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Article ; Online: Rotavirus VP4 Epitope of a Broadly Neutralizing Human Antibody Defined by Its Structure Bound with an Attenuated-Strain Virion.

Jenni, Simon / Li, Zongli / Wang, Yuhuan / Bessey, Theresa / Salgado, Eric N / Schmidt, Aaron G / Greenberg, Harry B / Jiang, Baoming / Harrison, Stephen C

Journal of virology

2022 Volume 96, Issue 16, Page(s) e0062722

Abstract: Rotavirus live-attenuated vaccines, both mono- and pentavalent, generate broadly heterotypic protection. B-cells isolated from adults encode neutralizing antibodies, some with affinity for VP5*, that afford broad protection in mice. We have mapped the ... ...

Abstract	Rotavirus live-attenuated vaccines, both mono- and pentavalent, generate broadly heterotypic protection. B-cells isolated from adults encode neutralizing antibodies, some with affinity for VP5, that afford broad protection in mice. We have mapped the epitope of one such antibody by determining the high-resolution cryo-EM structure of its antigen-binding fragment (Fab) bound to the virion of a candidate vaccine strain, CDC-9. The Fab contacts both the distal end of a VP5 β-barrel domain and the two VP8* lectin-like domains at the tip of a projecting spike. Its interactions with VP8* do not impinge on the likely receptor-binding site, suggesting that the mechanism of neutralization is at a step subsequent to initial attachment. We also examined structures of CDC-9 virions from two different stages of serial passaging. Nearly all the VP4 (cleaved to VP8/VP5) spikes on particles from the earlier passage (wild-type isolate) had transitioned from the "upright" conformation present on fully infectious virions to the "reversed" conformation that is probably the end state of membrane insertion, unable to mediate penetration, consistent with the very low
MeSH term(s)	Animals ; Broadly Neutralizing Antibodies/immunology ; Broadly Neutralizing Antibodies/ultrastructure ; Capsid Proteins/chemistry ; Capsid Proteins/immunology ; Capsid Proteins/ultrastructure ; Cryoelectron Microscopy ; Epitopes, B-Lymphocyte/immunology ; Epitopes, B-Lymphocyte/ultrastructure ; Humans ; Immunoglobulin Fab Fragments/immunology ; Immunoglobulin Fab Fragments/ultrastructure ; Mice ; Protein Conformation ; Rats ; Rotavirus/chemistry ; Rotavirus/classification ; Rotavirus/immunology ; Rotavirus/physiology ; Serial Passage ; Vaccines, Attenuated/chemistry ; Vaccines, Attenuated/immunology ; Vaccines, Attenuated/metabolism ; Virion/immunology ; Virion/metabolism ; Virion/ultrastructure
Chemical Substances	Broadly Neutralizing Antibodies ; Capsid Proteins ; Epitopes, B-Lymphocyte ; Immunoglobulin Fab Fragments ; VP4 protein, Rotavirus ; Vaccines, Attenuated
Language	English
Publishing date	2022-08-04
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't ; Research Support, N.I.H., Extramural
ZDB-ID	80174-4
ISSN	1098-5514 ; 0022-538X
ISSN (online)	1098-5514
ISSN	0022-538X
DOI	10.1128/jvi.00627-22
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Article ; Online: Functional refolding of the penetration protein on a non-enveloped virus.

Herrmann, Tobias / Torres, Raúl / Salgado, Eric N / Berciu, Cristina / Stoddard, Daniel / Nicastro, Daniela / Jenni, Simon / Harrison, Stephen C

Nature

2021 Volume 590, Issue 7847, Page(s) 666–670

Abstract: A non-enveloped virus requires a membrane lesion to deliver its genome into a target ... ...

Abstract	A non-enveloped virus requires a membrane lesion to deliver its genome into a target cell
MeSH term(s)	Animals ; Antigens, Viral/metabolism ; Capsid Proteins/chemistry ; Capsid Proteins/genetics ; Capsid Proteins/metabolism ; Capsid Proteins/ultrastructure ; Cell Line ; Cell Membrane/chemistry ; Cell Membrane/metabolism ; Cell Membrane/ultrastructure ; Cryoelectron Microscopy ; Disulfides/chemistry ; Disulfides/metabolism ; Models, Molecular ; Mutant Proteins/chemistry ; Mutant Proteins/genetics ; Mutant Proteins/metabolism ; Mutant Proteins/ultrastructure ; Mutation ; Protein Conformation ; Protein Refolding ; RNA-Binding Proteins/metabolism ; Rotavirus/chemistry ; Rotavirus/metabolism ; Rotavirus/physiology ; Rotavirus/ultrastructure ; Viral Nonstructural Proteins/metabolism ; Virion/chemistry ; Virion/metabolism ; Virion/ultrastructure ; Virus Internalization
Chemical Substances	Antigens, Viral ; Capsid Proteins ; Disulfides ; Mutant Proteins ; RNA-Binding Proteins ; VP4 protein, Rotavirus ; VP7 protein, Rotavirus ; Viral Nonstructural Proteins ; nsp1 protein, Rotavirus ; NS35 protein, rotavirus (138414-65-0)
Language	English
Publishing date	2021-01-13
Publishing country	England
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
ZDB-ID	120714-3
ISSN	1476-4687 ; 0028-0836
ISSN (online)	1476-4687
ISSN	0028-0836
DOI	10.1038/s41586-020-03124-4
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Article ; Online: Single-Particle Detection of Transcription following Rotavirus Entry.

Salgado, Eric N / Upadhyayula, Srigokul / Harrison, Stephen C

Journal of virology

2017 Volume 91, Issue 18

Abstract: Infectious rotavirus particles are triple-layered, icosahedral assemblies. The outer layer proteins, VP4 (cleaved to VP8* and VP5*) and VP7, surround a transcriptionally competent, double-layer particle (DLP), which they deliver into the cytosol. During ... ...

Abstract	Infectious rotavirus particles are triple-layered, icosahedral assemblies. The outer layer proteins, VP4 (cleaved to VP8* and VP5) and VP7, surround a transcriptionally competent, double-layer particle (DLP), which they deliver into the cytosol. During entry of rhesus rotavirus, VP8 interacts with cell surface gangliosides, allowing engulfment into a membrane vesicle by a clathrin-independent process. Escape into the cytosol and outer-layer shedding depend on interaction of a hydrophobic surface on VP5* with the membrane bilayer and on a large-scale conformational change. We report here experiments that detect the fate of released DLPs and their efficiency in initiating RNA synthesis. By replacing the outer layer with fluorescently tagged, recombinant proteins and also tagging the DLP, we distinguished particles that have lost their outer layer and entered the cytosol (uncoated) from those still within membrane vesicles. We used fluorescent
Language	English
Publishing date	2017-08-24
Publishing country	United States
Document type	Journal Article
ZDB-ID	80174-4
ISSN	1098-5514 ; 0022-538X
ISSN (online)	1098-5514
ISSN	0022-538X
DOI	10.1128/JVI.00651-17
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Article ; Online: Visualization of Calcium Ion Loss from Rotavirus during Cell Entry.

Salgado, Eric N / Garcia Rodriguez, Brian / Narayanaswamy, Nagarjun / Krishnan, Yamuna / Harrison, Stephen C

Journal of virology

2018 Volume 92, Issue 24

Abstract: Bound calcium ions stabilize many nonenveloped virions. Loss of ... ...

Abstract	Bound calcium ions stabilize many nonenveloped virions. Loss of Ca
MeSH term(s)	Animals ; Antigens, Viral/chemistry ; Antigens, Viral/metabolism ; Calcium/metabolism ; Capsid/chemistry ; Capsid/metabolism ; Capsid Proteins/chemistry ; Capsid Proteins/metabolism ; Cell Line ; Cytosol/virology ; Fluorescent Dyes/chemistry ; Microscopy, Confocal ; Protein Conformation ; Rotavirus/physiology ; Virus Internalization
Chemical Substances	Antigens, Viral ; Capsid Proteins ; Fluorescent Dyes ; VP2 protein, Rotavirus ; VP4 protein, Rotavirus ; VP6 protein, Rotavirus ; VP7 protein, Rotavirus ; Calcium (SY7Q814VUP)
Language	English
Publishing date	2018-11-27
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
ZDB-ID	80174-4
ISSN	1098-5514 ; 0022-538X
ISSN (online)	1098-5514
ISSN	0022-538X
DOI	10.1128/JVI.01327-18
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Article ; Online: Spatial Architecture of Myeloid and T Cells Orchestrates Immune Evasion and Clinical Outcome in Lung Cancer.

Enfield, Katey S S / Colliver, Emma / Lee, Claudia S Y / Magness, Alastair / Moore, David A / Sivakumar, Monica / Grigoriadis, Kristiana / Pich, Oriol / Karasaki, Takahiro / Hobson, Philip S / Levi, Dina / Veeriah, Selvaraju / Puttick, Clare / Nye, Emma L / Green, Mary / Dijkstra, Krijn K / Shimato, Masako / Akarca, Ayse U / Marafioti, Teresa /

Salgado, Roberto / Hackshaw, Allan / Consortium, TRACERx / Jamal-Hanjani, Mariam / van Maldegem, Febe / McGranahan, Nicholas / Glass, Benjamin / Pulaski, Hanna / Walk, Eric / Reading, James L / Quezada, Sergio A / Hiley, Crispin T / Downward, Julian / Sahai, Erik / Swanton, Charles / Angelova, Mihaela

Cancer discovery

2024

Abstract: ... lung cancer using imaging mass cytometry in the TRACERx study (n=81 patients/198 samples/2.3million cells ...

Abstract	Understanding the role of the tumour microenvironment (TME) in lung cancer is critical to improving patient outcome. We identified four histology-independent archetype TMEs in treatment-naive early-stage lung cancer using imaging mass cytometry in the TRACERx study (n=81 patients/198 samples/2.3million cells). In immune-hot adenocarcinomas, spatial niches of T cells and macrophages increased with clonal neoantigen burden, whereas such an increase was observed for niches of plasma and B cells in immune-excluded squamous cell carcinomas (LUSC). Immune-low TMEs were associated with fibroblast barriers to immune infiltration. The fourth archetype, characterised by sparse lymphocytes and high tumour-associated neutrophil (TAN) infiltration, had tumour cells spatially separated from vasculature and exhibited low spatial intratumour heterogeneity. TAN-High LUSC had frequent PIK3CA mutations. TAN-High tumours harboured recently expanded and metastasis-seeding subclones and had a shorter disease-free survival independent of stage. These findings delineate genomic, immune and physical barriers to immune surveillance and implicate neutrophil-rich TMEs in metastasis.
Language	English
Publishing date	2024-04-06
Publishing country	United States
Document type	Journal Article
ZDB-ID	2625242-9
ISSN	2159-8290 ; 2159-8274
ISSN (online)	2159-8290
ISSN	2159-8274
DOI	10.1158/2159-8290.CD-23-1380
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Zs.A 6916: Show issues

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Article ; Online: In situ Structure of Rotavirus VP1 RNA-Dependent RNA Polymerase.

Jenni, Simon / Salgado, Eric N / Herrmann, Tobias / Li, Zongli / Grant, Timothy / Grigorieff, Nikolaus / Trapani, Stefano / Estrozi, Leandro F / Harrison, Stephen C

Journal of molecular biology

2019 Volume 431, Issue 17, Page(s) 3124–3138

Abstract: Rotaviruses, like other non-enveloped, double-strand RNA viruses, package an RNA-dependent RNA polymerase (RdRp) with each duplex of their segmented genomes. Rotavirus cell entry results in loss of an outer protein layer and delivery into the cytosol of ... ...

Abstract	Rotaviruses, like other non-enveloped, double-strand RNA viruses, package an RNA-dependent RNA polymerase (RdRp) with each duplex of their segmented genomes. Rotavirus cell entry results in loss of an outer protein layer and delivery into the cytosol of an intact, inner capsid particle (the "double-layer particle," or DLP). The RdRp, designated VP1, is active inside the DLP; each VP1 achieves many rounds of mRNA transcription from its associated genome segment. Previous work has shown that one VP1 molecule lies close to each 5-fold axis of the icosahedrally symmetric DLP, just beneath the inner surface of its protein shell, embedded in tightly packed RNA. We have determined a high-resolution structure for the rotavirus VP1 RdRp in situ, by local reconstruction of density around individual 5-fold positions. We have analyzed intact virions ("triple-layer particles"), non-transcribing DLPs and transcribing DLPs. Outer layer dissociation enables the DLP to synthesize RNA, in vitro as well as in vivo, but appears not to induce any detectable structural change in the RdRp. Addition of NTPs, Mg
MeSH term(s)	Binding Sites ; Capsid Proteins/chemistry ; Models, Molecular ; Protein Conformation ; Protein Interaction Domains and Motifs ; RNA Replicase/chemistry ; RNA Replicase/metabolism ; RNA, Double-Stranded ; Rotavirus/genetics ; Rotavirus/metabolism ; Transcription, Genetic ; Viral Core Proteins ; Virus Replication
Chemical Substances	Capsid Proteins ; RNA, Double-Stranded ; VP1 protein, Rotavirus ; VP2 protein, Rotavirus ; Viral Core Proteins ; RNA Replicase (EC 2.7.7.48)
Language	English
Publishing date	2019-06-21
Publishing country	England
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
ZDB-ID	80229-3
ISSN	1089-8638 ; 0022-2836
ISSN (online)	1089-8638
ISSN	0022-2836
DOI	10.1016/j.jmb.2019.06.016
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Article ; Online: Two years of the COVID-19 pandemic: an anesthesiology perspective.

Schmidt, André P / Módolo, Norma S P / de Amorim, Célio G / Simões, Cláudia M / Kraychete, Durval C / Joaquim, Eduardo H G / Lineburger, Eric B / Papa, Fábio V / Fernandes, Fátima C / Mendes, Florentino F / Guimarães, Gabriel M N / Barros, Guilherme A M / Silva-Jr, João M / Navarro E Lima, Laís H / Azi, Liana M T A / Carvalho, Lorena I M / Stefani, Luciana C / Garcia, Luis V / Malbouisson, Luiz Marcelo S /

Salgado-Filho, Marcello F / Nascimento Junior, Paulo do / Alves, Rodrigo L / Carvalho, Vanessa H / Quintão, Vinicius C / Carmona, Maria José C

Brazilian journal of anesthesiology (Elsevier)

2022 Volume 72, Issue 2, Page(s) 165–168

MeSH term(s)	Anesthesiology ; COVID-19 ; Humans ; Pandemics ; SARS-CoV-2
Language	English
Publishing date	2022-02-19
Publishing country	Brazil
Document type	Editorial
ZDB-ID	1142792-9
ISSN	0104-0014 ; 0104-0014
ISSN (online)	0104-0014
ISSN	0104-0014
DOI	10.1016/j.bjane.2022.02.004
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Article ; Online: Examining the impact of a 9-component bundle and the INICC multidimensional approach on catheter-associated urinary tract infection rates in 32 countries across Asia, Eastern Europe, Latin America, and the Middle East.

Rosenthal, Victor D / Yin, Ruijie / Jin, Zhilin / Perez, Valentina / Kis, Matthew A / Abdulaziz-Alkhawaja, Safaa / Valderrama-Beltran, Sandra L / Gomez, Katherine / Rodas, Claudia M H / El-Sisi, Amal / Sahu, Suneeta / Kharbanda, Mohit / Rodrigues, Camilla / Myatra, Sheila N / Chawla, Rajesh / Sandhu, Kavita / Mehta, Yatin / Rajhans, Prasad / Arjun, Rajalakshmi /

Tai, Chian-Wern / Bhakta, Arpita / Mat Nor, Mohd-Basri / Aguirre-Avalos, Guadalupe / Sassoe-Gonzalez, Alejandro / Bat-Erdene, Ider / Acharya, Subhash P / Aguilar-de-Moros, Daisy / Carreazo, Nilton Yhuri / Duszynska, Wieslawa / Hlinkova, Sona / Yildizdas, Dincer / Kılıc, Esra K / Dursun, Oguz / Odek, Caglar / Deniz, Suna S O / Guclu, Ertugrul / Koksal, Iftihar / Medeiros, Eduardo A / Petrov, Michael M / Tao, Lili / Salgado, Estuardo / Dueñas, Lourdes / Daboor, Mohammad A / Raka, Lul / Omar, Abeer A / Ikram, Aamer / Horhat-Florin, George / Memish, Ziad A / Brown, Eric C

American journal of infection control

2024

Abstract: Background: Catheter-Associated Urinary Tract Infections (CAUTIs) frequently occur in the intensive care unit (ICU) and are correlated with a significant burden.: Methods: We implemented a strategy involving a 9-element bundle, education, ... ...

Abstract	Background: Catheter-Associated Urinary Tract Infections (CAUTIs) frequently occur in the intensive care unit (ICU) and are correlated with a significant burden. Methods: We implemented a strategy involving a 9-element bundle, education, surveillance of CAUTI rates and clinical outcomes, monitoring compliance with bundle components, feedback of CAUTI rates and performance feedback. This was executed in 299 ICUs across 32 low- and middle-income countries. The dependent variable was CAUTI per 1,000 UC days, assessed at baseline and throughout the intervention, in the second month, third month, 4 to 15 months, 16 to 27 months, and 28 to 39 months. Comparisons were made using a 2-sample t test, and the exposure-outcome relationship was explored using a generalized linear mixed model with a Poisson distribution. Results: Over the course of 978,364 patient days, 150,258 patients utilized 652,053 UC-days. The rates of CAUTI per 1,000 UC days were measured. The rates decreased from 14.89 during the baseline period to 5.51 in the second month (risk ratio [RR] = 0.37; 95% confidence interval [CI] = 0.34-0.39; P < .001), 3.79 in the third month (RR = 0.25; 95% CI = 0.23-0.28; P < .001), 2.98 in the 4 to 15 months (RR = 0.21; 95% CI = 0.18-0.22; P < .001), 1.86 in the 16 to 27 months (RR = 0.12; 95% CI = 0.11-0.14; P < .001), and 1.71 in the 28 to 39 months (RR = 0.11; 95% CI = 0.09-0.13; P < .001). Conclusions: Our intervention, without substantial costs or additional staffing, achieved an 89% reduction in CAUTI incidence in ICUs across 32 countries, demonstrating feasibility in ICUs of low- and middle-income countries.
Language	English
Publishing date	2024-03-02
Publishing country	United States
Document type	Journal Article
ZDB-ID	392362-9
ISSN	1527-3296 ; 0196-6553
ISSN (online)	1527-3296
ISSN	0196-6553
DOI	10.1016/j.ajic.2024.02.017
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Zs.A 1773: Show issues

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Article ; Online: Implementation of a retinal stroke-code protocol results in visual recovery in patients receiving reperfusion therapies.

Bustamante, Alejandro / Balboa, Marta / Ezcurra, Garbiñe / Sánchez-Fortún, Adrián / Ruiz, Judith / Castellví, Jordi / Castillo-Acedo, Susana / Matas, Èric / Bouchikh, Rachid / Martínez-Sánchez, Marina / Castaño, Carlos / Remollo, Sebastiá / Werner, Mariano / Salgado, Maria Carmen / Villodres, Samuel / Gea, Mireia / Millán, Mònica / Pérez de la Ossa, Natàlia / Ruiz-Bilbao, Susana

European stroke journal

2024 , Page(s) 23969873231221366

Abstract: Introduction: Reperfusion therapies represent promising treatments for patients with Central Retinal Artery Occlusion (CRAO), but access is limited due to low incidence and lack of protocols. We aimed to describe the benefit of implementing a Retinal ... ...

Abstract	Introduction: Reperfusion therapies represent promising treatments for patients with Central Retinal Artery Occlusion (CRAO), but access is limited due to low incidence and lack of protocols. We aimed to describe the benefit of implementing a Retinal Stroke-Code protocol regarding access to reperfusion, visual acuity and aetiological assessment. Patients and methods: Prospective cohort study performed at a Comprehensive Stroke Centre. Criteria for activation were sudden monocular, painless vision loss within 6 h from onset. Eligible patients received IAT when immediately available and IVT otherwise. All patients were followed by ophthalmologists to assess best-corrected visual acuity (BCVA) and visual complications, and by neurologists for aetiological workup. Visual amelioration was defined as improvement of at least one Early Treatment Diabetic Retinopathy Study (ETDRS) letter from baseline to 1 week. Results: Of 49 patients with CRAO, 15 (30.6%) received reperfusion therapies (12 IVT, 3 IAT). Presentation beyond 6 h was the main contraindication. Patients receiving reperfusion therapies had better rates of visual improvement (33.3% vs 5.9%, Conclusion: A comprehensive acute management of CRAO is feasible despite low incidence. In our study, reperfusion therapies were safe and associated with higher rates of visual recovery. A similar etiological workup than ischemic stroke led to of high proportion of underlying aetiologies.
Language	English
Publishing date	2024-01-08
Publishing country	England
Document type	Journal Article
ZDB-ID	2851287-X
ISSN	2396-9881 ; 2396-9873
ISSN (online)	2396-9881
ISSN	2396-9873
DOI	10.1177/23969873231221366
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Article: In situ Structure of Rotavirus VP1 RNA-Dependent RNA Polymerase

Jenni, Simon / Salgado, Eric N / Herrmann, Tobias / Li, Zongli / Grant, Timothy / Grigorieff, Nikolaus / Trapani, Stefano / Estrozi, Leandro F / Harrison, Stephen C

Journal of molecular biology. 2019 Aug. 09, v. 431, no. 17

2019

Abstract	Rotaviruses, like other non-enveloped, double-strand RNA viruses, package an RNA-dependent RNA polymerase (RdRp) with each duplex of their segmented genomes. Rotavirus cell entry results in loss of an outer protein layer and delivery into the cytosol of an intact, inner capsid particle (the “double-layer particle,” or DLP). The RdRp, designated VP1, is active inside the DLP; each VP1 achieves many rounds of mRNA transcription from its associated genome segment. Previous work has shown that one VP1 molecule lies close to each 5-fold axis of the icosahedrally symmetric DLP, just beneath the inner surface of its protein shell, embedded in tightly packed RNA. We have determined a high-resolution structure for the rotavirus VP1 RdRp in situ, by local reconstruction of density around individual 5-fold positions. We have analyzed intact virions (“triple-layer particles”), non-transcribing DLPs and transcribing DLPs. Outer layer dissociation enables the DLP to synthesize RNA, in vitro as well as in vivo, but appears not to induce any detectable structural change in the RdRp. Addition of NTPs, Mg2+, and S-adenosylmethionine, which allows active transcription, results in conformational rearrangements, in both VP1 and the DLP capsid shell protein, that allow a transcript to exit the polymerase and the particle. The position of VP1 (among the five symmetrically related alternatives) at one vertex does not correlate with its position at other vertices. This stochastic distribution of site occupancies limits long-range order in the 11-segment, double-strand RNA genome.
Keywords	RNA-directed RNA polymerase ; Rotavirus ; S-adenosylmethionine ; capsid ; cytosol ; dissociation ; genome ; magnesium ; messenger RNA ; transcription (genetics) ; virion
Language	English
Dates of publication	2019-0809
Size	p. 3124-3138.
Publishing place	Elsevier Ltd
Document type	Article
ZDB-ID	80229-3
ISSN	1089-8638 ; 0022-2836
ISSN (online)	1089-8638
ISSN	0022-2836
DOI	10.1016/j.jmb.2019.06.016
Database	NAL-Catalogue (AGRICOLA)

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