthaya S, Inayat H, Pierpont T, Elsaid I, Bloom J, Ortega J, Weiss R and Aye Y. Nuclear RNR-αAntagonizes Cell Proliferation by Directly Inhibiting ZRANB3. (2018). Nature Chemical Biology. 14:943-954.

57. Algamal M, Jafari N, Ahsan B, Ortega J and Melacini G. Atomic-Resolution Map of the Interactions between an Amyloid Inhibitory Protein and Aβ Peptides in the Monomeric and Protofibrillar States. (2017). JBC. 292(42):17158-17168. 
 
56. Ashton A, Chambers M, Chen S, Cheng A, Ebrahim M, Eng E, Hagen W, Koster A, López C, Lukoyanova N, Ortega J, Schrijver R, Renault L, Reyntjens S, Rice W, Scapin G, Siebert A, Stagg S, Grum-Tokars V, Wright E, Wu S, Yu Z, Zhou H, Carragher B and Clinton S.Potter. Best Practices for Managing Large CryoEM Facilities. (2017). J. Struct. Biol. 199(3):225-236. 
 
55. Ahmed R, VanSchouwen B, Jafari N, Ni X, Ortega J and Melacini G. A Molecular Mechanism for the EGCG-Induced Toxic to Non-Toxic Remodeling of Aβ Oligomers. (2017). JACS. 139(39):13720-13734.

54. Razi A and Ortega J. Ribosomal Proteins: Their role in the assembly, structure and function of the ribosome. (2017). eLS John Wiley & Sons Ltd, Chichester. http://www.els.net [doi: 10.1002/9780470015902.a0000535.pub2].

53. Manhart CM, Ranjha L, Ni X, White M. A, Ortega J, Surtees J, Cejka P, Alani A. The meiotic recombination endonuclease Mlh1-Mlh3 is activated by polymer formation and directed by Msh4-Msh5. (2017). PLoS Biology 15: e2001164

52. Razi A and Ortega J. The cryo-EM structure of YjeQ bound to the 30S subunit suggests a fidelity checkpoint function for this protein in ribosome assembly. (2017). PNAS. 114: E3396-E3403.

51. Razi A and Ortega J. Final touches and quality control on the assembly of the eukaryotic ribosome. (2017). EMBO J. 114: E3396-E3403. 

50. Razi A, Britton RA and Ortega J. The Impact of Recent Improvements in Cryo-electron Microscopy Technology on the Understanding of Bacterial Ribosome Assembly. (2017). Nucleic Acids Research. 45:1027-1040.

49. Shao S, Do TN, Razi A, Dzikovski BG, Ortega J, Karttunen M, Spernyak JA, and Lovell JF. Design of Hydrated Bilayers via Amine-Modified Porphyrin-phospholipids. Small. (2016). 13(1).

48. Ni X, Davis J.H, Jain N, Razi A, Benlekbir S, McArthur A, Rubinstein J, Britton R, Williamson J.R and Ortega J. YphC and YSxC GTPases contribute to the maturation of the central protuberance and functional core the 50S ribosomal subunit. (2016). Nucleic Acids Research. 44:8442-8455.

47. Thurlow B, Leong V, Davis J.H, Moraes T, Williamson J.R and Ortega J. Binding properties of YjeQ, RbfA, RimM and Era to assembly intermediates of the 30S subunit.  (2016). Nucleic Acids Research. 44:9918-9932

46. Carter KA, Luo D, Razi A, Geng J, Shao S, Ortega J, Lovell JF. Sphingomyelin Liposomes Containing Porphyrin-phospholipid for Irinotecan Chemophototherapy. (2016). Theranostics. 6:2329-2336

45. Mottillo E, Desjardins E, Crane J, Smith B, Green A, Ducommun S, Henriksen T, Rebalka I, Razi A, Sakamoto K, Scheele C, Kemp B, Hawke T, Ortega J, Granneman J and Steinberg G. Lack of Adipocyte AMPK Exacerbates Insulin Resistance and Hepatic Steatosis through Brown and Beige Adipose Tissue Function. (2016). Cell Metabolism. In press.

44. Luo D, Carter KA, Razi A, Shao S, Geng J, Shao S, Lin C, Ortega J, Lovell JF. Porphyrin-Liposomes with Tunable Leakiness. (2015). Journal of Controlled Release. 220:484-494.

43. Luo D, Carter KA, Razi A, Geng J, Shao S, Giraldo D, Sunar U, Ortega J, Lovell JF. Doxorubicin Encapsulated in Stealth Liposomes Conferred with Light-Triggered Drug Release. (2015). Biomaterials. 75:193-202.
 
42. Jeganathan A, Razi A, Thurlow B and OrtegaJ. YjeQ zinc finger domain monitors the conformation of the decoding center and catalyzes the release of RbfA during 30S ribosome subunit assembly. (2015). RNA. 21: 1203-1206.
 
41. Jeganathan A, Leong V, Huen J, Zhao L, Nano N, Houry WA & Ortega J. Yeast Rvb1 and Rvb2 proteins oligomerize as a conformationally variable dodecamer with low frequency. (2015). J. Mol. Biol. 427: 1975-1886.

40. Jones SE, Leong V, Ortega J & Elliot M. Development, antibiotic production and ribosome assembly are impacted by RNase J and RNase III in Streptomyces venezuelae. (2014). J. Bacteriol. 196(24) : 4253-67. 
 
39. Ban N, Beckman R, Cate J.H.D, Dinman J.D, Ellis S.R, Lafontaine, D.L.J, Lindahl L, Lijas A, McAlear M.A, Moore P, Noller H, Ortega J, Govind Panse V, Ramakrishnan V, Spahn, C.M.T., Steitz T.A, Tchorzewski M, Tollervey D, Williamson J.R, Wilson D, Yonath A, Yusopov M. A new system for naming ribosomal proteins. (2014). Current Opinion in Structural Biology. 24:165-169.
 
38. Carter K, Shao S, Hoopes M, Song W, Huang H, Zhang, G, Ahsan B, Pandey R. K, Pfeifer B. A, Ortega J, Kartunen M, Lovell J. Stable porphyrin-phospholipid doped liposomes permeabilized by near infrared light. (2014). Nature Communications. 5:3546. 
 
37. Jomaa A,, Jain N, Davis J.H, Achila D., , Gulati M, Williamson J.R, Britton R.A & Ortega J. Role of the GTPases RbgA in the late stages of assembly of the 50S subunit in Bacillus subtilis. (2014) Nucleic Acids Res. 42:3419-3435. 
 
36. Cheng C, Jomaa A, Ortega J & Alani E. Pch2 is a meiotic hexameric ATPase that binds to and alters Hop1 DNA binding properties. (2014). PNAS. 111:E44-53.

35. Sowole M, Alexopoulos J, Cheng Y-Q, Ortega J & Konermann L. Activation of the ClpP protease by acyldepsipeptide antibiotics: insights from hydrogen exchange mass spectrometry. (2013). J. Mol. Biol. 425:4508-4519.

34. Alexopoulos J, Ahsan B, Homchaudhuri L, Husain N, Cheng Y-Q & Ortega J. Structural determinants stabilizing the axial channel of ClpP for substrate translocation. (2013). Molecular Microbiology. 90: 167-180.
Leong V, Kent M, Jomaa A & Ortega J. Escherichia coli rimM and yjeQ null strains accumulate a structurally similar immature 30S subunits of comparable protein complement.  (2013). RNA. 19: 789-802.

33. Alexopoulos JA, Guarne A and Ortega J. ClpP: A Structurally Dynamic Protease Regulated by AAA+ Proteins. (2012). J Struct Biol. 179: 202-210.
32. Jomaa A, Stewart G, Mears JA, Kireeva I, Brown ED & Ortega J. Cryo-electron Microscopy Structure of the 30S Subunit in Complex with the YjeQ Biogenesis Factor. (2011). RNA. 17: 2026-2038. 

31. Capstick DS, Jomaa A, Christopher H, Ortega J & Elliot M. Dual amyloid domains promote different functioning of the chaplin proteins during Streptomyces aerial morphogenesis. (2011). PNAS. 108(24):9821-9826.

30. Iwanczyk J, Leong V & Ortega J. Factors Defining the Functional Oligomeric State of Escherichia coli DegP Protease. (2011). PLoS one. 6(4): e18994.
 
29. Jomaa A, Stewart G, Martín-Benito J, Zielke R, Campbell TL, Maddock JR, Brown ED & Ortega J. Understanding Ribosome Assembly: the Structure of in vivo Assembled Immature 30S Subunits Revealed by Cryo-electron Microscopy. (2011). RNA. 17: 697-709.