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1. Virology—the path forward

Author

Rasmussen, Angela L, Gronvall, Gigi K, Lowen, Anice C, Goodrum, Felicia, Alwine, James, Andersen, Kristian G, Anthony, Simon J, Baines, Joel, Banerjee, Arinjay, Broadbent, Andrew J, Brooke, Christopher B, Campos, Samuel K, Caposio, Patrizia, Casadevall, Arturo, Chan, Gary C, Cliffe, Anna R, Collins-McMillen, Donna, Connell, Nancy, Damania, Blossom, Daugherty, Matthew D, Debbink, Kari, Dermody, Terence S, DiMaio, Daniel, Duprex, W Paul, Emerman, Michael, Galloway, Denise A, Garry, Robert F, Goldstein, Stephen A, Greninger, Alexander L, Hartman, Amy L, Hogue, Brenda G, Horner, Stacy M, Hotez, Peter J, Jung, Jae U, Kamil, Jeremy P, Karst, Stephanie M, Laimins, Lou, Lakdawala, Seema S, Landais, Igor, Letko, Michael, Lindenbach, Brett, Liu, Shan-Lu, Luftig, Micah, McFadden, Grant, Mehle, Andrew, Morrison, Juliet, Moscona, Anne, Mühlberger, Elke, Munger, Joshua, Münger, Karl, Murphy, Eain, Neufeldt, Christopher J, Nikolich, Janko Z, O'Connor, Christine M, Pekosz, Andrew, Permar, Sallie R, Pfeiffer, Julie K, Popescu, Saskia V, Purdy, John G, Racaniello, Vincent R, Rice, Charles M, Runstadler, Jonathan A, Sapp, Martin J, Scott, Rona S, Smith, Gregory A, Sorrell, Erin M, Speranza, Emily, Streblow, Daniel, Tibbetts, Scott A, Toth, Zsolt, Van Doorslaer, Koenraad, Weiss, Susan R, White, Elizabeth A, White, Timothy M, Wobus, Christiane E, Worobey, Michael, Yamaoka, Satoko, and Yurochko, Andrew

Subjects
Agricultural, Veterinary and Food Sciences, Biological Sciences, Biomedical and Clinical Sciences, Coronaviruses, Prevention, Emerging Infectious Diseases, Infectious Diseases, Good Health and Well Being, Humans, Containment of Biohazards, COVID-19, United States, Viruses, Virology, Biomedical Research, virology, SARS-CoV-2, oversight, biosafety, emergence, Agricultural and Veterinary Sciences, Medical and Health Sciences, Agricultural, veterinary and food sciences, Biological sciences, Biomedical and clinical sciences
Abstract

In the United States (US), biosafety and biosecurity oversight of research on viruses is being reappraised. Safety in virology research is paramount and oversight frameworks should be reviewed periodically. Changes should be made with care, however, to avoid impeding science that is essential for rapidly reducing and responding to pandemic threats as well as addressing more common challenges caused by infectious diseases. Decades of research uniquely positioned the US to be able to respond to the COVID-19 crisis with astounding speed, delivering life-saving vaccines within a year of identifying the virus. We should embolden and empower this strength, which is a vital part of protecting the health, economy, and security of US citizens. Herein, we offer our perspectives on priorities for revised rules governing virology research in the US.

Published
2024

2. An advanced workflow for single particle imaging with the limited data at an X-ray free-electron laser

Author

Assalauova, Dameli, Kim, Young Yong, Bobkov, Sergey, Khubbutdinov, Ruslan, Rose, Max, Alvarez, Roberto, Andreasson, Jakob, Balaur, Eugeniu, Contreras, Alice, DeMirci, Hasan, Gelisio, Luca, Hajdu, Janos, Hunter, Mark S., Kurta, Ruslan P., Li, Haoyuan, McFadden, Matthew, Nazari, Reza, Schwander, Peter, Teslyuk, Anton, Walter, Peter, Xavier, P. Lourdu, Yoon, Chun Hong, Zaared, Sahba, Ilyin, Viacheslav A., Kirian, Richard A., Hogue, Brenda G., Aquila, Andrew, and Vartanyants, Ivan A.

Subjects
Physics - Biological Physics, Physics - Data Analysis, Statistics and Probability
Abstract

An improved analysis for single particle imaging (SPI) experiments, using the limited data, is presented here. Results are based on a study of bacteriophage PR772 performed at the AMO instrument at the Linac Coherent Light Source (LCLS) as part of the SPI initiative. Existing methods were modified to cope with the shortcomings of the experimental data: inaccessibility of information from the half of the detector and small fraction of single hits. General SPI analysis workflow was upgraded with the expectation-maximization based classification of diffraction patterns and mode decomposition on the final virus structure determination step. The presented processing pipeline allowed us to determine the three-dimensional structure of the bacteriophage PR772 without symmetry constraints with a spatial resolution of 6.9 nm. The obtained resolution was limited by the scattering intensity during the experiment and the relatively small number of single hits., Comment: 40 pages, 7 figures (main text), 2 tables (main text), 14 figures (supplementary information), 1 table (supplementary information)

Published
2020

3. Megahertz single-particle imaging at the European XFEL

Author

Sobolev, Egor, Zolotarev, Serguey, Giewekemeyer, Klaus, Bielecki, Johan, Okamoto, Kenta, Reddy, Hemanth K. N., Andreasson, Jakob, Ayyer, Kartik, Barak, Imrich, Bari, Sadia, Barty, Anton, Bean, Richard, Bobkov, Sergey, Chapman, Henry N., Chojnowski, Grzegorz, Daurer, Benedikt J., Dörner, Katerina, Ekeberg, Tomas, Flückiger, Leonie, Galzitskaya, Oxana, Gelisio, Luca, Hauf, Steffen, Hogue, Brenda G., Horke, Daniel A., Hosseinizadeh, Ahmad, Ilyin, Vyacheslav, Jung, Chulho, Kim, Chan, Kim, Yoonhee, Kirian, Richard A., Kirkwood, Henry, Kulyk, Olena, Letrun, Romain, Loh, Duane, Messerschmidt, Marc, Mühlig, Kerstin, Ourmazd, Abbas, Raab, Natascha, Rode, Andrei V., Rose, Max, Round, Adam, Sato, Takushi, Schubert, Robin, Schwander, Peter, Sellberg, Jonas A., Sikorski, Marcin, Silenzi, Alessandro, Song, Changyong, Spence, John C. H., Stern, Stephan, Sztuk-Dambietz, Jolanta, Teslyuk, Anthon, Timneanu, Nicusor, Trebbin, Martin, Uetrecht, Charlotte, Weinhausen, Britta, Williams, Garth J., Xavier, P Lourdu, Xu, Chen, Vartanyants, Ivan, Lamzin, Victor, Mancuso, Adrian, and Maia, Filipe R. N. C.

Subjects
Physics - Instrumentation and Detectors, Physics - Biological Physics
Abstract

The emergence of high repetition-rate X-ray free-electron lasers (XFELs) powered by superconducting accelerator technology enables the measurement of significantly more experimental data per day than was previously possible. The European XFEL will soon provide 27,000 pulses per second, more than two orders of magnitude more than any other XFEL. The increased pulse rate is a key enabling factor for single-particle X-ray diffractive imaging, which relies on averaging the weak diffraction signal from single biological particles. Taking full advantage of this new capability requires that all experimental steps, from sample preparation and delivery to the acquisition of diffraction patterns, are compatible with the increased pulse repetition rate. Here, we show that single-particle imaging can be performed using X-ray pulses at megahertz repetition rates. The obtained results pave the way towards exploiting high repetition-rate X-ray free-electron lasers for single-particle imaging at their full repetition rate.

Published
2019
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4. Low-signal limit of X-ray single particle imaging

Author

Ayyer, Kartik, Morgan, Andrew J., Aquila, Andrew A., DeMirci, Hasan, Hogue, Brenda G., Kirian, Richard A., Xavier, P. Lourdu, Yoon, Chun Hong, Chapman, Henry N., and Barty, Anton

Subjects
Electrical Engineering and Systems Science - Image and Video Processing, Physics - Optics
Abstract

An outstanding question in X-ray single particle imaging experiments has been the feasibility of imaging sub 10-nm-sized biomolecules under realistic experimental conditions where very few photons are expected to be measured in a single snapshot and instrument background may be significant relative to particle scattering. While analyses of simulated data have shown that the determination of an average image should be feasible using Bayesian methods such as the EMC algorithm, this has yet to be demonstrated using experimental data containing realistic non-isotropic instrument background, sample variability and other experimental factors. In this work, we show that the orientation and phase retrieval steps work at photon counts diluted to the signal levels one expects from smaller molecules or with weaker pulses, using data from experimental measurements of 60-nm PR772 viruses. Even when the signal is reduced to a fraction as little as 1/256, the virus electron density determined using ab initio phasing is of almost the same quality as the high-signal data. However, we are still limited by the total number of patterns collected, which may soon be mitigated by the advent of high repetition-rate sources like the European XFEL and LCLS-II., Comment: 19 pages, 9 figures

Published
2019
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5. Viral anti‐inflammatory serpin reduces immuno‐coagulopathic pathology in SARS‐CoV‐2 mouse models of infection

Author

Zhang, Liqiang, Li, Yize Henry, Kibler, Karen, Kraberger, Simona, Varsani, Arvind, Turk, Julie, Elmadbouly, Nora, Aliskevich, Emily, Spaccarelli, Laurel, Estifanos, Bereket, Enow, Junior, Zanetti, Isabela Rivabem, Saldevar, Nicholas, Lim, Efrem, Schlievert, Jessika, Browder, Kyle, Wilson, Anjali, Juan, Fernando Arcos, Pinteric, Aubrey, Garg, Aman, Monder, Henna, Saju, Rohan, Gisriel, Savanah, Jacobs, Bertram, Karr, Timothy L, Florsheim, Esther Borges, Kumar, Vivek, Wallen, John, Rahman, Masmudur, McFadden, Grant, Hogue, Brenda G, and Lucas, Alexandra R

Published
2023
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6. Megahertz single-particle imaging at the European XFEL

Author

Sobolev, Egor, Zolotarev, Sergei, Giewekemeyer, Klaus, Bielecki, Johan, Okamoto, Kenta, Reddy, Hemanth KN, Andreasson, Jakob, Ayyer, Kartik, Barak, Imrich, Bari, Sadia, Barty, Anton, Bean, Richard, Bobkov, Sergey, Chapman, Henry N, Chojnowski, Grzegorz, Daurer, Benedikt J, Dörner, Katerina, Ekeberg, Tomas, Flückiger, Leonie, Galzitskaya, Oxana, Gelisio, Luca, Hauf, Steffen, Hogue, Brenda G, Horke, Daniel A, Hosseinizadeh, Ahmad, Ilyin, Vyacheslav, Jung, Chulho, Kim, Chan, Kim, Yoonhee, Kirian, Richard A, Kirkwood, Henry, Kulyk, Olena, Küpper, Jochen, Letrun, Romain, Loh, N Duane, Lorenzen, Kristina, Messerschmidt, Marc, Mühlig, Kerstin, Ourmazd, Abbas, Raab, Natascha, Rode, Andrei V, Rose, Max, Round, Adam, Sato, Takushi, Schubert, Robin, Schwander, Peter, Sellberg, Jonas A, Sikorski, Marcin, Silenzi, Alessandro, Song, Changyong, Spence, John CH, Stern, Stephan, Sztuk-Dambietz, Jolanta, Teslyuk, Anthon, Timneanu, Nicusor, Trebbin, Martin, Uetrecht, Charlotte, Weinhausen, Britta, Williams, Garth J, Xavier, P Lourdu, Xu, Chen, Vartanyants, Ivan A, Lamzin, Victor S, Mancuso, Adrian, and Maia, Filipe RNC

Abstract

The emergence of high repetition-rate X-ray free-electron lasers (XFELs) powered by superconducting accelerator technology enables the measurement of significantly more experimental data per day than was previously possible. The European XFEL is expected to provide 27,000 pulses per second, over two orders of magnitude more than any other XFEL. The increased pulse rate is a key enabling factor for single-particle X-ray diffractive imaging, which relies on averaging the weak diffraction signal from single biological particles. Taking full advantage of this new capability requires that all experimental steps, from sample preparation and delivery to the acquisition of diffraction patterns, are compatible with the increased pulse repetition rate. Here, we show that single-particle imaging can be performed using X-ray pulses at megahertz repetition rates. The results obtained pave the way towards exploiting high repetition-rate X-ray free-electron lasers for single-particle imaging at their full repetition rate.

Published
2020

7. Diffraction data from aerosolized Coliphage PR772 virus particles imaged with the Linac Coherent Light Source

Author

Li, Haoyuan, Nazari, Reza, Abbey, Brian, Alvarez, Roberto, Aquila, Andrew, Ayyer, Kartik, Barty, Anton, Berntsen, Peter, Bielecki, Johan, Pietrini, Alberto, Bucher, Maximilian, Carini, Gabriella, Chapman, Henry N, Contreras, Alice, Daurer, Benedikt J, DeMirci, Hasan, Flűckiger, Leonie, Frank, Matthias, Hajdu, Janos, Hantke, Max F, Hogue, Brenda G, Hosseinizadeh, Ahmad, Hunter, Mark S, Jönsson, H Olof, Kirian, Richard A, Kurta, Ruslan P, Loh, Duane, Maia, Filipe RNC, Mancuso, Adrian P, Morgan, Andrew J, McFadden, Matthew, Muehlig, Kerstin, Munke, Anna, Reddy, Hemanth Kumar Narayana, Nettelblad, Carl, Ourmazd, Abbas, Rose, Max, Schwander, Peter, Marvin Seibert, M, Sellberg, Jonas A, Sierra, Raymond G, Sun, Zhibin, Svenda, Martin, Vartanyants, Ivan A, Walter, Peter, Westphal, Daniel, Williams, Garth, Xavier, P Lourdu, Yoon, Chun Hong, and Zaare, Sahba

Subjects
Chemical Sciences, Synchrotrons and Accelerators, Physical Sciences, Coliphages, Lasers, Particle Accelerators, Virion, X-Ray Diffraction
Abstract

Single Particle Imaging (SPI) with intense coherent X-ray pulses from X-ray free-electron lasers (XFELs) has the potential to produce molecular structures without the need for crystallization or freezing. Here we present a dataset of 285,944 diffraction patterns from aerosolized Coliphage PR772 virus particles injected into the femtosecond X-ray pulses of the Linac Coherent Light Source (LCLS). Additional exposures with background information are also deposited. The diffraction data were collected at the Atomic, Molecular and Optical Science Instrument (AMO) of the LCLS in 4 experimental beam times during a period of four years. The photon energy was either 1.2 or 1.7 keV and the pulse energy was between 2 and 4 mJ in a focal spot of about 1.3 μm x 1.7 μm full width at half maximum (FWHM). The X-ray laser pulses captured the particles in random orientations. The data offer insight into aerosolised virus particles in the gas phase, contain information relevant to improving experimental parameters, and provide a basis for developing algorithms for image analysis and reconstruction.

Published
2020

8. Single-particle imaging without symmetry constraints at an X-ray free-electron laser

Author

Rose, Max, Bobkov, Sergey, Ayyer, Kartik, Kurta, Ruslan P, Dzhigaev, Dmitry, Kim, Young Yong, Morgan, Andrew J, Yoon, Chun Hong, Westphal, Daniel, Bielecki, Johan, Sellberg, Jonas A, Williams, Garth, Maia, Filipe RNC, Yefanov, Olexander M, Ilyin, Vyacheslav, Mancuso, Adrian P, Chapman, Henry N, Hogue, Brenda G, Aquila, Andrew, Barty, Anton, and Vartanyants, Ivan A

Subjects
Inorganic Chemistry, Chemical Sciences, Physical Sciences, Bioengineering, XFELs, single-particle imaging, three-dimensional virus reconstructions, Atomic, Molecular, Nuclear, Particle and Plasma Physics, Condensed Matter Physics, Physical Chemistry (incl. Structural), Physical chemistry, Condensed matter physics
Abstract

The analysis of a single-particle imaging (SPI) experiment performed at the AMO beamline at LCLS as part of the SPI initiative is presented here. A workflow for the three-dimensional virus reconstruction of the PR772 bacteriophage from measured single-particle data is developed. It consists of several well defined steps including single-hit diffraction data classification, refined filtering of the classified data, reconstruction of three-dimensional scattered intensity from the experimental diffraction patterns by orientation determination and a final three-dimensional reconstruction of the virus electron density without symmetry constraints. The analysis developed here revealed and quantified nanoscale features of the PR772 virus measured in this experiment, with the obtained resolution better than 10 nm, with a clear indication that the structure was compressed in one direction and, as such, deviates from ideal icosahedral symmetry.

Published
2018

9. Correction for Rasmussen et al., “Virology—the path forward”

Author

Rasmussen, Angela L., primary, Gronvall, Gigi K., additional, Lowen, Anice C., additional, Goodrum, Felicia, additional, Alwine, James, additional, Andersen, Kristian G., additional, Anthony, Simon J., additional, Baines, Joel, additional, Banerjee, Arinjay, additional, Broadbent, Andrew J., additional, Brooke, Christopher B., additional, Campos, Samuel K., additional, Caposio, Patrizia, additional, Casadevall, Arturo, additional, Chan, Gary C., additional, Cliffe, Anna R., additional, Collins-McMillen, Donna, additional, Connell, Nancy, additional, Damania, Blossom, additional, Daugherty, Matthew D., additional, Debbink, Kari, additional, Dermody, Terence S., additional, DiMaio, Daniel, additional, Duprex, W. Paul, additional, Emerman, Michael, additional, Galloway, Denise A., additional, Garry, Robert F., additional, Goldstein, Stephen A., additional, Greninger, Alexander L., additional, Hartman, Amy L., additional, Hogue, Brenda G., additional, Horner, Stacy M., additional, Hotez, Peter J., additional, Jung, Jae U., additional, Kamil, Jeremy P., additional, Karst, Stephanie M., additional, Laimins, Lou, additional, Lakdawala, Seema S., additional, Landais, Igor, additional, Letko, Michael, additional, Lindenbach, Brett, additional, Liu, Shan-Lu, additional, Luftig, Micah, additional, McFadden, Grant, additional, Mehle, Andrew, additional, Morrison, Juliet, additional, Moscona, Anne, additional, Mühlberger, Elke, additional, Munger, Joshua, additional, Münger, Karl, additional, Murphy, Eain, additional, Neufeldt, Christopher J., additional, Nikolich, Janko Z., additional, O'Connor, Christine M., additional, Pekosz, Andrew, additional, Permar, Sallie R., additional, Pfeiffer, Julie K., additional, Popescu, Saskia V., additional, Purdy, John G., additional, Racaniello, Vincent R., additional, Rice, Charles M., additional, Runstadler, Jonathan A., additional, Sapp, Martin J., additional, Scott, Rona S., additional, Smith, Gregory A., additional, Sorrell, Erin M., additional, Speranza, Emily, additional, Streblow, Daniel, additional, Tibbetts, Scott A., additional, Toth, Zsolt, additional, Van Doorslaer, Koenraad, additional, Weiss, Susan R., additional, White, Elizabeth A., additional, White, Timothy M., additional, Wobus, Christiane E., additional, Worobey, Michael, additional, Yamaoka, Satoko, additional, and Yurochko, Andrew, additional

Published
2024
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10. Coronavirus M Protein Trafficking in Epithelial Cells Utilizes a Myosin Vb Splice Variant and Rab10

Author

Lapierre, Lynne, Roland, Joseph T., Manning, Elizabeth H., Caldwell, Catherine, Glenn, Honor L., Vidalain, Pierre-Olivier, Tangy, Frederic, Hogue, Brenda G., Haan, Cornelis de, Goldenring, James R., Lapierre, Lynne, Roland, Joseph T., Manning, Elizabeth H., Caldwell, Catherine, Glenn, Honor L., Vidalain, Pierre-Olivier, Tangy, Frederic, Hogue, Brenda G., Haan, Cornelis de, and Goldenring, James R.

Abstract

The membrane (M) glycoprotein of coronaviruses (CoVs) serves as the nidus for virion assembly. Using a yeast two-hybrid screen, we identified the interaction of the cytosolic tail of Murine Hepatitis Virus (MHV-CoV) M protein with Myosin Vb (MYO5B), specifically with the alternative splice variant of cellular MYO5B including exon D (MYO5B+D), which mediates interaction with Rab10. When co-expressed in human lung epithelial A549 and canine kidney epithelial MDCK cells, MYO5B+D co-localized with the MHV-CoV M protein, as well as with the M proteins from Porcine Epidemic Diarrhea Virus (PEDV-CoV), Middle East Respiratory Syndrome (MERS-CoV) and Severe Acute Respiratory Syndrome 2 (SARS-CoV-2). Co-expressed M proteins and MYO5B+D co-localized with endogenous Rab10 and Rab11a. We identified point mutations in MHV-CoV M that blocked the interaction with MYO5B+D in yeast 2-hybrid assays. One of these point mutations (E121K) was previously shown to block MHV-CoV virion assembly and its interaction with MYO5B+D. The E to K mutation at homologous positions in PEDV-CoV, MERS-CoV and SARS-CoV-2 M proteins also blocked colocalization with MYO5B+D. The knockdown of Rab10 blocked the co-localization of M proteins with MYO5B+D and was rescued by re-expression of CFP-Rab10. Our results suggest that CoV M proteins traffic through Rab10-containing systems, in association with MYO5B+D.

Published
2024

11. Coronavirus M Protein Trafficking in Epithelial Cells Utilizes a Myosin Vb Splice Variant and Rab10

Author

Virologie, Infectious Diseases and Immunology - Virology, Lapierre, Lynne, Roland, Joseph T., Manning, Elizabeth H., Caldwell, Catherine, Glenn, Honor L., Vidalain, Pierre-Olivier, Tangy, Frederic, Hogue, Brenda G., Haan, Cornelis de, Goldenring, James R., Virologie, Infectious Diseases and Immunology - Virology, Lapierre, Lynne, Roland, Joseph T., Manning, Elizabeth H., Caldwell, Catherine, Glenn, Honor L., Vidalain, Pierre-Olivier, Tangy, Frederic, Hogue, Brenda G., Haan, Cornelis de, and Goldenring, James R.

Published
2024

21. Treatment with anti-inflammatory viral serpin modulates immuno-thrombotic responses and improves outcomes in SARS-CoV-2 infected mice

Author

Zhang, Liqiang, primary, Li, Yize (Henry), additional, Kibler, Karen, additional, Kraberger, Simona, additional, Varsani, Arvind, additional, Turk, Julie, additional, Elmadbouly, Nora, additional, Aliskevich, Emily, additional, Spaccarelli, Laurel, additional, Estifanos, Bereket, additional, Enow, Junior, additional, Zanetti, Isabela Rivabem, additional, Saldevar, Nicholas, additional, Lim, Efrem, additional, Browder, Kyle, additional, Wilson, Anjali, additional, Juan, Fernando Arcos, additional, Pinteric, Aubrey, additional, Garg, Aman, additional, Gisriel, Savanah, additional, Jacobs, Bertram, additional, Karr, Timothy L., additional, Florsheim, Esther Borges, additional, Kumar, Vivek, additional, Wallen, John, additional, Rahman, Masmudur, additional, McFadden, Grant, additional, Hogue, Brenda G., additional, and Lucas, Alexandra R., additional

Published
2022
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23. Intranasal Immunization with a Vaccinia Virus Vaccine Vector Expressing Pre-Fusion Stabilized SARS-CoV-2 Spike Fully Protected Mice against Lethal Challenge with the Heavily Mutated Mouse-Adapted SARS2-N501YMA30 Strain of SARS-CoV-2

Author

Kibler, Karen V., primary, Szczerba, Mateusz, additional, Lake, Douglas, additional, Roeder, Alexa J., additional, Rahman, Masmudur, additional, Hogue, Brenda G., additional, Roy Wong, Lok-Yin, additional, Perlman, Stanley, additional, Li, Yize, additional, and Jacobs, Bertram L., additional

Published
2022
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29. Corrigendum: An advanced workflow for single-particle imaging with the limited data at an X-ray free-electron laser

Author

Assalauova, Dameli, Kim, Young Yong, Bobkov, Sergey, Khubbutdinov, Ruslan, Rose, Max, Alvarez, Roberto, Andreasson, Jakob, Balaur, Eugeniu, Contreras, Alice, DeMirci, Hasan, Gelisio, Luca, Hajdu, Janos, Hunter, Mark S., Kurta, Ruslan P., Li, Haoyuan, McFadden, Matthew, Nazari, Reza, Schwander, Peter, Teslyuk, Anton, Walter, Peter, Xavier, P. Lourdu, Yoon, Chun Hong, Zaare, Sahba, Ilyin, Viacheslav A., Kirian, Richard A., Hogue, Brenda G., Aquila, Andrew, and Vartanyants, Ivan A.

Subjects
ddc:530
Abstract

IUCrJ 9(2), 328 (2022). doi:10.1107/S2052252522000501, An error in Fig. 3(c) of the article by Assalauova et al. [IUCrJ (2020), 7, 1102–1113] is corrected., Published by Chester

Published
2022
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30. An advanced workflow for single-particle imaging with the limited data at an X-ray free-electron laser. Corrigendum

Author

Assalauova, Dameli, primary, Kim, Young Yong, additional, Bobkov, Sergey, additional, Khubbutdinov, Ruslan, additional, Rose, Max, additional, Alvarez, Roberto, additional, Andreasson, Jakob, additional, Balaur, Eugeniu, additional, Contreras, Alice, additional, DeMirci, Hasan, additional, Gelisio, Luca, additional, Hajdu, Janos, additional, Hunter, Mark S., additional, Kurta, Ruslan P., additional, Li, Haoyuan, additional, McFadden, Matthew, additional, Nazari, Reza, additional, Schwander, Peter, additional, Teslyuk, Anton, additional, Walter, Peter, additional, Xavier, P. Lourdu, additional, Yoon, Chun Hong, additional, Zaare, Sahba, additional, Ilyin, Viacheslav A., additional, Kirian, Richard A., additional, Hogue, Brenda G., additional, Aquila, Andrew, additional, and Vartanyants, Ivan A., additional

Published
2022
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33. Intranasal immunization with a vaccinia virus vaccine vector expressing pre-fusion stabilized SARS-CoV-2 spike fully protected mice against lethal challenge with the heavily mutated mouse-adapted SARS2-N501YMA30 strain of SARS-CoV-2

Author

Kibler, Karen V., primary, Szczerba, Mateusz, additional, Lake, Douglas, additional, Roeder, Alexa J., additional, Rahman, Masmudur, additional, Hogue, Brenda G., additional, Wong, Lok-Yin Roy, additional, Perlman, Stanley, additional, Li, Yize, additional, and Jacobs, Bertram L., additional

Published
2021
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37. Intranasal Immunization with a Vaccinia Virus Vaccine Vector Expressing Pre-Fusion Stabilized SARS-CoV-2 Spike Fully Protected Mice against Lethal Challenge with the Heavily Mutated Mouse-Adapted SARS2-N501Y MA30 Strain of SARS-CoV-2.

Author

Kibler, Karen V., Szczerba, Mateusz, Lake, Douglas, Roeder, Alexa J., Rahman, Masmudur, Hogue, Brenda G., Roy Wong, Lok-Yin, Perlman, Stanley, Li, Yize, and Jacobs, Bertram L.

Subjects
VACCINIA, VIRAL vaccines, SARS-CoV-2 Omicron variant, SARS-CoV-2, IMMUNIZATION, ADENOVIRUS diseases
Abstract

The Omicron SARS-CoV-2 variant has been designated as a variant of concern because its spike protein is heavily mutated. In particular, the Omicron spike is mutated at five positions (K417, N440, E484, Q493, and N501) that have been associated with escape from neutralizing antibodies induced by either infection with or immunization against the early Washington strain of SARS-CoV-2. The mouse-adapted strain of SARS-CoV-2, SARS2-N501YMA30, contains a spike that is also heavily mutated, with mutations at four of the five positions in the Omicron spike associated with neutralizing antibody escape (K417, E484, Q493, and N501). In this manuscript, we show that intranasal immunization with a pre-fusion stabilized Washington strain spike, expressed from a highly attenuated, replication-competent vaccinia virus construct, NYVAC-KC, fully protected mice against symptoms and death from SARS2-N501YMA30. Similarly, immunization by scarification on the skin fully protected against death, but not from mild disease. This data demonstrates that the Washington strain spike, when expressed from a highly attenuated, replication-competent poxvirus—administered without parenteral injection—can fully protect against the heavily mutated mouse-adapted SARS2-N501YMA30. [ABSTRACT FROM AUTHOR]

Published
2022
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38. An advanced workflow for single-particle imaging with the limited data at an X-ray free-electron laser

Author

Assalauova, Dameli, primary, Kim, Young Yong, additional, Bobkov, Sergey, additional, Khubbutdinov, Ruslan, additional, Rose, Max, additional, Alvarez, Roberto, additional, Andreasson, Jakob, additional, Balaur, Eugeniu, additional, Contreras, Alice, additional, DeMirci, Hasan, additional, Gelisio, Luca, additional, Hajdu, Janos, additional, Hunter, Mark S., additional, Kurta, Ruslan P., additional, Li, Haoyuan, additional, McFadden, Matthew, additional, Nazari, Reza, additional, Schwander, Peter, additional, Teslyuk, Anton, additional, Walter, Peter, additional, Xavier, P. Lourdu, additional, Yoon, Chun Hong, additional, Zaare, Sahba, additional, Ilyin, Viacheslav A., additional, Kirian, Richard A., additional, Hogue, Brenda G., additional, Aquila, Andrew, additional, and Vartanyants, Ivan A., additional

Published
2020
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41. An advanced workflow for single-particle imaging with the limited data at an X-ray free-electron laser

Author

Demirci, Hasan (ORCID 0000-0002-9135-5397 & YÖK ID 307350), Assalauova, Dameli; Kim, Young Yong; Bobkov, Sergey; Khubbutdinov, Ruslan; Rose, Max; Alvarez, Roberto; Andreasson, Jakob; Balaur, Eugeniu; Contreras, Alice; Gelisio, Luca; Hajdu, Janos; Hunter, Mark S.; Kurta, Ruslan P.; Li, Haoyuan; McFadden, Matthew; Nazari, Reza; Schwander, Peter; Teslyuk, Anton; Walter, Peter; Xavier, P. Lourdu; Yoon, Chun Hong; Zaare, Sahba; Ilyin, Viacheslav A.; Kirian, Richard A.; Hogue, Brenda G.; Aquila, Andrew; Vartanyants, Ivan A., College of Sciences, Department of Molecular Biology and Genetics, Demirci, Hasan (ORCID 0000-0002-9135-5397 & YÖK ID 307350), Assalauova, Dameli; Kim, Young Yong; Bobkov, Sergey; Khubbutdinov, Ruslan; Rose, Max; Alvarez, Roberto; Andreasson, Jakob; Balaur, Eugeniu; Contreras, Alice; Gelisio, Luca; Hajdu, Janos; Hunter, Mark S.; Kurta, Ruslan P.; Li, Haoyuan; McFadden, Matthew; Nazari, Reza; Schwander, Peter; Teslyuk, Anton; Walter, Peter; Xavier, P. Lourdu; Yoon, Chun Hong; Zaare, Sahba; Ilyin, Viacheslav A.; Kirian, Richard A.; Hogue, Brenda G.; Aquila, Andrew; Vartanyants, Ivan A., College of Sciences, and Department of Molecular Biology and Genetics

Abstract

An improved analysis for single-particle imaging (SPI) experiments, using the limited data, is presented here. Results are based on a study of bacteriophage PR772 performed at the Atomic, Molecular and Optical Science instrument at the Linac Coherent Light Source as part of the SPI initiative. Existing methods were modified to cope with the shortcomings of the experimental data: inaccessibility of information from half of the detector and a small fraction of single hits. The general SPI analysis workflow was upgraded with the expectation-maximization based classification of diffraction patterns and mode decomposition on the final virus-structure determination step. The presented processing pipeline allowed us to determine the 3D structure of bacteriophage PR772 without symmetry constraints with a spatial resolution of 6.9 nm. The obtained resolution was limited by the scattering intensity during the experiment and the relatively small number of single hits., European Union (European Union); Horizon 2020; European Research Council (ERC); Frontiers in Attosecond X-ray Science: Imaging and Spectroscopy (AXSIS); Scientific and Technological Research Council of Turkey (TÜBİTAK); Helmholtz Associations Initiative Networking Fund; Russian Science Foundation; US National Science Foundation (NSF) Science and Technology Center BioXFEL Award; European Regional Development Fund (ADONIS); Ministry of Education, Youth and Sports; National Program of Sustainability II; Human Frontier Science Program; Joachim Herz Stiftung Fellowship; Swedish Research Council; Knut and Alice Wallenberg Foundation; European Research Council (ERC); Röntgen–Ångström Cluster; Structural Dynamics of Biomolecular Systems; European Regional Development Fund; Australian Research Council Centre of Excellence in Advanced Molecular Imaging

Published
2020

43. Low-signal limit of X-ray single particle diffractive imaging

Author

Ayyer, Kartik, primary, Morgan, Andrew J., additional, Aquila, Andrew, additional, DeMirci, Hasan, additional, Hogue, Brenda G., additional, Kirian, Richard A., additional, Xavier, P. Lourdu, additional, Yoon, Chun Hong, additional, Chapman, Henry N., additional, and Barty, Anton, additional

Published
2019
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44. Low-signal limit of X-ray single particle diffractive imaging

Author

Demirci, Hasan (ORCID 0000-0002-9135-5397 & YÖK ID 307350), Ayyer, Kartik; Morgan, Andrew J.; Aquila, Andrew; Hogue, Brenda G.; Kirian, Richard A.; Xavier, P. Lourdu; Yoon, Chun Hong; Chapman, Henry N.; Barty, Anton, College of Sciences, Department of Molecular Biology and Genetics, Demirci, Hasan (ORCID 0000-0002-9135-5397 & YÖK ID 307350), Ayyer, Kartik; Morgan, Andrew J.; Aquila, Andrew; Hogue, Brenda G.; Kirian, Richard A.; Xavier, P. Lourdu; Yoon, Chun Hong; Chapman, Henry N.; Barty, Anton, College of Sciences, and Department of Molecular Biology and Genetics

Abstract

An outstanding question in X-ray single particle imaging experiments has been the feasibility of imaging sub 10-nm-sized biomolecules under realistic experimental conditions where very few photons are expected to be measured in a single snapshot and instrument background may be significant relative to particle scattering. While analyses of simulated data have shown that the determination of an average image should be feasible using Bayesian methods such as the EMC algorithm, this has yet to be demonstrated using experimental data containing realistic non-isotropic instrument background, sample variability and other experimental factors. In this work, we show that the orientation and phase retrieval steps work at photon counts diluted to the signal levels one expects from smaller molecules or with weaker pulses, using data from experimental measurements of 60-nm PR772 viruses. Even when the signal is reduced to a fraction as little as 1/256, the virus electron density determined using ab initio phasing is of almost the same quality as the high-signal data. However, we are still limited by the total number of patterns collected, which may soon be mitigated by the advent of high repetition-rate sources like the European XFEL and LCLS-II., Basic Energy Sciences; National Science Foundation BioXFEL award; European Research Council (ERC); European Union (European Union); Human Frontier Science Program; Exzellenzclusters Entzundungsforschung; Helmholtz Association; Australian Research Council

Published
2019

45. Rapid sample delivery for megahertz serial crystallography at X-ray FELs

Author

Wiedorn, Max Oliver, Awel, Salah, Morgan, Andrew J., Ayyer, Kartik, Gevorkov, Yaroslav, Fleckenstein, Holger, Roth, Nils, Adriano, Luigi, Bean, Richard, Beyerlein, Kenneth R., Chen, Joe, Coe, Jesse, Cruz-Mazo, Francisco, Ekeberg, Tomas, Graceffa, Rita, Heymann, Michael, Horke, Daniel A., Knoška, Juraj, Mariani, Valerio, Nazari, Reza, Oberthür, Dominik, Samanta, Amit K., Sierra, Raymond G., Stan, Claudiu A., Yefanov, Oleksandr, Rompotis, Dimitrios, Correa, Jonathan, Erk, Benjamin, Treusch, Rolf, Schulz, Joachim, Hogue, Brenda G., Gañán-Calvo, Alfonso M., Fromme, Petra, Küpper, Jochen, Rode, Andrei V., Bajt, Saša, Kirian, Richard A., Chapman, Henry N., Wiedorn, Max Oliver, Awel, Salah, Morgan, Andrew J., Ayyer, Kartik, Gevorkov, Yaroslav, Fleckenstein, Holger, Roth, Nils, Adriano, Luigi, Bean, Richard, Beyerlein, Kenneth R., Chen, Joe, Coe, Jesse, Cruz-Mazo, Francisco, Ekeberg, Tomas, Graceffa, Rita, Heymann, Michael, Horke, Daniel A., Knoška, Juraj, Mariani, Valerio, Nazari, Reza, Oberthür, Dominik, Samanta, Amit K., Sierra, Raymond G., Stan, Claudiu A., Yefanov, Oleksandr, Rompotis, Dimitrios, Correa, Jonathan, Erk, Benjamin, Treusch, Rolf, Schulz, Joachim, Hogue, Brenda G., Gañán-Calvo, Alfonso M., Fromme, Petra, Küpper, Jochen, Rode, Andrei V., Bajt, Saša, Kirian, Richard A., and Chapman, Henry N.

Abstract

Liquid microjets are a common means of delivering protein crystals to the focus of X-ray free-electron lasers (FELs) for serial femtosecond crystallography measurements. The high X-ray intensity in the focus initiates an explosion of the microjet and sample. With the advent of X-ray FELs with megahertz rates, the typical velocities of these jets must be increased significantly in order to replenish the damaged material in time for the subsequent measurement with the next X-ray pulse. This work reports the results of a megahertz serial diffraction experiment at the FLASH FEL facility using 4.3 nm radiation. The operation of gas-dynamic nozzles that produce liquid microjets with velocities greater than 80 m s-1 was demonstrated. Furthermore, this article provides optical images of X-ray-induced explosions together with Bragg diffraction from protein microcrystals exposed to trains of X-ray pulses repeating at rates of up to 4.5 MHz. The results indicate the feasibility for megahertz serial crystallography measurements with hard X-rays and give guidance for the design of such experiments.

Published
2019

47. Evaluation of the performance of classification algorithms for XFEL single-particle imaging data

Author

Shi, Yingchen, primary, Yin, Ke, additional, Tai, Xuecheng, additional, DeMirci, Hasan, additional, Hosseinizadeh, Ahmad, additional, Hogue, Brenda G., additional, Li, Haoyuan, additional, Ourmazd, Abbas, additional, Schwander, Peter, additional, Vartanyants, Ivan A., additional, Yoon, Chun Hong, additional, Aquila, Andrew, additional, and Liu, Haiguang, additional

Published
2019
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48. Rapid sample delivery for megahertz serial crystallography at X-ray FELs

Author

Wiedorn, Max O., primary, Awel, Salah, additional, Morgan, Andrew J., additional, Ayyer, Kartik, additional, Gevorkov, Yaroslav, additional, Fleckenstein, Holger, additional, Roth, Nils, additional, Adriano, Luigi, additional, Bean, Richard, additional, Beyerlein, Kenneth R., additional, Chen, Joe, additional, Coe, Jesse, additional, Cruz-Mazo, Francisco, additional, Ekeberg, Tomas, additional, Graceffa, Rita, additional, Heymann, Michael, additional, Horke, Daniel A., additional, Knoška, Juraj, additional, Mariani, Valerio, additional, Nazari, Reza, additional, Oberthür, Dominik, additional, Samanta, Amit K., additional, Sierra, Raymond G., additional, Stan, Claudiu A., additional, Yefanov, Oleksandr, additional, Rompotis, Dimitrios, additional, Correa, Jonathan, additional, Erk, Benjamin, additional, Treusch, Rolf, additional, Schulz, Joachim, additional, Hogue, Brenda G., additional, Gañán-Calvo, Alfonso M., additional, Fromme, Petra, additional, Küpper, Jochen, additional, Rode, Andrei V., additional, Bajt, Saša, additional, Kirian, Richard A., additional, and Chapman, Henry N., additional

Published
2018
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