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  1. Article ; Online: Antibody-mediated neutralization of SARS-CoV-2.

    Gruell, Henning / Vanshylla, Kanika / Weber, Timm / Barnes, Christopher O / Kreer, Christoph / Klein, Florian

    Immunity

    2022  Volume 55, Issue 6, Page(s) 925–944

    Abstract: Neutralizing antibodies can block infection, clear pathogens, and are essential to provide long-term immunity. Since the onset of the pandemic, SARS-CoV-2 neutralizing antibodies have been comprehensively investigated and critical information on their ... ...

    Abstract Neutralizing antibodies can block infection, clear pathogens, and are essential to provide long-term immunity. Since the onset of the pandemic, SARS-CoV-2 neutralizing antibodies have been comprehensively investigated and critical information on their development, function, and potential use to prevent and treat COVID-19 have been revealed. With the emergence of SARS-CoV-2 immune escape variants, humoral immunity is being challenged, and a detailed understanding of neutralizing antibodies is essential to guide vaccine design strategies as well as antibody-mediated therapies. In this review, we summarize some of the key findings on SARS-CoV-2 neutralizing antibodies, with a focus on their clinical application.
    MeSH term(s) Antibodies, Neutralizing ; Antibodies, Viral ; COVID-19 ; Humans ; Neutralization Tests ; SARS-CoV-2 ; Vaccination
    Chemical Substances Antibodies, Neutralizing ; Antibodies, Viral
    Language English
    Publishing date 2022-05-13
    Publishing country United States
    Document type Journal Article ; Review ; Research Support, Non-U.S. Gov't
    ZDB-ID 1217235-2
    ISSN 1097-4180 ; 1074-7613
    ISSN (online) 1097-4180
    ISSN 1074-7613
    DOI 10.1016/j.immuni.2022.05.005
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  2. Article ; Online: Author Correction: SARS-CoV-2 neutralizing antibody structures inform therapeutic strategies.

    Barnes, Christopher O / Jette, Claudia A / Abernathy, Morgan E / Dam, Kim-Marie A / Esswein, Shannon R / Gristick, Harry B / Malyutin, Andrey G / Sharaf, Naima G / Huey-Tubman, Kathryn E / Lee, Yu E / Robbiani, Davide F / Nussenzweig, Michel C / West, Anthony P / Bjorkman, Pamela J

    Nature

    2024  Volume 628, Issue 8008, Page(s) E2

    Language English
    Publishing date 2024-04-18
    Publishing country England
    Document type Published Erratum
    ZDB-ID 120714-3
    ISSN 1476-4687 ; 0028-0836
    ISSN (online) 1476-4687
    ISSN 0028-0836
    DOI 10.1038/s41586-024-07344-w
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  3. Article ; Online: Vaccine design via antigen reorientation.

    Xu, Duo / Carter, Joshua J / Li, Chunfeng / Utz, Ashley / Weidenbacher, Payton A B / Tang, Shaogeng / Sanyal, Mrinmoy / Pulendran, Bali / Barnes, Christopher O / Kim, Peter S

    Nature chemical biology

    2024  

    Abstract: A major challenge in creating universal influenza vaccines is to focus immune responses away from the immunodominant, variable head region of hemagglutinin (HA-head) and toward the evolutionarily conserved stem region (HA-stem). Here we introduce an ... ...

    Abstract A major challenge in creating universal influenza vaccines is to focus immune responses away from the immunodominant, variable head region of hemagglutinin (HA-head) and toward the evolutionarily conserved stem region (HA-stem). Here we introduce an approach to control antigen orientation via site-specific insertion of aspartate residues that facilitates antigen binding to alum. We demonstrate the generalizability of this approach with antigens from Ebola, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and influenza viruses and observe enhanced neutralizing antibody responses in all cases. We then reorient an H2 HA in an 'upside-down' configuration to increase the exposure and immunogenicity of HA-stem. The reoriented H2 HA (reoH2HA) on alum induced stem-directed antibodies that cross-react with both group 1 and group 2 influenza A subtypes. Electron microscopy polyclonal epitope mapping (EMPEM) revealed that reoH2HA (group 1) elicits cross-reactive antibodies targeting group 2 HA-stems. Our results highlight antigen reorientation as a generalizable approach for designing epitope-focused vaccines.
    Language English
    Publishing date 2024-01-15
    Publishing country United States
    Document type Journal Article
    ZDB-ID 2202962-X
    ISSN 1552-4469 ; 1552-4450
    ISSN (online) 1552-4469
    ISSN 1552-4450
    DOI 10.1038/s41589-023-01529-6
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  4. Article: Discovery and engineering of the antibody response against a prominent skin commensal.

    Bousbaine, Djenet / Bauman, Katherine D / Chen, Y Erin / Yu, Victor K / Lalgudi, Pranav V / Naziripour, Arash / Veinbachs, Alessandra / Phung, Jennie L / Nguyen, Tam T D / Swenson, Joyce M / Lee, Yue E / Dimas, Alex / Jain, Sunit / Meng, Xiandong / Pham, Thi Phuong Thao / Zhao, Aishan / Barkal, Layla / Gribonika, Inta / Van Rompay, Koen K A /
    Belkaid, Yasmine / Barnes, Christopher O / Fischbach, Michael A

    bioRxiv : the preprint server for biology

    2024  

    Abstract: The ubiquitous skin ... ...

    Abstract The ubiquitous skin colonist
    Language English
    Publishing date 2024-01-23
    Publishing country United States
    Document type Preprint
    DOI 10.1101/2024.01.23.576900
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  5. Article ; Online: HIV-1 CD4-binding site germline antibody-Env structures inform vaccine design.

    Dam, Kim-Marie A / Barnes, Christopher O / Gristick, Harry B / Schoofs, Till / Gnanapragasam, Priyanthi N P / Nussenzweig, Michel C / Bjorkman, Pamela J

    Nature communications

    2022  Volume 13, Issue 1, Page(s) 6123

    Abstract: BG24, a VRC01-class broadly neutralizing antibody (bNAb) against HIV-1 Env with relatively few somatic hypermutations (SHMs), represents a promising target for vaccine strategies to elicit CD4-binding site (CD4bs) bNAbs. To understand how SHMs correlate ... ...

    Abstract BG24, a VRC01-class broadly neutralizing antibody (bNAb) against HIV-1 Env with relatively few somatic hypermutations (SHMs), represents a promising target for vaccine strategies to elicit CD4-binding site (CD4bs) bNAbs. To understand how SHMs correlate with BG24 neutralization of HIV-1, we report 4.1 Å and 3.4 Å single-particle cryo-EM structures of two inferred germline (iGL) BG24 precursors complexed with engineered Env-based immunogens lacking CD4bs N-glycans. Structures reveal critical Env contacts by BG24
    MeSH term(s) Antibodies, Neutralizing ; Binding Sites ; Broadly Neutralizing Antibodies ; CD4 Antigens ; Germ Cells ; HIV Antibodies ; HIV Infections/prevention & control ; HIV-1/genetics ; Humans ; Polysaccharides ; env Gene Products, Human Immunodeficiency Virus
    Chemical Substances Antibodies, Neutralizing ; Broadly Neutralizing Antibodies ; CD4 Antigens ; HIV Antibodies ; Polysaccharides ; env Gene Products, Human Immunodeficiency Virus
    Language English
    Publishing date 2022-10-17
    Publishing country England
    Document type Journal Article ; Research Support, U.S. Gov't, Non-P.H.S. ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
    ZDB-ID 2553671-0
    ISSN 2041-1723 ; 2041-1723
    ISSN (online) 2041-1723
    ISSN 2041-1723
    DOI 10.1038/s41467-022-33860-2
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  6. Article: Structural basis of transcription: RNA Polymerase II substrate binding and metal coordination at 3.0 Å using a free-electron laser.

    Lin, Guowu / Barnes, Christopher O / Weiss, Simon / Dutagaci, Bercem / Qiu, Chenxi / Feig, Michael / Song, Jihnu / Lyubimov, Artem / Cohen, Aina E / Kaplan, Craig D / Calero, Guillermo

    bioRxiv : the preprint server for biology

    2023  

    Abstract: Catalysis and translocation of multi-subunit DNA-directed RNA polymerases underlie all cellular mRNA synthesis. RNA polymerase II (Pol II) synthesizes eukaryotic pre-mRNAs from a DNA template strand buried in its active site. Structural details of ... ...

    Abstract Catalysis and translocation of multi-subunit DNA-directed RNA polymerases underlie all cellular mRNA synthesis. RNA polymerase II (Pol II) synthesizes eukaryotic pre-mRNAs from a DNA template strand buried in its active site. Structural details of catalysis at near atomic resolution and precise arrangement of key active site components have been elusive. Here we present the free electron laser (FEL) structure of a matched ATP-bound Pol II, revealing the full active site interaction network at the highest resolution to date, including the trigger loop (TL) in the closed conformation, bonafide occupancy of both site A and B Mg
    Language English
    Publishing date 2023-09-22
    Publishing country United States
    Document type Preprint
    DOI 10.1101/2023.09.22.559052
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  7. Article ; Online: SARS-CoV-2 lineage B.1.526 emerging in the New York region detected by software utility created to query the spike mutational landscape

    West, Anthony P / Barnes, Christopher O / Yang, Zhi / Bjorkman, Pamela J

    bioRxiv

    Abstract: Wide-scale SARS-CoV-2 genome sequencing is critical to monitoring and understanding viral evolution during the ongoing pandemic. Variants first detected in the United Kingdom, South Africa, and Brazil have spread to multiple countries. We have developed ... ...

    Abstract Wide-scale SARS-CoV-2 genome sequencing is critical to monitoring and understanding viral evolution during the ongoing pandemic. Variants first detected in the United Kingdom, South Africa, and Brazil have spread to multiple countries. We have developed a software tool, Variant Database (VDB), for quickly examining the changing landscape of spike mutations. Using this tool, we detected an emerging lineage of viral isolates in the New York region that shares mutations with previously reported variants. The most common sets of spike mutations in this lineage (now designated as B.1.526) are L5F, T95I, D253G, E484K or S477N, D614G, and A701V. This lineage appeared in late November 2020, and isolates from this lineage account for ~5% of coronavirus genomes sequenced and deposited from New York during late January 2021.
    Keywords covid19
    Language English
    Publishing date 2021-02-15
    Publisher Cold Spring Harbor Laboratory
    Document type Article ; Online
    DOI 10.1101/2021.02.14.431043
    Database COVID19

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  8. Article: A sampling strategy for genome sequencing the British terrestrial arthropod fauna.

    Crowley, Liam / Allen, Heather / Barnes, Ian / Boyes, Douglas / Broad, Gavin R / Fletcher, Christopher / Holland, Peter W H / Januszczak, Inez / Lawniczak, Mara / Lewis, Owen T / Macadam, Craig R / Mulhair, Peter O / Pereira da Conceicoa, Lyndall / Price, Benjamin W / Raper, Chris / Sivell, Olga / Sivess, Laura

    Wellcome open research

    2023  Volume 8, Page(s) 123

    Abstract: The Darwin Tree of Life (DToL) project aims to sequence and assemble high-quality genomes from all eukaryote species in Britain and Ireland, with the first phase of the project concentrating on family-level coverage plus species of particular ecological, ...

    Abstract The Darwin Tree of Life (DToL) project aims to sequence and assemble high-quality genomes from all eukaryote species in Britain and Ireland, with the first phase of the project concentrating on family-level coverage plus species of particular ecological, biomedical or evolutionary interest. We summarise the processes involved in (1) assessing the UK arthropod fauna and the status of individual species on UK lists; (2) prioritising and collecting species for initial genome sequencing; (3) handling methods to ensure that high-quality genomic DNA is preserved; and (4) compiling standard operating procedures for processing specimens for genome sequencing, identification verification and voucher specimen curation. We briefly explore some lessons learned from the pilot phase of DToL and the impact of the Covid-19 pandemic.
    Language English
    Publishing date 2023-03-20
    Publishing country England
    Document type Journal Article
    ISSN 2398-502X
    ISSN 2398-502X
    DOI 10.12688/wellcomeopenres.18925.1
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  9. Article ; Online: Desert diversity: genome sequence of

    Barnes, October / Workman, Christopher J / Patterson, Noah C / Oesch, Riley / Johnson, Katie L / Goncz, Kaarin / Sharbrough, Joel / DeVeaux, Linda C

    Microbiology resource announcements

    2024  Volume 13, Issue 4, Page(s) e0124523

    Abstract: Lytic bacteriophages Mossy and Erutan were directly isolated from desert soil ... ...

    Abstract Lytic bacteriophages Mossy and Erutan were directly isolated from desert soil on
    Language English
    Publishing date 2024-03-12
    Publishing country United States
    Document type Journal Article
    ISSN 2576-098X
    ISSN (online) 2576-098X
    DOI 10.1128/mra.01245-23
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  10. Article ; Online: Cryo-EM structures of HIV-1 trimer bound to CD4-mimetics BNM-III-170 and M48U1 adopt a CD4-bound open conformation

    Claudia A. Jette / Christopher O. Barnes / Sharon M. Kirk / Bruno Melillo / Amos B. Smith / Pamela J. Bjorkman

    Nature Communications, Vol 12, Iss 1, Pp 1-

    2021  Volume 10

    Abstract: Conformational changes of HIV’s Env protein are required for its function in fusing the viral and host cell membranes. Here the authors describe how two small molecules alter the confirmation of Env trimers, and show they can induce structural changes ... ...

    Abstract Conformational changes of HIV’s Env protein are required for its function in fusing the viral and host cell membranes. Here the authors describe how two small molecules alter the confirmation of Env trimers, and show they can induce structural changes similar to those occur upon receptor binding.
    Keywords Science ; Q
    Language English
    Publishing date 2021-03-01T00:00:00Z
    Publisher Nature Portfolio
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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