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2. Vaccine induction of heterologous HIV-1-neutralizing antibody B cell lineages in humans

Author

Williams, Wilton B., Alam, S. Munir, Ofek, Gilad, Erdmann, Nathaniel, Montefiori, David C., Seaman, Michael S., Wagh, Kshitij, Korber, Bette, Edwards, Robert J., Mansouri, Katayoun, Eaton, Amanda, Cain, Derek W., Martin, Mitchell, Hwang, JongIn, Arus-Altuz, Aria, Lu, Xiaozhi, Cai, Fangping, Jamieson, Nolan, Parks, Robert, Barr, Maggie, Foulger, Andrew, Anasti, Kara, Patel, Parth, Sammour, Salam, Parsons, Ruth J., Huang, Xiao, Lindenberger, Jared, Fetics, Susan, Janowska, Katarzyna, Niyongabo, Aurelie, Janus, Benjamin M., Astavans, Anagh, Fox, Christopher B., Mohanty, Ipsita, Evangelous, Tyler, Chen, Yue, Berry, Madison, Kirshner, Helene, Van Itallie, Elizabeth, Saunders, Kevin O., Wiehe, Kevin, Cohen, Kristen W., McElrath, M. Juliana, Corey, Lawrence, Acharya, Priyamvada, Walsh, Stephen R., Baden, Lindsey R., and Haynes, Barton F.

Published
2024
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3. The inner disk of RY Tau: evidence of stellar occultation by the disk atmosphere at the sublimation rim from K-band continuum interferometry

Author

Davies, Claire L., Kraus, Stefan, Harries, Tim J., Monnier, John D., Kloppenborg, Brian, Aarnio, Alicia, Baron, Fabien, Lopez, Rebeca Garcia, Millan-Gabet, Rafael, Parks, Robert, Pedretti, Ettore, Perraut, Karine, Sturmann, Judit, Sturmann, Laszlo, Brummelaar, Theo A. ten, and Touhami, Yamina

Subjects
Astrophysics - Solar and Stellar Astrophysics, Astrophysics - Earth and Planetary Astrophysics, Astrophysics - Astrophysics of Galaxies
Abstract

We present models of the inner region of the circumstellar disk of RY Tau which aim to explain our near-infrared ($K$-band: $2.1\,\mu$m) interferometric observations while remaining consistent with the optical to near-infrared portions of the spectral energy distribution. Our sub-milliarcsecond resolution CHARA Array observations are supplemented with shorter baseline, archival data from PTI, KI and VLTI/GRAVITY and modeled using an axisymmetric Monte Carlo radiative transfer code. The $K$-band visibilities are well-fit by models incorporating a central star illuminating a disk with an inner edge shaped by dust sublimation at $0.210\pm0.005\,$au, assuming a viewing geometry adopted from millimeter interferometry ($65^{\circ}$ inclined with a disk major axis position angle of $23^{\circ}$). This sublimation radius is consistent with that expected of Silicate grains with a maximum size of $0.36-0.40\,\mu$m contributing to the opacity and is an order of magnitude further from the star than the theoretical magnetospheric truncation radius. The visibilities on the longest baselines probed by CHARA indicate that we lack a clear line-of-sight to the stellar photosphere. Instead, our analysis shows that the central star is occulted by the disk surface layers close to the sublimation rim. While we do not see direct evidence of temporal variability in our multi-epoch CHARA observations, we suggest the aperiodic photometric variability of RY~Tau is likely related temporal and/or azimuthal variations in the structure of the disk surface layers., Comment: Accepted for publication in The Astrophysical Journal

Published
2020
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4. Vaccine-mediated protection against Merbecovirus and Sarbecovirus challenge in mice

Author

Martinez, David R., Schäfer, Alexandra, Gavitt, Tyler D., Mallory, Michael L., Lee, Esther, Catanzaro, Nicholas J., Chen, Haiyan, Gully, Kendra, Scobey, Trevor, Korategere, Pooja, Brown, Alecia, Smith, Lena, Parks, Robert, Barr, Maggie, Newman, Amanda, Bowman, Cindy, Powers, John M., Soderblom, Erik J., Mansouri, Katayoun, Edwards, Robert J., Baric, Ralph S., Haynes, Barton F., and Saunders, Kevin O.

Published
2023
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5. Correction for Kibler et al., “Replication-Competent NYVAC-KC Yields Improved Immunogenicity to HIV-1 Antigens in Rhesus Macaques Compared to Nonreplicating NYVAC”

Author

Kibler, Karen V, Asbach, Benedikt, Perdiguero, Beatriz, García-Arriaza, Juan, Yates, Nicole L, Parks, Robert, Stanfield-Oakley, Sherry, Ferrari, Guido, Montefiori, David C, Tomaras, Georgia D, Roederer, Mario, Foulds, Kathryn E, Forthal, Donald N, Seaman, Michael S, Self, Steve, Gottardo, Raphael, Phogat, Sanjay, Tartaglia, James, Barnett, Susan, Cristillo, Anthony D, Weiss, Deborah, Galmin, Lindsey, Ding, Song, Heeney, Jonathan L, Esteban, Mariano, Wagner, Ralf, Pantaleo, Giuseppe, and Jacobs, Bertram L

Subjects
Medical Microbiology, Biomedical and Clinical Sciences, Immunology, Good Health and Well Being, Biological Sciences, Agricultural and Veterinary Sciences, Medical and Health Sciences, Virology, Agricultural, veterinary and food sciences, Biological sciences, Biomedical and clinical sciences
Abstract

Volume 93, no. 3, e01513-18, 2019, https://doi.org/10.1128/JVI.01513-18. The article was originally published on 17 January 2019 with a standard copyright line (“© 2019 American Society for Microbiology. All Rights Reserved.”). We elected to pay for open access for the article after publication, necessitating replacement of the original copyright line with “© 2019 Kibler et al. This is an open-access article distributed under the terms of the Creative Commons Attribution 4.0 International license.” This change was made to the online version of the article on 21 August 2019.

Published
2019

6. A HIV-1 Gp41 Peptide-Liposome Vaccine Elicits Neutralizing Epitope-Targeted Antibody Responses in Healthy Individuals

Author

Erdmann, Nathan B., primary, Williams, Wilton B, additional, Walsh, Stephen R., additional, Grunenberg, Nicole, additional, Edlefsen, Paul T., additional, Goepfert, Paul A., additional, Cain, Derek W., additional, Cohen, Kristen W., additional, Maenza, Janine, additional, Mayer, Kenneth H., additional, Tieu, Hong Van, additional, Sobieszczyk, Magdalena E., additional, Swann, Edith, additional, Lu, Helen, additional, De Rosa, Stephen C., additional, Sagawa, Zachary, additional, Moody, M. Anthony, additional, Fox, Christopher B., additional, Ferrari, Guido, additional, Edwards, R. J., additional, Acharya, Priyamvada, additional, Alam, S. Munir, additional, Parks, Robert, additional, Barr, Margaret, additional, Tomaras, Georgia D., additional, Montefiori, David C., additional, Gilbert, Peter B., additional, McElrath, M. Juliana, additional, Corey, Lawrence, additional, Haynes, Barton F., additional, and Baden, Lindsey R., additional

Published
2024
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7. Breadth of SARS-CoV-2 neutralization and protection induced by a nanoparticle vaccine

Author

Li, Dapeng, Martinez, David R., Schäfer, Alexandra, Chen, Haiyan, Barr, Maggie, Sutherland, Laura L., Lee, Esther, Parks, Robert, Mielke, Dieter, Edwards, Whitney, Newman, Amanda, Bock, Kevin W., Minai, Mahnaz, Nagata, Bianca M., Gagne, Matthew, Douek, Daniel C., DeMarco, C. Todd, Denny, Thomas N., Oguin, III, Thomas H., Brown, Alecia, Rountree, Wes, Wang, Yunfei, Mansouri, Katayoun, Edwards, Robert J., Ferrari, Guido, Sempowski, Gregory D., Eaton, Amanda, Tang, Juanjie, Cain, Derek W., Santra, Sampa, Pardi, Norbert, Weissman, Drew, Tomai, Mark A., Fox, Christopher B., Moore, Ian N., Andersen, Hanne, Lewis, Mark G., Golding, Hana, Seder, Robert, Khurana, Surender, Baric, Ralph S., Montefiori, David C., Saunders, Kevin O., and Haynes, Barton F.

Published
2022
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8. Mouse and human antibodies bind HLA-E-leader peptide complexes and enhance NK cell cytotoxicity

Author

Li, Dapeng, Brackenridge, Simon, Walters, Lucy C., Swanson, Olivia, Harlos, Karl, Rozbesky, Daniel, Cain, Derek W., Wiehe, Kevin, Scearce, Richard M., Barr, Maggie, Mu, Zekun, Parks, Robert, Quastel, Max, Edwards, Robert J., Wang, Yunfei, Rountree, Wes, Saunders, Kevin O., Ferrari, Guido, Borrow, Persephone, Jones, E. Yvonne, Alam, S. Munir, Azoitei, Mihai L., Gillespie, Geraldine M., McMichael, Andrew J., and Haynes, Barton F.

Published
2022
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9. Replication-Competent NYVAC-KC Yields Improved Immunogenicity to HIV-1 Antigens in Rhesus Macaques Compared to Nonreplicating NYVAC.

Author

Kibler, Karen V, Asbach, Benedikt, Perdiguero, Beatriz, García-Arriaza, Juan, Yates, Nicole L, Parks, Robert, Stanfield-Oakley, Sherry, Ferrari, Guido, Montefiori, David C, Tomaras, Georgia D, Roederer, Mario, Foulds, Kathryn E, Forthal, Donald N, Seaman, Michael S, Self, Steve, Gottardo, Raphael, Phogat, Sanjay, Tartaglia, James, Barnett, Susan, Cristillo, Anthony D, Weiss, Deborah, Galmin, Lindsey, Ding, Song, Heeney, Jonathan L, Esteban, Mariano, Wagner, Ralf, Pantaleo, Giuseppe, and Jacobs, Bertram L

Subjects
Medical Microbiology, Biomedical and Clinical Sciences, Immunology, Vaccine Related (AIDS), Biotechnology, Prevention, Immunization, HIV/AIDS, Vaccine Related, Infectious Diseases, Prevention of disease and conditions, and promotion of well-being, 3.4 Vaccines, Infection, Good Health and Well Being, Animals, Antibodies, Neutralizing, CD4-Positive T-Lymphocytes, HIV Antibodies, HIV Antigens, HIV Infections, HIV-1, Humans, Macaca mulatta, Male, Vaccination, Vaccinia virus, Viral Vaccines, Virus Replication, env Gene Products, Human Immunodeficiency Virus, Gag-Pol-Nef, HIV, NYVAC, NYVAC-KC, T cell response, antibody responses, gp140, nonhuman primates, vaccines, Biological Sciences, Agricultural and Veterinary Sciences, Medical and Health Sciences, Virology, Agricultural, veterinary and food sciences, Biological sciences, Biomedical and clinical sciences
Abstract

As part of the continuing effort to develop an effective HIV vaccine, we generated a poxviral vaccine vector (previously described) designed to improve on the results of the RV144 phase III clinical trial. The construct, NYVAC-KC, is a replication-competent, attenuated recombinant of the vaccinia virus strain NYVAC. NYVAC is a vector that has been used in many previous clinical studies but is replication deficient. Here, we report a side-by-side comparison of replication-restricted NYVAC and replication-competent NYVAC-KC in a nonhuman primate study, which utilized a prime-boost regimen similar to that of RV144. NYVAC-C and NYVAC-C-KC express the HIV-1 antigens gp140, and Gag/Gag-Pol-Nef-derived virus-like particles (VLPs) from clade C and were used as the prime, with recombinant virus plus envelope protein used as the boost. In nearly every T and B cell immune assay against HIV-1, including neutralization and antibody binding, NYVAC-C-KC induced a greater immune response than NYVAC-C, indicating that replication competence in a poxvirus may improve upon the modestly successful regimen used in the RV144 clinical trial.IMPORTANCE Though the RV144 phase III clinical trial showed promise that an effective vaccine against HIV-1 is possible, a successful vaccine will require improvement over the vaccine candidate (ALVAC) used in the RV144 study. With that goal in mind, we have tested in nonhuman primates an attenuated but replication-competent vector, NYVAC-KC, in direct comparison to its parental vector, NYVAC, which is replication restricted in human cells, similar to the ALVAC vector used in RV144. We have utilized a prime-boost regimen for administration of the vaccine candidate that is similar to the one used in the RV144 study. The results of this study indicate that a replication-competent poxvirus vector may improve upon the effectiveness of the RV144 clinical trial vaccine candidate.

Published
2019

10. Priming with a Potent HIV-1 DNA Vaccine Frames the Quality of Immune Responses prior to a Poxvirus and Protein Boost.

Author

Asbach, Benedikt, Kibler, Karen V, Köstler, Josef, Perdiguero, Beatriz, Yates, Nicole L, Stanfield-Oakley, Sherry, Tomaras, Georgia D, Kao, Shing-Fen, Foulds, Kathryn E, Roederer, Mario, Seaman, Michael S, Montefiori, David C, Parks, Robert, Ferrari, Guido, Forthal, Donald N, Phogat, Sanjay, Tartaglia, James, Barnett, Susan W, Self, Steven G, Gottardo, Raphael, Cristillo, Anthony D, Weiss, Deborah E, Galmin, Lindsey, Ding, Song, Heeney, Jonathan L, Esteban, Mariano, Jacobs, Bertram L, Pantaleo, Giuseppe, and Wagner, Ralf

Subjects
Medical Microbiology, Biomedical and Clinical Sciences, Immunology, Prevention, Vaccine Related, HIV/AIDS, Biotechnology, Immunization, Rare Diseases, Vaccine Related (AIDS), Prevention of disease and conditions, and promotion of well-being, 3.4 Vaccines, Infection, Good Health and Well Being, Animals, Antibodies, Neutralizing, HIV Antibodies, HIV Antigens, HIV Infections, HIV-1, Humans, Macaca mulatta, Male, Poxviridae, T-Lymphocytes, Vaccination, Vaccines, DNA, Vaccinia virus, Viral Vaccines, Virus Replication, DNA vaccine, Gag-Pol-Nef, NYVAC, NYVAC-KC, T cell responses, antibody responses, gp140, human immunodeficiency virus, nonhuman primates, vaccine, Biological Sciences, Agricultural and Veterinary Sciences, Medical and Health Sciences, Virology, Agricultural, veterinary and food sciences, Biological sciences, Biomedical and clinical sciences
Abstract

The use of heterologous immunization regimens and improved vector systems has led to increases in immunogenicity of HIV-1 vaccine candidates in nonhuman primates. In order to resolve interrelations between different delivery modalities, three different poxvirus boost regimens were compared. Three groups of rhesus macaques were each primed with the same DNA vaccine encoding Gag, Pol, Nef, and gp140. The groups were then boosted with either the vaccinia virus strain NYVAC or a variant with improved replication competence in human cells, termed NYVAC-KC. The latter was administered either by scarification or intramuscularly. Finally, macaques were boosted with adjuvanted gp120 protein to enhance humoral responses. The regimen elicited very potent CD4+ and CD8+ T cell responses in a well-balanced manner, peaking 2 weeks after the boost. T cells were broadly reactive and polyfunctional. All animals exhibited antigen-specific humoral responses already after the poxvirus boost, which further increased following protein administration. Polyclonal reactivity of IgG antibodies was highest against HIV-1 clade C Env proteins, with considerable cross-reactivity to other clades. Substantial effector functional activities (antibody-dependent cell-mediated cytotoxicity and antibody-dependent cell-mediated virus inhibition) were observed in serum obtained after the last protein boost. Notably, major differences between the groups were absent, indicating that the potent priming induced by the DNA vaccine initially framed the immune responses in such a way that the subsequent boosts with NYVAC and protein led only to an increase in the response magnitudes without skewing the quality. This study highlights the importance of selecting the best combination of vector systems in heterologous prime-boost vaccination regimens.IMPORTANCE The evaluation of HIV vaccine efficacy trials indicates that protection would most likely correlate with a polyfunctional immune response involving several effector functions from all arms of the immune system. Heterologous prime-boost regimens have been shown to elicit vigorous T cell and antibody responses in nonhuman primates that, however, qualitatively and quantitatively differ depending on the respective vector systems used. The present study evaluated a DNA prime and poxvirus and protein boost regimen and compared how two poxvirus vectors with various degrees of replication capacity and two different delivery modalities-conventional intramuscular delivery and percutaneous delivery by scarification-impact several immune effectors. It was found that despite the different poxvirus boosts, the overall immune responses in the three groups were similar, suggesting the potent DNA priming as the major determining factor of immune responses. These findings emphasize the importance of selecting optimal priming agents in heterologous prime-boost vaccination settings.

Published
2019

11. The transcription factor CREB1 is a mechanistic driver of immunogenicity and reduced HIV-1 acquisition following ALVAC vaccination

Author

Tomalka, Jeffrey Alan, Pelletier, Adam Nicolas, Fourati, Slim, Latif, Muhammad Bilal, Sharma, Ashish, Furr, Kathryn, Carlson, Kevin, Lifton, Michelle, Gonzalez, Ana, Wilkinson, Peter, Franchini, Genoveffa, Parks, Robert, Letvin, Norman, Yates, Nicole, Seaton, Kelly, Tomaras, Georgia, Tartaglia, Jim, Robb, Merlin L., Michael, Nelson L., Koup, Richard, Haynes, Barton, Santra, Sampa, and Sekaly, Rafick Pierre

Published
2021
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12. Discovery and Characterization of a Pan-betacoronavirus S2-binding antibody

Author

Johnson, Nicole V., primary, Wall, Steven C., additional, Kramer, Kevin J., additional, Holt, Clinton M., additional, Periasamy, Sivakumar, additional, Richardson, Simone, additional, Suryadevara, Naveenchandra, additional, Andreano, Emanuele, additional, Paciello, Ida, additional, Pierleoni, Giulio, additional, Piccini, Giulia, additional, Huang, Ying, additional, Ge, Pan, additional, Allen, James D., additional, Uno, Naoko, additional, Shiakolas, Andrea R., additional, Pilewski, Kelsey A., additional, Nargi, Rachel S., additional, Sutton, Rachel E., additional, Abu-Shmais, Alexandria A., additional, Parks, Robert, additional, Haynes, Barton F., additional, Carnahan, Robert H., additional, Crowe, James E., additional, Montomoli, Emanuele, additional, Rappuoli, Rino, additional, Bukreyev, Alexander, additional, Ross, Ted M., additional, Sautto, Giuseppe A., additional, McLellan, Jason S., additional, and Georgiev, Ivelin S., additional

Published
2024
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13. Neutralizing antibody vaccine for pandemic and pre-emergent coronaviruses

Author

Saunders, Kevin O., Lee, Esther, Parks, Robert, Martinez, David R., Li, Dapeng, Chen, Haiyan, Edwards, Robert J., Gobeil, Sophie, Barr, Maggie, Mansouri, Katayoun, Alam, S. Munir, Sutherland, Laura L., Cai, Fangping, Sanzone, Aja M., Berry, Madison, Manne, Kartik, and Bock, Kevin W.

Subjects
Viral antibodies -- Usage -- Health aspects, Viral vaccines -- Dosage and administration, Antibodies -- Usage -- Health aspects, Coronaviruses -- Health aspects -- Control, Environmental issues, Science and technology, Zoology and wildlife conservation
Abstract

Betacoronaviruses caused the outbreaks of severe acute respiratory syndrome (SARS) and Middle East respiratory syndrome, as well as the current pandemic of SARS coronavirus 2 (SARS-CoV-2).sup.1-4. Vaccines that elicit protective immunity against SARS-CoV-2 and betacoronaviruses that circulate in animals have the potential to prevent future pandemics. Here we show that the immunization of macaques with nanoparticles conjugated with the receptor-binding domain of SARS-CoV-2, and adjuvanted with 3M-052 and alum, elicits cross-neutralizing antibody responses against bat coronaviruses, SARS-CoV and SARS-CoV-2 (including the B.1.1.7, P.1 and B.1.351 variants). Vaccination of macaques with these nanoparticles resulted in a 50% inhibitory reciprocal serum dilution (ID.sub.50) neutralization titre of 47,216 (geometric mean) for SARS-CoV-2, as well as in protection against SARS-CoV-2 in the upper and lower respiratory tracts. Nucleoside-modified mRNAs that encode a stabilized transmembrane spike or monomeric receptor-binding domain also induced cross-neutralizing antibody responses against SARS-CoV and bat coronaviruses, albeit at lower titres than achieved with the nanoparticles. These results demonstrate that current mRNA-based vaccines may provide some protection from future outbreaks of zoonotic betacoronaviruses, and provide a multimeric protein platform for the further development of vaccines against multiple (or all) betacoronaviruses. Immunization of macaques with nanoparticle-conjugated receptor-binding domain of SARS-CoV-2 adjuvanted with 3M-052 and alum results in cross-neutralizing antibodies against bat coronaviruses, SARS-CoV and SARS-CoV-2 variants, and may provide a platform for developing pan-coronavirus vaccines., Author(s): Kevin O. Saunders [sup.1] [sup.2] [sup.3] [sup.4] , Esther Lee [sup.1] [sup.5] , Robert Parks [sup.1] [sup.5] , David R. Martinez [sup.6] , Dapeng Li [sup.1] [sup.5] , Haiyan [...]

Published
2021
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14. Broadly neutralizing antibody induction by non-stabilized SARS-CoV-2 Spike mRNA vaccination in nonhuman primates

Author

Malewana, R. Dilshan, primary, Stalls, Victoria, additional, May, Aaron, additional, Lu, Xiaozhi, additional, Martinez, David R, additional, Schafer, Alexandra, additional, Li, Dapeng, additional, Barr, Maggie, additional, Sutherland, Laura L, additional, Lee, Esther, additional, Parks, Robert, additional, Beck, Whitney Edwards, additional, Newman, Amanda, additional, Bock, Kevin W, additional, Minai, Mahnaz, additional, Nagata, Bianca M, additional, DeMarco, C. Todd, additional, Denny, Thomas N, additional, Oguin, Thomas H, additional, Rountree, Wes, additional, Wang, Yunfei, additional, Mansouri, Katayoun, additional, Edwards, Robert J, additional, Sempowski, Gregory D, additional, Eaton, Amanda, additional, Muramatsu, Hiromi, additional, Henderson, Rory, additional, Tam, Ying, additional, Barbosa, Christopher, additional, Tang, Juanjie, additional, Cain, Derek W, additional, Santra, Sampa, additional, Moore, Ian N, additional, Andersen, Hanne, additional, Lewis, Mark G, additional, Golding, Hana, additional, Seder, Robert, additional, Khurana, Surender, additional, Montefiori, David C, additional, Pardi, Norbert, additional, Weissman, Drew, additional, Baric, Ralph S, additional, Acharya, Priyamvada, additional, Haynes, Barton F, additional, and Saunders, Kevin O, additional

Published
2023
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16. Interferometry of $\epsilon$ Aurigae: Characterization of the asymmetric eclipsing disk

Author

Kloppenborg, Brian, Stencel, Robert, Monnier, John D., Schaefer, Gail, Baron, Fabien, Tycner, Chris, Zavala, Robert T., Hutter, Donald, Zhao, Ming, Che, Xiao, Brummelaar, Theo ten, Farrington, Chris, Parks, Robert, McAlister, Hal, Sturmann, Judit, Sturmann, Laszlo, Sallave-Goldfinger, P. J., Turner, Nils, Pedretti, Ettoree, and Thureau, Nathalie

Subjects
Astrophysics - Solar and Stellar Astrophysics
Abstract

We report on a total of 106 nights of optical interferometric observations of the $\epsilon$ Aurigae system taken during the last 14 years by four beam combiners at three different interferometric facilities. This long sequence of data provides an ideal assessment of the system prior to, during, and after the recent 2009-2011 eclipse. We have reconstructed model-independent images from the 10 in-eclipse epochs which show that a disk-like object is indeed responsible for the eclipse. Using new 3D, time-dependent modeling software, we derive the properties of the F-star (diameter, limb darkening), determine previously unknown orbital elements ($\Omega$, $i$), and access the global structures of the optically thick portion of the eclipsing disk using both geometric models and approximations of astrophysically relevant density distributions. These models may be useful in future hydrodynamical modeling of the system. Lastly, we address several outstanding research questions including mid-eclipse brightening, possible shrinking of the F-type primary, and any warps or sub-features within the disk., Comment: 105 pages, 57 figures. This is an author-created, un-copyedited version of an article accepted for publication in Astrophysical Journal Supplement Series. IOP Publishing Ltd is not responsible for any errors or omissions in this version of the manuscript or any version derived from it

Published
2015
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17. Author Correction: Lipid nanoparticle encapsulated nucleoside-modified mRNA vaccines elicit polyfunctional HIV-1 antibodies comparable to proteins in nonhuman primates

Author

Saunders, Kevin O., Pardi, Norbert, Parks, Robert, Santra, Sampa, Mu, Zekun, Sutherland, Laura, Scearce, Richard, Barr, Maggie, Eaton, Amanda, Hernandez, Giovanna, Goodman, Derrick, Hogan, Michael J., Tombacz, Istvan, Gordon, David N., Rountree, R. Wes, Wang, Yunfei, Lewis, Mark G., Pierson, Theodore C., Barbosa, Chris, Tam, Ying, Matyas, Gary R., Rao, Mangala, Beck, Zoltan, Shen, Xiaoying, Ferrari, Guido, Tomaras, Georgia D., Montefiori, David C., Weissman, Drew, and Haynes, Barton F.

Published
2021
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18. Lipid nanoparticle encapsulated nucleoside-modified mRNA vaccines elicit polyfunctional HIV-1 antibodies comparable to proteins in nonhuman primates

Author

Saunders, Kevin O., Pardi, Norbert, Parks, Robert, Santra, Sampa, Mu, Zekun, Sutherland, Laura, Scearce, Richard, Barr, Maggie, Eaton, Amanda, Hernandez, Giovanna, Goodman, Derrick, Hogan, Michael J., Tombacz, Istvan, Gordon, David N., Rountree, R. Wes, Wang, Yunfei, Lewis, Mark G., Pierson, Theodore C., Barbosa, Chris, Tam, Ying, Matyas, Gary R., Rao, Mangala, Beck, Zoltan, Shen, Xiaoying, Ferrari, Guido, Tomaras, Georgia D., Montefiori, David C., Weissman, Drew, and Haynes, Barton F.

Published
2021
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21. The Gathering Gift of a River: Responding to the Questions of the Ecological Food Web of the Eel River

Author

Parks, Robert A.

Subjects
Philosophy, Ecology, Philosophy of science, Action, Ecology, Eel River, Philosophy, Philosophy of science, Praxis
Abstract

In this dissertation, I respond to questions that call me before them. I respond, inevitably incompletely, with my limited awareness and sensitivity, and—undoubtedly—with areas of blindness of which I am not aware. I begin with the question: What are the ecological food webs of the Eel River? Faithful, trusting, and lawful response requires me—but never forces me or acts upon me such that I am made to respond—to begin once and again, never anew, but always moving faringly and practically, with trust and faith, along the way these questions open before me. (Q1) What are the ecological food webs of the Eel River? I respond: Given epistemologically-metaphysically, and, thereof, scientifically-epistemologically, the ecological food webs of the Eel River are actions-reactions, and thus actings-reactings, the activities-reactivities that these actings-reactings comprise, and, thus, interactions, interacting, and interactivities. In epistemological-metaphysical sense and sensibility, the ecological food webs of the Eel River, as actions-reactions, are forces forcing and being forced forcefully. (Q2) What is the ecological food web of the Eel River? I respond: The ecological food web of the Eel River is the food web of the Eel River. Regardless of one or another of their actions-reactions, and forgivingly of these when they harm, the food web of the Eel River is the meeting-coming-together, safe-keeping, and faring together in this small opening-region of the world of the beings given to exist and, thus, to fare-existingly in and around the Eel River, including the river. The food web of the Eel River is, then, the giving-gathering of those beings, as they come to existing, into the opening revealing of sense, sensibility, and, thereof—for some of them, at least, and in degrees, probably—the commonly sensing understanding to which they are given, that they may learn to existingly-abide together familiarly, among and with one another—with varying degrees of awareness, with various sensitivities and proclivities, perhaps with kindness, perhaps befriendingly, perhaps with love in each and all of its senses—but, regardless, openingly nourishing one another, as they are, and as each of them fares its way existingly through the world together with the others, for the limited time they are given. Responding to these two questions leads me along a sinuous path of analyzing, thinking, and responding to the research and explanations of several ecologists who have researched the ecological food webs of the Eel River. These ecologists’ research and explanations, as well as the questions that have arisen for me from their research and explanations, lead me into an engagement with several historically foundational works of the science-epistemology of ecology, particular those written during the twentieth century. I pay especial attention to Principles of Animal Ecology (1949) to help me learn what outstandingly scrupulous ecologists understand science, ecology, an ecological community, an ecological food web, and a biological organism to be. From these readings, I respond, perhaps most importantly, to the questions of what action, activity, and practice are. Finally, when analyzed scientifically-epistemologically, I find a consistency of scientific-epistemological problems in the ecological explanations of the literature I study. This consistency and continuity seem important, and I note them throughout. I do not, however, attempt to resolve these problems or explain why these scientific-epistemological problems are what they are, and continue ubiquitously as I have found them to—if, that is, they are scientific-epistemological problems at all. With attention and thorough analysis, I have judged them to be scientific-epistemological problems. I have so judged after thorough and meticulous attempts to piece together the scientific-epistemological consistency and coherency of what ecologists explain.

Published
2022

24. COVID-19 Diagnosis and SARS-CoV-2 Strain Identification by a Rapid, Multiplexed, Point-of-Care Antibody Microarray

Author

Heggestad, Jacob T., primary, Britton, Rhett J., additional, Kinnamon, David S., additional, Liu, Jason, additional, Anderson, Jack G., additional, Joh, Daniel Y., additional, Quinn, Zachary, additional, Fontes, Cassio M., additional, Hucknall, Angus M., additional, Parks, Robert, additional, Sempowski, Gregory D., additional, Denny, Thomas N., additional, Burke, Thomas W., additional, Haynes, Barton F., additional, Woods, Christopher W., additional, and Chilkoti, Ashutosh, additional

Published
2023
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25. Vaccine Induction of Heterologous HIV-1 Neutralizing Antibody B Cell Lineages in Humans

Author

Williams, Wilton B., primary, Alam, S. Munir, additional, Ofek, Gilad, additional, Erdmann, Nathaniel, additional, Montefiori, David, additional, Seaman, Michael S., additional, Wagh, Kshitij, additional, Korber, Bette, additional, Edwards, Robert J., additional, Mansouri, Katayoun, additional, Eaton, Amanda, additional, Cain, Derek W., additional, Martin, Mitchell, additional, Parks, Robert, additional, Barr, Maggie, additional, Foulger, Andrew, additional, Anasti, Kara, additional, Patel, Parth, additional, Sammour, Salam, additional, Parsons, Ruth J., additional, Huang, Xiao, additional, Lindenberger, Jared, additional, Fetics, Susan, additional, Janowska, Katarzyna, additional, Niyongabo, Aurelie, additional, Janus, Benjamin M., additional, Astavans, Anagh, additional, Fox, Christopher B., additional, Mohanty, Ipsita, additional, Evangelous, Tyler, additional, Chen, Yue, additional, Berry, Madison, additional, Kirshner, Helene, additional, Van Itallie, Elizabeth, additional, Saunders, Kevin, additional, Wiehe, Kevin, additional, Cohen, Kristen W., additional, McElrath, M. Juliana, additional, Corey, Lawrence, additional, Acharya, Priyamvada, additional, Walsh, Stephen R., additional, Baden, Lindsey R., additional, and Haynes, Barton F., additional

Published
2023
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28. Immune checkpoint modulation enhances HIV-1 antibody induction

Author

Bradley, Todd, Kuraoka, Masayuki, Yeh, Chen-Hao, Tian, Ming, Chen, Huan, Cain, Derek W., Chen, Xuejun, Cheng, Cheng, Ellebedy, Ali H., Parks, Robert, Barr, Maggie, Sutherland, Laura L., Scearce, Richard M., Bowman, Cindy M., Bouton-Verville, Hilary, Santra, Sampa, Wiehe, Kevin, Lewis, Mark G., Ogbe, Ane, Borrow, Persephone, Montefiori, David, Bonsignori, Mattia, Anthony Moody, M., Verkoczy, Laurent, Saunders, Kevin O., Ahmed, Rafi, Mascola, John R., Kelsoe, Garnett, Alt, Frederick W., and Haynes, Barton F.

Published
2020
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31. Structure-Based Stabilization of SOSIP Env Enhances Recombinant Ectodomain Durability and Yield

Author

Wrapp, Daniel, primary, Mu, Zekun, additional, Thakur, Bhishem, additional, Janowska, Katarzyna, additional, Ajayi, Oluwatobi, additional, Barr, Maggie, additional, Parks, Robert, additional, Mansouri, Katayoun, additional, Edwards, Robert J., additional, Hahn, Beatrice H., additional, Acharya, Priyamvada, additional, Saunders, Kevin O., additional, and Haynes, Barton F., additional

Published
2023
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33. Diversion of HIV-1 vaccine–induced immunity by gp41-microbiota cross-reactive antibodies

Author

Williams, Wilton B., Liao, Hua-Xin, Moody, M. Anthony, Kepler, Thomas B., Alam, S. Munir, Gao, Feng, Wiehe, Kevin, Trama, Ashley M., Jones, Kathryn, Zhang, Ruijun, Song, Hongshuo, Marshall, Dawn J., Whitesides, John F., Sawatzki, Kaitlin, Hua, Axin, Liu, Pinghuang, Tay, Matthew Z., Seaton, Kelly E., Shen, Xiaoying, Foulger, Andrew, Lloyd, Krissey E., Parks, Robert, Pollara, Justin, Ferrari, Guido, Yu, Jae-Sung, Vandergrift, Nathan, Montefiori, David C., Sobieszczyk, Magdalena E., Hammer, Scott, Karuna, Shelly, Gilbert, Peter, Grove, Doug, Grunenberg, Nicole, McElrath, M. Juliana, Mascola, John R., Koup, Richard A., Corey, Lawrence, Nabel, Gary J., Morgan, Cecilia, Churchyard, Gavin, Maenza, Janine, Keefer, Michael, Graham, Barney S., Baden, Lindsey R., Tomaras, Georgia D., and Haynes, Barton F.

Published
2015

36. IDLV-HIV-1 Env vaccination in non-human primates induces affinity maturation of antigen-specific memory B cells

Author

Blasi, Maria, Negri, Donatella, LaBranche, Celia, Alam, S. Munir, Baker, Erich J., Brunner, Elizabeth C., Gladden, Morgan A., Michelini, Zuleika, Vandergrift, Nathan A., Wiehe, Kevin J., Parks, Robert, Shen, Xiaoying, Bonsignori, Mattia, Tomaras, Georgia D., Ferrari, Guido, Montefiori, David C., Santra, Sampa, Haynes, Barton F., Moody, Michael A., Cara, Andrea, and Klotman, Mary E.

Published
2018
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37. An antibody from single human V H -rearranging mouse neutralizes all SARS-CoV-2 variants through BA.5 by inhibiting membrane fusion

Author

Luo, Sai, primary, Zhang, Jun, additional, Kreutzberger, Alex J. B., additional, Eaton, Amanda, additional, Edwards, Robert J., additional, Jing, Changbin, additional, Dai, Hai-Qiang, additional, Sempowski, Gregory D., additional, Cronin, Kenneth, additional, Parks, Robert, additional, Ye, Adam Yongxin, additional, Mansouri, Katayoun, additional, Barr, Maggie, additional, Pishesha, Novalia, additional, Williams, Aimee Chapdelaine, additional, Vieira Francisco, Lucas, additional, Saminathan, Anand, additional, Peng, Hanqin, additional, Batra, Himanshu, additional, Bellusci, Lorenza, additional, Khurana, Surender, additional, Alam, S. Munir, additional, Montefiori, David C., additional, Saunders, Kevin O., additional, Tian, Ming, additional, Ploegh, Hidde, additional, Kirchhausen, Tom, additional, Chen, Bing, additional, Haynes, Barton F., additional, and Alt, Frederick W., additional

Published
2022
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41. Structural basis for breadth development in a HIV-1 neutralizing antibody

Author

Henderson, Rory, primary, Zhou, Ye, additional, Stalls, Victoria, additional, Wiehe, Kevin, additional, Saunders, Kevin O., additional, Wagh, Kshitij, additional, Anasti, Kara, additional, Barr, Maggie, additional, Parks, Robert, additional, Alam, S. Munir, additional, Korber, Bette, additional, Haynes, Barton F., additional, Bartesaghi, Alberto, additional, and Acharya, Priyamvada, additional

Published
2022
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42. Stabilized HIV-1 envelope immunization induces neutralizing antibodies to the CD4bs and protects macaques against mucosal infection

Author

Saunders, Kevin O., primary, Edwards, Robert J., additional, Tilahun, Kedamawit, additional, Manne, Kartik, additional, Lu, Xiaozhi, additional, Cain, Derek W., additional, Wiehe, Kevin, additional, Williams, Wilton B., additional, Mansouri, Katayoun, additional, Hernandez, Giovanna E., additional, Sutherland, Laura, additional, Scearce, Richard, additional, Parks, Robert, additional, Barr, Maggie, additional, DeMarco, Todd, additional, Eater, Chloe M., additional, Eaton, Amanda, additional, Morton, Georgeanna, additional, Mildenberg, Benjamin, additional, Wang, Yunfei, additional, Rountree, R. Wes, additional, Tomai, Mark A., additional, Fox, Christopher B., additional, Moody, M. Anthony, additional, Alam, S. Munir, additional, Santra, Sampa, additional, Lewis, Mark G., additional, Denny, Thomas N., additional, Shaw, George M., additional, Montefiori, David C., additional, Acharya, Priyamvada, additional, and Haynes, Barton F., additional

Published
2022
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44. Humanized antibody potently neutralizes all SARS-CoV-2 variants by a novel mechanism

Author

Luo, Sai, primary, Zhang, Jun, additional, Kreutzberger, Alex J.B., additional, Eaton, Amanda, additional, Edwards, Robert J., additional, Jing, Changbin, additional, Dai, Hai-Qiang, additional, Sempowski, Gregory D., additional, Cronin, Kenneth, additional, Parks, Robert, additional, Ye, Adam Yongxin, additional, Mansouri, Katayoun, additional, Barr, Maggie, additional, Pishesha, Novalia, additional, Williams, Aimee Chapdelaine, additional, Francisco, Lucas Vieira, additional, Saminathan, Anand, additional, Peng, Hanqin, additional, Batra, Himanshu, additional, Bellusci, Lorenza, additional, Khurana, Surender, additional, Alam, S. Munir, additional, Montefiori, David C., additional, Saunders, Kevin O., additional, Tian, Ming, additional, Ploegh, Hidde, additional, Kirchhausen, Tom, additional, Chen, Bing, additional, Haynes, Barton F., additional, and Alt, Frederick W., additional

Published
2022
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45. Parallel Induction of CH505 B Cell Ontogeny-Guided Neutralizing Antibodies and tHIVconsvX Conserved Mosaic-Specific T Cells against HIV-1

Author

Wee, Edmund G., primary, Moyo, Nathifa A., additional, Saunders, Kevin O., additional, LaBranche, Celia, additional, Donati, Filippo, additional, Capucci, Silvia, additional, Parks, Robert, additional, Borthwick, Nicola, additional, Hannoun, Zara, additional, Montefiori, David C., additional, Haynes, Barton F., additional, and Hanke, Tomáš, additional

Published
2022
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46. Mimicry of an HIV broadly neutralizing antibody epitope with a synthetic glycopeptide

Author

Alam, S. Munir, Aussedat, Baptiste, Vohra, Yusuf, Ryan Meyerhoff, R., Cale, Evan M., Walkowicz, William E., Radakovich, Nathan A., Anasti, Kara, Armand, Lawrence, Parks, Robert, Sutherland, Laura, Scearce, Richard, Joyce, M. Gordon, Pancera, Marie, Druz, Aliaksandr, Georgiev, Ivelin S., Von Holle, Tarra, Eaton, Amanda, Fox, Christopher, Reed, Steven G., Louder, Mark, Bailer, Robert T., Morris, Lynn, Abdool-Karim, Salim S., Cohen, Myron, Liao, Hua-Xin, Montefiori, David C., Park, Peter K., Fernández-Tejada, Alberto, Wiehe, Kevin, Santra, Sampa, Kepler, Thomas B., Saunders, Kevin O., Sodroski, Joseph, Kwong, Peter D., Mascola, John R., Bonsignori, Mattia, Moody, M. Anthony, Danishefsky, Samuel, and Haynes, Barton F.

Published
2017
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47. Potent and broad HIV-neutralizing antibodies in memory B cells and plasma

Author

Williams, LaTonya D., Ofek, Gilad, Schätzle, Sebastian, McDaniel, Jonathan R., Lu, Xiaozhi, Nicely, Nathan I., Wu, Liming, Lougheed, Caleb S., Bradley, Todd, Louder, Mark K., McKee, Krisha, Bailer, Robert T., O’Dell, Sijy, Georgiev, Ivelin S., Seaman, Michael S., Parks, Robert J., Marshall, Dawn J., Anasti, Kara, Yang, Guang, Nie, Xiaoyan, Tumba, Nancy L., Wiehe, Kevin, Wagh, Kshitij, Korber, Bette, Kepler, Thomas B., Munir Alam, S., Morris, Lynn, Kamanga, Gift, Cohen, Myron S., Bonsignori, Mattia, Xia, Shi-Mao, Montefiori, David C., Kelsoe, Garnett, Gao, Feng, Mascola, John R., Moody, M. Anthony, Saunders, Kevin O., Liao, Hua-Xin, Tomaras, Georgia D., Georgiou, George, and Haynes, Barton F.

Published
2017
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49. Dual-affinity re-targeting proteins direct T cell-mediated cytolysis of latently HIV-infected cells

Author

Sung, Julia A.M., Pickeral, Joy, Liu, Liqin, Stanfield-Oakley, Sherry A., Lam, Chia-Ying Kao, Garrido, Carolina, Pollara, Justin, LaBranche, Celia, Bonsignori, Mattia, Moody, M. Anthony, Yang, Yinhua, Parks, Robert, Archin, Nancie, Allard, Brigitte, Kirchherr, Jennifer, Kuruc, JoAnn D., Gay, Cynthia L., Cohen, Myron S., Ochsenbauer, Christina, Soderberg, Kelly, Liao, Hua-Xin, Montefiori, David, Moore, Paul, Johnson, Syd, Koenig, Scott, Haynes, Barton F., Nordstrom, Jeffrey L., Margolis, David M., and Ferrari, Guido

Subjects
T cells -- Genetic aspects, Viral proteins -- Properties, Immune response -- Regulation, HIV infection -- Genetic aspects -- Development and progression, Health care industry
Abstract

Enhancement of HIV-specific Immunity Is likely required to eliminate latent HIV Infection. Here, we have developed an Immunotherapeutic modality aimed to improve T cell-mediated clearance of HIV-1-infected cells. Specifically, we employed Dual-Affinity Re-Targeting (DART) proteins, which are bispecific, antibody-based molecules that can bind 2 distinct cell-surface molecules simultaneously. We designed DARTs with a monovalent HIV-1 envelope-binding (Env-binding) arm that was derived from broadly binding, antibody-dependent cellular cytotoxicity-mediating antibodies known to bind to HIV- infected target cells coupled to a monovalent CD3 binding arm designed to engage cytolytic effector T cells (referred to as HIVxCD3 DARTs). Thus, these DARTs redirected polyclonal T cells to specifically engage with and kill Env-expressing cells, including [CD4.sup.+] T cells infected with different HIV-1 subtypes, thereby obviating the requirement for HIV- specific immunity. Using lymphocytes from patients on suppressive antiretroviral therapy (ART), we demonstrated that DARTs mediate [CD8.sup.+] T cell clearance of [CD4.sup.+] T cells that are superinfected with the HIV-1 strain JR-CSF or infected with autologous reservoir viruses isolated from HIV-infected-patient resting [CD4.sup.+] T cells. Moreover, DARTs mediated [CD8.sup.+] T cell clearance of HIV from resting [CD4.sup.+] T cell cultures following induction of latent virus expression. Combined with HIV latency reversing agents, HIVxCD3 DARTs have the potential to be effective immunotherapeutic agents to clear latent HIV-1 reservoirs in HIV-infected individuals., Introduction The inability of antiretroviral therapy (ART) to eradicate HIV was first suggested by the demonstration of latent infection of resting [CD4.sup.+] T cells (1) and then by the recovery [...]

Published
2015
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