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Article ; Online: Hypoxia: Uncharged tRNA to the Rescue!

Mulroney, Thomas E / Pöyry, Tuija / Willis, Anne E

2021 Volume 31, Issue 1, Page(s) R25–R27

Abstract: A new study has identified genes that protect Caenorhabditis elegans from hypoxic stress. Genomic approaches and whole-organism proteomics reveal a regulatory interaction between a threonyl-tRNA synthetase and ribosome biogenesis that modulates global ... ...

Abstract	A new study has identified genes that protect Caenorhabditis elegans from hypoxic stress. Genomic approaches and whole-organism proteomics reveal a regulatory interaction between a threonyl-tRNA synthetase and ribosome biogenesis that modulates global translation and hypoxic sensitivity.
MeSH term(s)	Amino Acyl-tRNA Synthetases/genetics ; Animals ; Caenorhabditis elegans/genetics ; Hypoxia/genetics ; RNA, Transfer/genetics ; Threonine-tRNA Ligase
Chemical Substances	RNA, Transfer (9014-25-9) ; Amino Acyl-tRNA Synthetases (EC 6.1.1.-) ; Threonine-tRNA Ligase (EC 6.1.1.3)
Language	English
Publishing date	2021-01-11
Publishing country	England
Document type	Editorial ; Comment
ZDB-ID	1071731-6
ISSN	1879-0445 ; 0960-9822
ISSN (online)	1879-0445
ISSN	0960-9822
DOI	10.1016/j.cub.2020.10.067
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Article: Unresolved stalled ribosome complexes restrict cell-cycle progression after genotoxic stress

Stoneley, Mark / Harvey, Robert F. / Mulroney, Thomas E. / Mordue, Ryan / Jukes-Jones, Rebekah / Cain, Kelvin / Lilley, Kathryn S. / Sawarkar, Ritwick / Willis, Anne E.

Molecular cell. 2022 Jan. 24,

2022

Abstract: During the translation surveillance mechanism known as ribosome-associated quality control, the ASC-1 complex (ASCC) disassembles ribosomes stalled on the mRNA. Here, we show that there are two distinct classes of stalled ribosome. Ribosomes stalled by ... ...

Abstract	During the translation surveillance mechanism known as ribosome-associated quality control, the ASC-1 complex (ASCC) disassembles ribosomes stalled on the mRNA. Here, we show that there are two distinct classes of stalled ribosome. Ribosomes stalled by translation elongation inhibitors or methylated mRNA are short lived in human cells because they are split by the ASCC. In contrast, although ultraviolet light and 4-nitroquinoline 1-oxide induce ribosome stalling by damaging mRNA, and the ASCC is recruited to these stalled ribosomes, we found that they are refractory to the ASCC. Consequently, unresolved UV- and 4NQO-stalled ribosomes persist in human cells. We show that ribosome stalling activates cell-cycle arrest, partly through ZAK-p38ᴹᴬᴾᴷ signaling, and that this cell-cycle delay is prolonged when the ASCC cannot resolve stalled ribosomes. Thus, we propose that the sensitivity of stalled ribosomes to the ASCC influences the kinetics of stall resolution, which in turn controls the adaptive stress response.
Keywords	cell cycle checkpoints ; humans ; methylation ; monitoring ; mutagens ; quality control ; ribosomes ; stress response ; ultraviolet radiation
Language	English
Dates of publication	2022-0124
Publishing place	Elsevier Inc.
Document type	Article
Note	Pre-press version
ZDB-ID	1415236-8
ISSN	1097-4164 ; 1097-2765
ISSN (online)	1097-4164
ISSN	1097-2765
DOI	10.1016/j.molcel.2022.01.019
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Article: Translation of

von der Haar, Tobias / Mulroney, Thomas E / Hedayioglu, Fabio / Kurusamy, Sathishkumar / Rust, Maria / Lilley, Kathryn S / Thaventhiran, James E / Willis, Anne E / Smales, C Mark

Frontiers in molecular biosciences

2023 Volume 10, Page(s) 1128067

Abstract: ... In ... ...

Abstract	In vitro
Language	English
Publishing date	2023-02-08
Publishing country	Switzerland
Document type	Journal Article ; Review
ZDB-ID	2814330-9
ISSN	2296-889X
ISSN	2296-889X
DOI	10.3389/fmolb.2023.1128067
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Article ; Online: Development of a colorimetric assay for the detection of SARS-CoV-2 3CLpro activity.

Garland, Gavin D / Harvey, Robert F / Mulroney, Thomas E / Monti, Mie / Fuller, Stewart / Haigh, Richard / Gerber, Pehuén Pereyra / Barer, Michael R / Matheson, Nicholas J / Willis, Anne E

The Biochemical journal

2022 Volume 479, Issue 8, Page(s) 901–920

Abstract: Diagnostic testing continues to be an integral component of the strategy to contain the Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) global pandemic, the causative agent of Coronavirus Disease 2019 (COVID-19). The SARS-CoV-2 genome ... ...

Abstract	Diagnostic testing continues to be an integral component of the strategy to contain the Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) global pandemic, the causative agent of Coronavirus Disease 2019 (COVID-19). The SARS-CoV-2 genome encodes the 3C-like protease (3CLpro) which is essential for coronavirus replication. This study adapts an in vitro colorimetric gold nanoparticle (AuNP) based protease assay to specifically detect the activity of SARS-CoV-2 3CLpro as a purified recombinant protein and as a cellular protein exogenously expressed in HEK293T human cells. We also demonstrate that the specific sensitivity of the assay for SARS-CoV-2 3CLpro can be improved by use of an optimised peptide substrate and through hybrid dimerisation with inactive 3CLpro mutant monomers. These findings highlight the potential for further development of the AuNP protease assay to detect SARS-CoV-2 3CLpro activity as a novel, accessible and cost-effective diagnostic test for SARS-CoV-2 infection at the point-of-care. Importantly, this versatile assay could also be easily adapted to detect specific protease activity associated with other viruses or diseases conditions.
MeSH term(s)	Antiviral Agents ; COVID-19/diagnosis ; Colorimetry ; Coronavirus 3C Proteases ; Gold ; HEK293 Cells ; Humans ; Metal Nanoparticles ; Peptide Hydrolases ; Protease Inhibitors ; SARS-CoV-2
Chemical Substances	Antiviral Agents ; Protease Inhibitors ; Gold (7440-57-5) ; Peptide Hydrolases (EC 3.4.-) ; Coronavirus 3C Proteases (EC 3.4.22.28)
Language	English
Publishing date	2022-04-04
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2969-5
ISSN	1470-8728 ; 0006-2936 ; 0306-3275 ; 0264-6021
ISSN (online)	1470-8728
ISSN	0006-2936 ; 0306-3275 ; 0264-6021
DOI	10.1042/BCJ20220105
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Article ; Online: Unresolved stalled ribosome complexes restrict cell-cycle progression after genotoxic stress.

Stoneley, Mark / Harvey, Robert F / Mulroney, Thomas E / Mordue, Ryan / Jukes-Jones, Rebekah / Cain, Kelvin / Lilley, Kathryn S / Sawarkar, Ritwick / Willis, Anne E

Molecular cell

2022 Volume 82, Issue 8, Page(s) 1557–1572.e7

Abstract	During the translation surveillance mechanism known as ribosome-associated quality control, the ASC-1 complex (ASCC) disassembles ribosomes stalled on the mRNA. Here, we show that there are two distinct classes of stalled ribosome. Ribosomes stalled by translation elongation inhibitors or methylated mRNA are short lived in human cells because they are split by the ASCC. In contrast, although ultraviolet light and 4-nitroquinoline 1-oxide induce ribosome stalling by damaging mRNA, and the ASCC is recruited to these stalled ribosomes, we found that they are refractory to the ASCC. Consequently, unresolved UV- and 4NQO-stalled ribosomes persist in human cells. We show that ribosome stalling activates cell-cycle arrest, partly through ZAK-p38
MeSH term(s)	DNA Damage ; Humans ; Protein Biosynthesis ; RNA, Messenger/genetics ; RNA, Messenger/metabolism ; Ribosomes/genetics ; Ribosomes/metabolism
Chemical Substances	RNA, Messenger
Language	English
Publishing date	2022-02-17
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	1415236-8
ISSN	1097-4164 ; 1097-2765
ISSN (online)	1097-4164
ISSN	1097-2765
DOI	10.1016/j.molcel.2022.01.019
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Article ; Online: A protease-activatable luminescent biosensor and reporter cell line for authentic SARS-CoV-2 infection.

Gerber, Pehuén Pereyra / Duncan, Lidia M / Greenwood, Edward Jd / Marelli, Sara / Naamati, Adi / Teixeira-Silva, Ana / Crozier, Thomas Wm / Gabaev, Ildar / Zhan, Jun R / Mulroney, Thomas E / Horner, Emily C / Doffinger, Rainer / Willis, Anne E / Thaventhiran, James Ed / Protasio, Anna V / Matheson, Nicholas J

PLoS pathogens

2022 Volume 18, Issue 2, Page(s) e1010265

Abstract: Efforts to define serological correlates of protection against COVID-19 have been hampered by the lack of a simple, scalable, standardised assay for SARS-CoV-2 infection and antibody neutralisation. Plaque assays remain the gold standard, but are ... ...

Abstract	Efforts to define serological correlates of protection against COVID-19 have been hampered by the lack of a simple, scalable, standardised assay for SARS-CoV-2 infection and antibody neutralisation. Plaque assays remain the gold standard, but are impractical for high-throughput screening. In this study, we show that expression of viral proteases may be used to quantitate infected cells. Our assays exploit the cleavage of specific oligopeptide linkers, leading to the activation of cell-based optical biosensors. First, we characterise these biosensors using recombinant SARS-CoV-2 proteases. Next, we confirm their ability to detect viral protease expression during replication of authentic virus. Finally, we generate reporter cells stably expressing an optimised luciferase-based biosensor, enabling viral infection to be measured within 24 h in a 96- or 384-well plate format, including variants of concern. We have therefore developed a luminescent SARS-CoV-2 reporter cell line, and demonstrated its utility for the relative quantitation of infectious virus and titration of neutralising antibodies.
MeSH term(s)	Biosensing Techniques/methods ; COVID-19/diagnosis ; COVID-19/virology ; COVID-19 Testing/methods ; Cell Line ; Humans ; Luminescent Measurements/methods ; Peptide Hydrolases/analysis ; Peptide Hydrolases/genetics ; Peptide Hydrolases/metabolism ; SARS-CoV-2/enzymology ; SARS-CoV-2/genetics ; SARS-CoV-2/physiology ; Viral Proteins/analysis ; Viral Proteins/genetics ; Viral Proteins/metabolism ; Virus Replication
Chemical Substances	Viral Proteins ; Peptide Hydrolases (EC 3.4.-)
Language	English
Publishing date	2022-02-10
Publishing country	United States
Document type	Evaluation Study ; Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2205412-1
ISSN	1553-7374 ; 1553-7374
ISSN (online)	1553-7374
ISSN	1553-7374
DOI	10.1371/journal.ppat.1010265
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Nature

2023 Volume 625, Issue 7993, Page(s) 189–194

Abstract: In vitro-transcribed (IVT) mRNAs are modalities that can combat human disease, exemplified by their use as vaccines for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). IVT mRNAs are transfected into target cells, where they are translated ... ...

Abstract	In vitro-transcribed (IVT) mRNAs are modalities that can combat human disease, exemplified by their use as vaccines for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). IVT mRNAs are transfected into target cells, where they are translated into recombinant protein, and the biological activity or immunogenicity of the encoded protein exerts an intended therapeutic effect
MeSH term(s)	Animals ; Humans ; Mice ; BNT162 Vaccine/adverse effects ; BNT162 Vaccine/genetics ; BNT162 Vaccine/immunology ; Frameshifting, Ribosomal/genetics ; RNA, Messenger/chemistry ; RNA, Messenger/genetics ; RNA, Messenger/metabolism ; Pseudouridine/analogs & derivatives ; Pseudouridine/metabolism ; Ribosomes/metabolism ; Protein Biosynthesis
Chemical Substances	BNT162 Vaccine ; RNA, Messenger ; 1-methylpseudouridine (13860-38-3) ; Pseudouridine (1445-07-4)
Language	English
Publishing date	2023-12-06
Publishing country	England
Document type	Journal Article
ZDB-ID	120714-3
ISSN	1476-4687 ; 0028-0836
ISSN (online)	1476-4687
ISSN	0028-0836
DOI	10.1038/s41586-023-06800-3
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Article ; Online: The cell stress response: extreme times call for post-transcriptional measures.

Pizzinga, Mariavittoria / Harvey, Robert F / Garland, Gavin D / Mordue, Ryan / Dezi, Veronica / Ramakrishna, Manasa / Sfakianos, Aristeidis / Monti, Mie / Mulroney, Thomas E / Poyry, Tuija / Willis, Anne E

Wiley interdisciplinary reviews. RNA

2019 Volume 11, Issue 3, Page(s) e1578

Abstract: Following cell stress, a wide range of molecular pathways are initiated to orchestrate the stress response and enable adaptation to an environmental or intracellular perturbation. The post-transcriptional regulation strategies adopted during the stress ... ...

Abstract	Following cell stress, a wide range of molecular pathways are initiated to orchestrate the stress response and enable adaptation to an environmental or intracellular perturbation. The post-transcriptional regulation strategies adopted during the stress response result in a substantial reorganization of gene expression, designed to prepare the cell for either acclimatization or programmed death, depending on the nature and intensity of the stress. Fundamental to the stress response is a rapid repression of global protein synthesis, commonly mediated by phosphorylation of translation initiation factor eIF2α. Recent structural and biochemical information have added unprecedented detail to our understanding of the molecular mechanisms underlying this regulation. During protein synthesis inhibition, the translation of stress-specific mRNAs is nonetheless enhanced, often through the interaction between RNA-binding proteins and specific RNA regulatory elements. Recent studies investigating the unfolded protein response (UPR) provide some important insights into how posttranscriptional events are spatially and temporally fine-tuned in order to elicit the most appropriate response and to coordinate the transition from an early, acute stage into the chronic state of adaptation. Importantly, cancer cells are known to hi-jack adaptive stress response pathways, particularly the UPR, to survive and proliferate in the unfavorable tumor environment. In this review, we consider the implications of recent research into stress-dependent post-transcriptional regulation and make the case for the exploration of the stress response as a strategy to identify novel targets in the development of cancer therapies. This article is categorized under: RNA in Disease and Development > RNA in Disease RNA Evolution and Genomics > RNA and Ribonucleoprotein Evolution Translation > Translation Mechanisms > Translation Regulation.
MeSH term(s)	Animals ; Eukaryotic Initiation Factor-2/genetics ; Eukaryotic Initiation Factor-2/metabolism ; Humans ; Neoplasms/genetics ; Neoplasms/metabolism ; Neoplasms/pathology ; RNA Processing, Post-Transcriptional/genetics ; RNA, Messenger/genetics ; RNA, Messenger/metabolism ; Unfolded Protein Response/genetics
Chemical Substances	Eukaryotic Initiation Factor-2 ; RNA, Messenger
Language	English
Publishing date	2019-11-21
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't ; Review
ZDB-ID	2634714-3
ISSN	1757-7012 ; 1757-7004
ISSN (online)	1757-7012
ISSN	1757-7004
DOI	10.1002/wrna.1578
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Article ; Online: Accelerated waning of the humoral response to COVID-19 vaccines in obesity.

van der Klaauw, Agatha A / Horner, Emily C / Pereyra-Gerber, Pehuén / Agrawal, Utkarsh / Foster, William S / Spencer, Sarah / Vergese, Bensi / Smith, Miriam / Henning, Elana / Ramsay, Isobel D / Smith, Jack A / Guillaume, Stephane M / Sharpe, Hayley J / Hay, Iain M / Thompson, Sam / Innocentin, Silvia / Booth, Lucy H / Robertson, Chris / McCowan, Colin /

Kerr, Steven / Mulroney, Thomas E / O'Reilly, Martin J / Gurugama, Thevinya P / Gurugama, Lihinya P / Rust, Maria A / Ferreira, Alex / Ebrahimi, Soraya / Ceron-Gutierrez, Lourdes / Scotucci, Jacopo / Kronsteiner, Barbara / Dunachie, Susanna J / Klenerman, Paul / Park, Adrian J / Rubino, Francesco / Lamikanra, Abigail A / Stark, Hannah / Kingston, Nathalie / Estcourt, Lise / Harvala, Heli / Roberts, David J / Doffinger, Rainer / Linterman, Michelle A / Matheson, Nicholas J / Sheikh, Aziz / Farooqi, I Sadaf / Thaventhiran, James E D

Nature medicine

2023 Volume 29, Issue 5, Page(s) 1146–1154

Abstract: Obesity is associated with an increased risk of severe Coronavirus Disease 2019 (COVID-19) infection and mortality. COVID-19 vaccines reduce the risk of serious COVID-19 outcomes; however, their effectiveness in people with obesity is incompletely ... ...

Abstract	Obesity is associated with an increased risk of severe Coronavirus Disease 2019 (COVID-19) infection and mortality. COVID-19 vaccines reduce the risk of serious COVID-19 outcomes; however, their effectiveness in people with obesity is incompletely understood. We studied the relationship among body mass index (BMI), hospitalization and mortality due to COVID-19 among 3.6 million people in Scotland using the Early Pandemic Evaluation and Enhanced Surveillance of COVID-19 (EAVE II) surveillance platform. We found that vaccinated individuals with severe obesity (BMI > 40 kg/m
MeSH term(s)	Humans ; COVID-19 Vaccines ; Obesity, Morbid ; Longitudinal Studies ; Prospective Studies ; COVID-19/epidemiology ; COVID-19/prevention & control ; SARS-CoV-2 ; Obesity/epidemiology ; Antibodies, Neutralizing ; Antibodies, Viral ; Vaccination
Chemical Substances	COVID-19 Vaccines ; Antibodies, Neutralizing ; Antibodies, Viral
Language	English
Publishing date	2023-05-11
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't ; Research Support, N.I.H., Extramural
ZDB-ID	1220066-9
ISSN	1546-170X ; 1078-8956
ISSN (online)	1546-170X
ISSN	1078-8956
DOI	10.1038/s41591-023-02343-2
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Article ; Online: Age-associated B cells predict impaired humoral immunity after COVID-19 vaccination in patients receiving immune checkpoint blockade.

Yam-Puc, Juan Carlos / Hosseini, Zhaleh / Horner, Emily C / Gerber, Pehuén Pereyra / Beristain-Covarrubias, Nonantzin / Hughes, Robert / Lulla, Aleksei / Rust, Maria / Boston, Rebecca / Ali, Magda / Fischer, Katrin / Simmons-Rosello, Edward / O'Reilly, Martin / Robson, Harry / Booth, Lucy H / Kahanawita, Lakmini / Correa-Noguera, Andrea / Favara, David / Ceron-Gutierrez, Lourdes /

Keller, Baerbel / Craxton, Andrew / Anderson, Georgina S F / Sun, Xiao-Ming / Elmer, Anne / Saunders, Caroline / Bermperi, Areti / Jose, Sherly / Kingston, Nathalie / Mulroney, Thomas E / Piñon, Lucia P G / Chapman, Michael A / Grigoriadou, Sofia / MacFarlane, Marion / Willis, Anne E / Patil, Kiran R / Spencer, Sarah / Staples, Emily / Warnatz, Klaus / Buckland, Matthew S / Hollfelder, Florian / Hyvönen, Marko / Döffinger, Rainer / Parkinson, Christine / Lear, Sara / Matheson, Nicholas J / Thaventhiran, James E D

Nature communications

2023 Volume 14, Issue 1, Page(s) 3292

Abstract: Age-associated B cells (ABC) accumulate with age and in individuals with different immunological disorders, including cancer patients treated with immune checkpoint blockade and those with inborn errors of immunity. Here, we investigate whether ABCs from ...

Abstract	Age-associated B cells (ABC) accumulate with age and in individuals with different immunological disorders, including cancer patients treated with immune checkpoint blockade and those with inborn errors of immunity. Here, we investigate whether ABCs from different conditions are similar and how they impact the longitudinal level of the COVID-19 vaccine response. Single-cell RNA sequencing indicates that ABCs with distinct aetiologies have common transcriptional profiles and can be categorised according to their expression of immune genes, such as the autoimmune regulator (AIRE). Furthermore, higher baseline ABC frequency correlates with decreased levels of antigen-specific memory B cells and reduced neutralising capacity against SARS-CoV-2. ABCs express high levels of the inhibitory FcγRIIB receptor and are distinctive in their ability to bind immune complexes, which could contribute to diminish vaccine responses either directly, or indirectly via enhanced clearance of immune complexed-antigen. Expansion of ABCs may, therefore, serve as a biomarker identifying individuals at risk of suboptimal responses to vaccination.
MeSH term(s)	Humans ; Immunity, Humoral ; Immune Checkpoint Inhibitors ; COVID-19 Vaccines ; COVID-19/prevention & control ; SARS-CoV-2 ; Vaccination ; Antigen-Antibody Complex ; Antibodies, Viral
Chemical Substances	Immune Checkpoint Inhibitors ; COVID-19 Vaccines ; Antigen-Antibody Complex ; Antibodies, Viral
Language	English
Publishing date	2023-06-27
Publishing country	England
Document type	Journal Article ; 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/s41467-023-38810-0
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