Virus:Article Title: Multivalent antigen display on nanoparticle immunogens increases B cell clonotype diversity and neutralization breadth to pneumoviruses.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Polyclonal goat anti-human IgD FITC Southern Biotech Cat2030-02, RRID:AB_2795624 Mouse anti-human IgG BV786 (G18-145) BD Biosciences Cat#564230, RRID:AB_2738684 Mouse F(ab’)2 anti-human IgM, unlabeled Southern Biotech Cat#9023-01, RRID:AB_2796589 Anti-RSV-F site Ø (D25) McLellan et al.36 N/A Anti-RSV-F site I (ADI-14457) Gilman et al.28 N/A Anti-RSV-F site II (Palivizumab) McLellan et al.37 N/A Anti-RSV-F site II (Motavizumab) McLellan et al.37 N/A Anti-RSV-F site III (MPE8) Corti et al.41 N/A Anti-RSV-F site IV (101F) McLellan et al.37 N/A Anti-RSV-F site V (hRSV90) Mousa et al.58 N/A Anti-RSV-F site V (CR9501) Gilman et al.59 N/A Anti-RSV-F site I (4D7) Flynn et al.60 N/A Anti-RSV-F quaternary (AM14) Gilman et al.61 N/A Anti-RSV-F LOR antibodies This paper Table S1 Bacterial and virus strains Recombinant RSV A2 mKATE Hotard et al.62 N/A Recombinant MPV A2 GFP ViraTree Cat#M121 Biological samples Antiserum to Respiratory Syncytial Virus WHO 1st International Standard NIBSC Cat#16/284 Healthy human blood (buffy coats) from anonymous donors Karolinska University Hospital, Stockholm, Sweden N/A Chemicals, peptides, and recombinant proteins I53-50A Bale et al.63 N/A I53-50B.4PT1 Bale et al.63 N/A DS-Cav1-I53-50A Marcandalli et al.4 N/A RSV preF (DS-Cav1) McLellan et al.23 N/A RSV preF (SC-DM) Krarup et al.45 N/A RSV postF (RSV-F dFP) McLellan et al.37 N/A MPV preF (115-BV) Battles et al.55 N/A High Sensitivity NeutrAvidin-conjugated HRP Thermo Scientific Cat#31030 Streptavidin-conjugated APC Biolegend Cat#405243 Streptavidin-conjugated BV421 Biolegend Cat#405225 Streptavidin-conjugated ALP Mabtech Cat#3310-10-1000 FcR Blocking Reagent, human Miltenyi Cat#130-059-901 1-Step Ultra TMB-ELISA Substrate Solution Thermo Scientific Cat#34029 BCIP/NBT substrate Mabtech Cat#3650-10 RSV F (DS-Cav1) overlapping peptides This paper N/A Brefeldin A Invitrogen Cat#B7450 Staphylococcal enterotoxin B (SEB) Sigma Cat#S4881 CpG class B (ODN 2006) Invivogen Cat#tlrl-2006 Pokeweed mitogen Sigma Cat#L8777 Protein A from Staphylococcus aureus Cowan strain Sigma Cat#P7155 Liberase TL Research Grade Sigma Cat#5401020001 Deoxyribonuclease I (DNase I) from bovine pancreas Sigma Cat#DN25 Trypsin Gibco Cat#15090046 Sodium thiocyanate (NaSCN) Sigma Cat#467871 (Continued on next page) Immunity 56, 2425–2441.e1–e14, October 10, 2023 e2 .. REAGENT or RESOURCE SOURCE IDENTIFIER Indian-origin rhesus macaques (outbred) Bioqual, Inc., Rockville, MD, USA N/A Oligonucleotides Primers used for RT-PCR and nested PCRs Sundling et al.64; Sundling et al.65 N/A Primers used for library preparation Phad et al.40; Vázquez Bernat et al.66; Vázquez Bernat et al.67 N/A Random hexamers Invitrogen Cat#48190011 dNTP kit Invitrogen Cat#10297018 Recombinant DNA pLVX-ZsGreen-hIgM-VH Gift from Adrian McDermott N/A pLVX-mCherry-hIgM-VK Gift from Adrian McDermott N/A psPAX2 plasmid Gift from Didier Trono Addgene plasmid # 12260, RRID:Addgene_12260 pMD2.G plasmid Gift from Didier Trono Addgene plasmid # 12259, RRID:Addgene_12259 Software and algorithms FlowJo v10 FlowJo, LLC RRID:SCR_008520, https://www.flowjo.com/ solutions/flowjo/ Prism v9 GraphPad RRID:SCR_002798, https://www.graphpad.com/ scientific-software/prism/ Illustrator v27.7 Adobe RRID:SCR_010279, https://www.adobe.com/ products/illustrator.html ForteBio Data Analysis Software, version 12 Sartorius https://www.sartorius.com/en/products/ protein-analysis/octet-bli-detection/ octet-systems-software IgDiscover v0.15.1 Corcoran et al.68 https://docs.igdiscover.se/en/stable/ MUSCLE v5.1 Edgar69 https://www.drive5.com/muscle/ Fasttree v2.1.11 Price et al.70 http://www.microbesonline.org/fasttree/ R v4.2.2 CRAN https://www.r-project.org/ scifer v0.9.3 Bioconductor https://doi.org/10.18129/B9.bioc.scifer vegan v2.6.4 CRAN https://cran.r-project.org/web/packages/ vegan/index.html Recon v3.0 Kaplinsky et al.71 http://arnaoutlab.github.io/Recon/ treeio v1.22.0 Wang et al.72 https://doi.org/10.18129/B9.bioc.treeio ggtree v.3.6.0 Yu et al.73 https://doi.org/10.18129/B9.bioc.ggtree Code rendered as a webpage and raw code This paper https://rodrigarc.github.io/ RSV-NP-repertoire/ Leginon v3.4 Suloway et al.74 https://emg.nysbc.org/redmine/projects/ leginon/wiki/Leginon_Homepage CTFFIND v4 Mindell and Grigorieff75 https://grigoriefflab.umassmed.edu/ctffind4 cisTEM v1.0.0 Grant et al.76 https://cistem.org/ RELION v3.1 Kimanius et al.77; Scheres78; Zivanov et al.79 https://github.com/3dem/relion EPU v2 Thermo Scientific https://www.thermofisher.com/us/en/ home/electron-microscopy/products/ software-em-3d-vis/epu-software.html CryoSPARC v3.2 Punjani et al.80 https://cryosparc.com/download Other Squalene oil-in-water emulsion (SWE) adjuvant Vaccine Formulation Institute (VFI), Lausanne, Switzerland N/A Carbon Square Mesh, Cu, 400 Mesh, TH Electron Microscopy Sciences Cat#CF400-Cu-TH Immunity 56, 2425–2441.e1–e14, October 10, 2023 e4
Recombinant:Article Title: Multivalent antigen display on nanoparticle immunogens increases B cell clonotype diversity and neutralization breadth to pneumoviruses.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Polyclonal goat anti-human IgD FITC Southern Biotech Cat2030-02, RRID:AB_2795624 Mouse anti-human IgG BV786 (G18-145) BD Biosciences Cat#564230, RRID:AB_2738684 Mouse F(ab’)2 anti-human IgM, unlabeled Southern Biotech Cat#9023-01, RRID:AB_2796589 Anti-RSV-F site Ø (D25) McLellan et al.36 N/A Anti-RSV-F site I (ADI-14457) Gilman et al.28 N/A Anti-RSV-F site II (Palivizumab) McLellan et al.37 N/A Anti-RSV-F site II (Motavizumab) McLellan et al.37 N/A Anti-RSV-F site III (MPE8) Corti et al.41 N/A Anti-RSV-F site IV (101F) McLellan et al.37 N/A Anti-RSV-F site V (hRSV90) Mousa et al.58 N/A Anti-RSV-F site V (CR9501) Gilman et al.59 N/A Anti-RSV-F site I (4D7) Flynn et al.60 N/A Anti-RSV-F quaternary (AM14) Gilman et al.61 N/A Anti-RSV-F LOR antibodies This paper Table S1 Bacterial and virus strains Recombinant RSV A2 mKATE Hotard et al.62 N/A Recombinant MPV A2 GFP ViraTree Cat#M121 Biological samples Antiserum to Respiratory Syncytial Virus WHO 1st International Standard NIBSC Cat#16/284 Healthy human blood (buffy coats) from anonymous donors Karolinska University Hospital, Stockholm, Sweden N/A Chemicals, peptides, and recombinant proteins I53-50A Bale et al.63 N/A I53-50B.4PT1 Bale et al.63 N/A DS-Cav1-I53-50A Marcandalli et al.4 N/A RSV preF (DS-Cav1) McLellan et al.23 N/A RSV preF (SC-DM) Krarup et al.45 N/A RSV postF (RSV-F dFP) McLellan et al.37 N/A MPV preF (115-BV) Battles et al.55 N/A High Sensitivity NeutrAvidin-conjugated HRP Thermo Scientific Cat#31030 Streptavidin-conjugated APC Biolegend Cat#405243 Streptavidin-conjugated BV421 Biolegend Cat#405225 Streptavidin-conjugated ALP Mabtech Cat#3310-10-1000 FcR Blocking Reagent, human Miltenyi Cat#130-059-901 1-Step Ultra TMB-ELISA Substrate Solution Thermo Scientific Cat#34029 BCIP/NBT substrate Mabtech Cat#3650-10 RSV F (DS-Cav1) overlapping peptides This paper N/A Brefeldin A Invitrogen Cat#B7450 Staphylococcal enterotoxin B (SEB) Sigma Cat#S4881 CpG class B (ODN 2006) Invivogen Cat#tlrl-2006 Pokeweed mitogen Sigma Cat#L8777 Protein A from Staphylococcus aureus Cowan strain Sigma Cat#P7155 Liberase TL Research Grade Sigma Cat#5401020001 Deoxyribonuclease I (DNase I) from bovine pancreas Sigma Cat#DN25 Trypsin Gibco Cat#15090046 Sodium thiocyanate (NaSCN) Sigma Cat#467871 (Continued on next page) Immunity 56, 2425–2441.e1–e14, October 10, 2023 e2 .. REAGENT or RESOURCE SOURCE IDENTIFIER Indian-origin rhesus macaques (outbred) Bioqual, Inc., Rockville, MD, USA N/A Oligonucleotides Primers used for RT-PCR and nested PCRs Sundling et al.64; Sundling et al.65 N/A Primers used for library preparation Phad et al.40; Vázquez Bernat et al.66; Vázquez Bernat et al.67 N/A Random hexamers Invitrogen Cat#48190011 dNTP kit Invitrogen Cat#10297018 Recombinant DNA pLVX-ZsGreen-hIgM-VH Gift from Adrian McDermott N/A pLVX-mCherry-hIgM-VK Gift from Adrian McDermott N/A psPAX2 plasmid Gift from Didier Trono Addgene plasmid # 12260, RRID:Addgene_12260 pMD2.G plasmid Gift from Didier Trono Addgene plasmid # 12259, RRID:Addgene_12259 Software and algorithms FlowJo v10 FlowJo, LLC RRID:SCR_008520, https://www.flowjo.com/ solutions/flowjo/ Prism v9 GraphPad RRID:SCR_002798, https://www.graphpad.com/ scientific-software/prism/ Illustrator v27.7 Adobe RRID:SCR_010279, https://www.adobe.com/ products/illustrator.html ForteBio Data Analysis Software, version 12 Sartorius https://www.sartorius.com/en/products/ protein-analysis/octet-bli-detection/ octet-systems-software IgDiscover v0.15.1 Corcoran et al.68 https://docs.igdiscover.se/en/stable/ MUSCLE v5.1 Edgar69 https://www.drive5.com/muscle/ Fasttree v2.1.11 Price et al.70 http://www.microbesonline.org/fasttree/ R v4.2.2 CRAN https://www.r-project.org/ scifer v0.9.3 Bioconductor https://doi.org/10.18129/B9.bioc.scifer vegan v2.6.4 CRAN https://cran.r-project.org/web/packages/ vegan/index.html Recon v3.0 Kaplinsky et al.71 http://arnaoutlab.github.io/Recon/ treeio v1.22.0 Wang et al.72 https://doi.org/10.18129/B9.bioc.treeio ggtree v.3.6.0 Yu et al.73 https://doi.org/10.18129/B9.bioc.ggtree Code rendered as a webpage and raw code This paper https://rodrigarc.github.io/ RSV-NP-repertoire/ Leginon v3.4 Suloway et al.74 https://emg.nysbc.org/redmine/projects/ leginon/wiki/Leginon_Homepage CTFFIND v4 Mindell and Grigorieff75 https://grigoriefflab.umassmed.edu/ctffind4 cisTEM v1.0.0 Grant et al.76 https://cistem.org/ RELION v3.1 Kimanius et al.77; Scheres78; Zivanov et al.79 https://github.com/3dem/relion EPU v2 Thermo Scientific https://www.thermofisher.com/us/en/ home/electron-microscopy/products/ software-em-3d-vis/epu-software.html CryoSPARC v3.2 Punjani et al.80 https://cryosparc.com/download Other Squalene oil-in-water emulsion (SWE) adjuvant Vaccine Formulation Institute (VFI), Lausanne, Switzerland N/A Carbon Square Mesh, Cu, 400 Mesh, TH Electron Microscopy Sciences Cat#CF400-Cu-TH Immunity 56, 2425–2441.e1–e14, October 10, 2023 e4
Blocking Assay:Article Title: Multivalent antigen display on nanoparticle immunogens increases B cell clonotype diversity and neutralization breadth to pneumoviruses.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Polyclonal goat anti-human IgD FITC Southern Biotech Cat2030-02, RRID:AB_2795624 Mouse anti-human IgG BV786 (G18-145) BD Biosciences Cat#564230, RRID:AB_2738684 Mouse F(ab’)2 anti-human IgM, unlabeled Southern Biotech Cat#9023-01, RRID:AB_2796589 Anti-RSV-F site Ø (D25) McLellan et al.36 N/A Anti-RSV-F site I (ADI-14457) Gilman et al.28 N/A Anti-RSV-F site II (Palivizumab) McLellan et al.37 N/A Anti-RSV-F site II (Motavizumab) McLellan et al.37 N/A Anti-RSV-F site III (MPE8) Corti et al.41 N/A Anti-RSV-F site IV (101F) McLellan et al.37 N/A Anti-RSV-F site V (hRSV90) Mousa et al.58 N/A Anti-RSV-F site V (CR9501) Gilman et al.59 N/A Anti-RSV-F site I (4D7) Flynn et al.60 N/A Anti-RSV-F quaternary (AM14) Gilman et al.61 N/A Anti-RSV-F LOR antibodies This paper Table S1 Bacterial and virus strains Recombinant RSV A2 mKATE Hotard et al.62 N/A Recombinant MPV A2 GFP ViraTree Cat#M121 Biological samples Antiserum to Respiratory Syncytial Virus WHO 1st International Standard NIBSC Cat#16/284 Healthy human blood (buffy coats) from anonymous donors Karolinska University Hospital, Stockholm, Sweden N/A Chemicals, peptides, and recombinant proteins I53-50A Bale et al.63 N/A I53-50B.4PT1 Bale et al.63 N/A DS-Cav1-I53-50A Marcandalli et al.4 N/A RSV preF (DS-Cav1) McLellan et al.23 N/A RSV preF (SC-DM) Krarup et al.45 N/A RSV postF (RSV-F dFP) McLellan et al.37 N/A MPV preF (115-BV) Battles et al.55 N/A High Sensitivity NeutrAvidin-conjugated HRP Thermo Scientific Cat#31030 Streptavidin-conjugated APC Biolegend Cat#405243 Streptavidin-conjugated BV421 Biolegend Cat#405225 Streptavidin-conjugated ALP Mabtech Cat#3310-10-1000 FcR Blocking Reagent, human Miltenyi Cat#130-059-901 1-Step Ultra TMB-ELISA Substrate Solution Thermo Scientific Cat#34029 BCIP/NBT substrate Mabtech Cat#3650-10 RSV F (DS-Cav1) overlapping peptides This paper N/A Brefeldin A Invitrogen Cat#B7450 Staphylococcal enterotoxin B (SEB) Sigma Cat#S4881 CpG class B (ODN 2006) Invivogen Cat#tlrl-2006 Pokeweed mitogen Sigma Cat#L8777 Protein A from Staphylococcus aureus Cowan strain Sigma Cat#P7155 Liberase TL Research Grade Sigma Cat#5401020001 Deoxyribonuclease I (DNase I) from bovine pancreas Sigma Cat#DN25 Trypsin Gibco Cat#15090046 Sodium thiocyanate (NaSCN) Sigma Cat#467871 (Continued on next page) Immunity 56, 2425–2441.e1–e14, October 10, 2023 e2 .. REAGENT or RESOURCE SOURCE IDENTIFIER Indian-origin rhesus macaques (outbred) Bioqual, Inc., Rockville, MD, USA N/A Oligonucleotides Primers used for RT-PCR and nested PCRs Sundling et al.64; Sundling et al.65 N/A Primers used for library preparation Phad et al.40; Vázquez Bernat et al.66; Vázquez Bernat et al.67 N/A Random hexamers Invitrogen Cat#48190011 dNTP kit Invitrogen Cat#10297018 Recombinant DNA pLVX-ZsGreen-hIgM-VH Gift from Adrian McDermott N/A pLVX-mCherry-hIgM-VK Gift from Adrian McDermott N/A psPAX2 plasmid Gift from Didier Trono Addgene plasmid # 12260, RRID:Addgene_12260 pMD2.G plasmid Gift from Didier Trono Addgene plasmid # 12259, RRID:Addgene_12259 Software and algorithms FlowJo v10 FlowJo, LLC RRID:SCR_008520, https://www.flowjo.com/ solutions/flowjo/ Prism v9 GraphPad RRID:SCR_002798, https://www.graphpad.com/ scientific-software/prism/ Illustrator v27.7 Adobe RRID:SCR_010279, https://www.adobe.com/ products/illustrator.html ForteBio Data Analysis Software, version 12 Sartorius https://www.sartorius.com/en/products/ protein-analysis/octet-bli-detection/ octet-systems-software IgDiscover v0.15.1 Corcoran et al.68 https://docs.igdiscover.se/en/stable/ MUSCLE v5.1 Edgar69 https://www.drive5.com/muscle/ Fasttree v2.1.11 Price et al.70 http://www.microbesonline.org/fasttree/ R v4.2.2 CRAN https://www.r-project.org/ scifer v0.9.3 Bioconductor https://doi.org/10.18129/B9.bioc.scifer vegan v2.6.4 CRAN https://cran.r-project.org/web/packages/ vegan/index.html Recon v3.0 Kaplinsky et al.71 http://arnaoutlab.github.io/Recon/ treeio v1.22.0 Wang et al.72 https://doi.org/10.18129/B9.bioc.treeio ggtree v.3.6.0 Yu et al.73 https://doi.org/10.18129/B9.bioc.ggtree Code rendered as a webpage and raw code This paper https://rodrigarc.github.io/ RSV-NP-repertoire/ Leginon v3.4 Suloway et al.74 https://emg.nysbc.org/redmine/projects/ leginon/wiki/Leginon_Homepage CTFFIND v4 Mindell and Grigorieff75 https://grigoriefflab.umassmed.edu/ctffind4 cisTEM v1.0.0 Grant et al.76 https://cistem.org/ RELION v3.1 Kimanius et al.77; Scheres78; Zivanov et al.79 https://github.com/3dem/relion EPU v2 Thermo Scientific https://www.thermofisher.com/us/en/ home/electron-microscopy/products/ software-em-3d-vis/epu-software.html CryoSPARC v3.2 Punjani et al.80 https://cryosparc.com/download Other Squalene oil-in-water emulsion (SWE) adjuvant Vaccine Formulation Institute (VFI), Lausanne, Switzerland N/A Carbon Square Mesh, Cu, 400 Mesh, TH Electron Microscopy Sciences Cat#CF400-Cu-TH Immunity 56, 2425–2441.e1–e14, October 10, 2023 e4
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