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Article ; Online: Corrigendum: Brief research report: impact of vaccination on antibody responses and mortality from severe COVID-19.

Adhikari, Bindu / Bednash, Joseph S / Horowitz, Jeffrey C / Rubinstein, Mark P / Vlasova, Anastasia N

2024 Volume 15, Page(s) 1384209

Abstract: This corrects the article DOI: 10.3389/fimmu.2024.1325243.]. ...

Abstract	[This corrects the article DOI: 10.3389/fimmu.2024.1325243.].
Language	English
Publishing date	2024-02-28
Publishing country	Switzerland
Document type	Published Erratum
ZDB-ID	2606827-8
ISSN	1664-3224 ; 1664-3224
ISSN (online)	1664-3224
ISSN	1664-3224
DOI	10.3389/fimmu.2024.1384209
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Article ; Online: Brief research report: impact of vaccination on antibody responses and mortality from severe COVID-19.

Adhikari, Bindu / Bednash, Joseph S / Horowitz, Jeffrey C / Rubinstein, Mark P / Vlasova, Anastasia N

Frontiers in immunology

2024 Volume 15, Page(s) 1325243

Abstract: Introduction: While it is established that vaccination reduces risk of hospitalization, there is conflicting data on whether it improves outcome among hospitalized COVID-19 patients. This study evaluated clinical outcomes and antibody (Ab) responses to ... ...

Abstract	Introduction: While it is established that vaccination reduces risk of hospitalization, there is conflicting data on whether it improves outcome among hospitalized COVID-19 patients. This study evaluated clinical outcomes and antibody (Ab) responses to severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) infection/vaccines in patients with acute respiratory failure (ARF) and various comorbidities. Methods: In this single-center study, 152 adult patients were admitted to Ohio State University hospital with ARF (05/2020 - 11/2022) including 112 COVID-19-positive and 40 COVID-19-negative patients. Of the COVID-19 positive patients, 23 were vaccinated for SARS-CoV-2 (Vax), and 89 were not (NVax). Of the NVax COVID-19 patients, 46 were admitted before and 43 after SARS-CoV-2 vaccines were approved. SARS-CoV-2 Ab levels were measured/analyzed based on various demographic and clinical parameters of COVID-19 patients. Additionally, total IgG4 Ab concentrations were compared between the Vax and NVax patients. Results: While mortality rates were 36% (n=25) and 27% (n=15) for non-COVID-19 NVax and Vax patients, respectively, in COVID-19 patients mortality rates were 37% (NVax, n=89) and 70% (Vax, n=23). Among COVID-19 patients, mortality rate was significantly higher among Vax vs. NVax patients (p=0.002). The Charlson's Comorbidity Index score (CCI) was also significantly higher among Vax vs. NVax COVID-19 patients. However, the mortality risk remained significantly higher (p=0.02) when we compared COVID-19 Vax vs. NVax patients with similar CCI score, suggesting that additional factors may increase risk of mortality. Higher levels of SARS-CoV-2 Abs were noted among survivors, suggestive of their protective role. We observed a trend for increased total IgG4 Ab, which promotes immune tolerance, in the Vax vs. NVax patients in week 3. Conclusion: Although our cohort size is small, our results suggest that vaccination status of hospital-admitted COVID-19 patients may not be instructive in determining mortality risk. This may reflect that within the general population, those individuals at highest risk for COVID-19 mortality/immune failure are likely to be vaccinated. Importantly, the value of vaccination may be in preventing hospitalization as opposed to stratifying outcome among hospitalized patients, although our data do not address this possibility. Additional research to identify factors predictive of aberrant immunogenic responses to vaccination is warranted.
MeSH term(s)	Adult ; Humans ; COVID-19 ; SARS-CoV-2 ; Antibody Formation ; COVID-19 Vaccines ; Research Report ; Vaccination ; Immunoglobulin G
Chemical Substances	COVID-19 Vaccines ; Immunoglobulin G
Language	English
Publishing date	2024-02-07
Publishing country	Switzerland
Document type	Journal Article ; Research Support, N.I.H., Extramural
ZDB-ID	2606827-8
ISSN	1664-3224 ; 1664-3224
ISSN (online)	1664-3224
ISSN	1664-3224
DOI	10.3389/fimmu.2024.1325243
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Article ; Online: Regulation of inflammasomes by ubiquitination.

Bednash, Joseph S / Mallampalli, Rama K

Cellular & molecular immunology

2016 Volume 13, Issue 6, Page(s) 722–728

Abstract: Inflammasomes are multi-protein complexes that regulate the innate immune response by facilitating the release of inflammatory cytokines in response to pathogen exposure or cellular damage. Pro-inflammatory inflammasome signaling is vital to host defense ...

Abstract	Inflammasomes are multi-protein complexes that regulate the innate immune response by facilitating the release of inflammatory cytokines in response to pathogen exposure or cellular damage. Pro-inflammatory inflammasome signaling is vital to host defense and helps initiate the process of tissue repair following an insult to the host, but can be injurious, when excessive or chronic. As such, inflammasome activity is tightly regulated. Here we discuss one critical mechanism of inflammasome regulation, ubiquitination, that functions as a universal modulator of protein stability and trafficking. Recent studies have provided important insights into the regulation of inflammasome activation by protein ubiquitination. We review the molecular regulation of inflammasome function, specifically, as it relates to ubiquitination, and discuss the implications for the development of therapeutics to specifically target aberrant inflammasome signaling.
MeSH term(s)	Animals ; Humans ; Inflammasomes/metabolism ; Models, Biological ; Ubiquitin/metabolism ; Ubiquitination
Chemical Substances	Inflammasomes ; Ubiquitin
Language	English
Publishing date	2016-04-11
Publishing country	China
Document type	Journal Article ; Review ; Research Support, Non-U.S. Gov't
ZDB-ID	2435097-7
ISSN	2042-0226 ; 1672-7681
ISSN (online)	2042-0226
ISSN	1672-7681
DOI	10.1038/cmi.2016.15
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Article ; Online: Targeting Deubiquitinases in Cancer.

Bednash, Joseph S / Mallampalli, Rama K

Methods in molecular biology (Clifton, N.J.)

2016 Volume 1731, Page(s) 295–305

Abstract: The ubiquitin-proteasome system (UPS) is a complex and robust metabolic pathway that contributes to the regulation of many key cellular processes including the cell cycle, cell division, and response to external stimuli. Ubiquitin ligases, which tag ... ...

Abstract	The ubiquitin-proteasome system (UPS) is a complex and robust metabolic pathway that contributes to the regulation of many key cellular processes including the cell cycle, cell division, and response to external stimuli. Ubiquitin ligases, which tag proteins with ubiquitin, are opposed by deubiquitinase enzymes (DUBs). The relative activity of these enzymes allows for a dynamic balance that determines the abundance and activity of cellular proteins. Targeting the UPS in cancer has proven successful, as evidenced by use of bortezomib, a proteasome inhibitor, in multiple myeloma. However, no pharmacologic inhibitor of the upstream enzymes has yet to reach clinical trials for the treatment of malignancy. Here we present an in vitro DUB assay for use in drug discovery and development that provides a biologically relevant platform for screening and developing lead or tool compounds targeting DUBs.
MeSH term(s)	Antineoplastic Agents/pharmacology ; Apoptosis/drug effects ; Deubiquitinating Enzymes/antagonists & inhibitors ; Deubiquitinating Enzymes/metabolism ; Drug Discovery/instrumentation ; Drug Discovery/methods ; Drug Screening Assays, Antitumor/instrumentation ; Drug Screening Assays, Antitumor/methods ; Enzyme Assays/instrumentation ; Enzyme Assays/methods ; HEK293 Cells ; Humans ; Molecular Targeted Therapy/methods ; Neoplasms/drug therapy ; Protease Inhibitors/pharmacology ; Proteasome Endopeptidase Complex/metabolism ; Ubiquitin/metabolism
Chemical Substances	Antineoplastic Agents ; Protease Inhibitors ; Ubiquitin ; Deubiquitinating Enzymes (EC 3.4.19.12) ; Proteasome Endopeptidase Complex (EC 3.4.25.1)
Language	English
Publishing date	2016-10-07
Publishing country	United States
Document type	Journal Article
ISSN	1940-6029
ISSN (online)	1940-6029
DOI	10.1007/978-1-4939-7595-2_25
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Article ; Online: MicroID2: A Novel Biotin Ligase Enables Rapid Proximity-Dependent Proteomics.

Johnson, Benjamin S / Chafin, Lexie / Farkas, Daniela / Adair, Jessica / Elhance, Ajit / Farkas, Laszlo / Bednash, Joseph S / Londino, James D

Molecular & cellular proteomics : MCP

2022 Volume 21, Issue 7, Page(s) 100256

Abstract: Identifying protein-protein and other proximal interactions is central to dissecting signaling and regulatory processes in cells. BioID is a proximity-dependent biotinylation method that uses an "abortive" biotin ligase to detect proximal interactions in ...

Abstract	Identifying protein-protein and other proximal interactions is central to dissecting signaling and regulatory processes in cells. BioID is a proximity-dependent biotinylation method that uses an "abortive" biotin ligase to detect proximal interactions in cells in a highly reproducible manner. Recent advancements in proximity-dependent biotinylation tools have improved efficiency and timing of labeling, allowing for measurement of interactions on a cellular timescale. However, issues of size, stability, and background labeling of these constructs persist. Here we modified the structure of BioID2, derived from Aquifex aeolicus BirA, to create a smaller, highly active, biotin ligase that we named MicroID2. Truncation of the C terrminus of BioID2 and addition of mutations to alleviate blockage of biotin/ATP binding at the active site of BioID2 resulted in a smaller and highly active construct with lower background labeling. Several additional point mutations improved the function of our modified MicroID2 construct compared with BioID2 and other biotin ligases, including TurboID and miniTurbo. MicroID2 is the smallest biotin ligase reported so far (180 amino acids [AAs] for MicroID2 versus 257 AAs for miniTurbo and 338 AAs for TurboID), yet it demonstrates only slightly less labeling activity than TurboID and outperforms miniTurbo. MicroID2 also had lower background labeling than TurboID. For experiments where precise temporal control of labeling is essential, we in addition developed a MicroID2 mutant, termed lbMicroID2 (low background MicroID2), that has lower labeling efficiency but significantly reduced biotin scavenging compared with BioID2. Finally, we demonstrate utility of MicroID2 in mass spectrometry experiments by localizing MicroID2 constructs to subcellular organelles and measuring proximal interactions.
MeSH term(s)	Biotin ; Biotinylation ; Ligases ; Mass Spectrometry ; Protein Interaction Mapping/methods ; Proteomics/methods
Chemical Substances	Biotin (6SO6U10H04) ; Ligases (EC 6.-)
Language	English
Publishing date	2022-06-08
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
ZDB-ID	2075924-1
ISSN	1535-9484 ; 1535-9476
ISSN (online)	1535-9484
ISSN	1535-9476
DOI	10.1016/j.mcpro.2022.100256
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Zs.A 5599: Show issues

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Article ; Online: Immune evasion, infectivity, and fusogenicity of SARS-CoV-2 BA.2.86 and FLip variants.

Qu, Panke / Xu, Kai / Faraone, Julia N / Goodarzi, Negin / Zheng, Yi-Min / Carlin, Claire / Bednash, Joseph S / Horowitz, Jeffrey C / Mallampalli, Rama K / Saif, Linda J / Oltz, Eugene M / Jones, Daniel / Gumina, Richard J / Liu, Shan-Lu

Cell

2024 Volume 187, Issue 3, Page(s) 585–595.e6

Abstract: Evolution of SARS-CoV-2 requires the reassessment of current vaccine measures. Here, we characterized BA.2.86 and XBB-derived variant FLip by investigating their neutralization alongside D614G, BA.1, BA.2, BA.4/5, XBB.1.5, and EG.5.1 by sera from 3-dose- ... ...

Abstract	Evolution of SARS-CoV-2 requires the reassessment of current vaccine measures. Here, we characterized BA.2.86 and XBB-derived variant FLip by investigating their neutralization alongside D614G, BA.1, BA.2, BA.4/5, XBB.1.5, and EG.5.1 by sera from 3-dose-vaccinated and bivalent-vaccinated healthcare workers, XBB.1.5-wave-infected first responders, and monoclonal antibody (mAb) S309. We assessed the biology of the variant spikes by measuring viral infectivity and membrane fusogenicity. BA.2.86 is less immune evasive compared to FLip and other XBB variants, consistent with antigenic distances. Importantly, distinct from XBB variants, mAb S309 was unable to neutralize BA.2.86, likely due to a D339H mutation based on modeling. BA.2.86 had relatively high fusogenicity and infectivity in CaLu-3 cells but low fusion and infectivity in 293T-ACE2 cells compared to some XBB variants, suggesting a potentially different conformational stability of BA.2.86 spike. Overall, our study underscores the importance of SARS-CoV-2 variant surveillance and the need for updated COVID-19 vaccines.
MeSH term(s)	Humans ; Antibodies, Monoclonal ; Antibodies, Neutralizing ; Antibodies, Viral ; COVID-19/immunology ; COVID-19 Vaccines ; Immune Evasion ; SARS-CoV-2/classification ; SARS-CoV-2/physiology
Chemical Substances	Antibodies, Monoclonal ; Antibodies, Neutralizing ; Antibodies, Viral ; COVID-19 Vaccines
Language	English
Publishing date	2024-01-08
Publishing country	United States
Document type	Journal Article
ZDB-ID	187009-9
ISSN	1097-4172 ; 0092-8674
ISSN (online)	1097-4172
ISSN	0092-8674
DOI	10.1016/j.cell.2023.12.026
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Zs.A 1167: Show issues			Location: Je nach Verfügbarkeit (siehe Angabe bei Bestand) bis Jg. 1994: Bestellungen von Artikeln über das Online-Bestellformular Jg. 1995 - 2021: Lesesall (1.OG) ab Jg. 2022: Lesesaal (EG)
Zs.MG 58: Show issues

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Article ; Online: Distinct patterns of SARS-CoV-2 BA.2.87.1 and JN.1 variants in immune evasion, antigenicity, and cell-cell fusion.

Li, Pei / Liu, Yajie / Faraone, Julia N / Hsu, Cheng Chih / Chamblee, Michelle / Zheng, Yi-Min / Carlin, Claire / Bednash, Joseph S / Horowitz, Jeffrey C / Mallampalli, Rama K / Saif, Linda J / Oltz, Eugene M / Jones, Daniel / Li, Jianrong / Gumina, Richard J / Liu, Shan-Lu

mBio

2024 , Page(s) e0075124

Abstract: The rapid evolution of SARS-CoV-2 variants presents a constant challenge to the global vaccination effort. In this study, we conducted a comprehensive investigation into two newly emerged variants, BA.2.87.1 and JN.1, focusing on their neutralization ... ...

Abstract	The rapid evolution of SARS-CoV-2 variants presents a constant challenge to the global vaccination effort. In this study, we conducted a comprehensive investigation into two newly emerged variants, BA.2.87.1 and JN.1, focusing on their neutralization resistance, infectivity, antigenicity, cell-cell fusion, and spike processing. Neutralizing antibody (nAb) titers were assessed in diverse cohorts, including individuals who received a bivalent mRNA vaccine booster, patients infected during the BA.2.86/JN.1-wave, and hamsters vaccinated with XBB.1.5-monovalent vaccine. We found that BA.2.87.1 shows much less nAb escape from WT-BA.4/5 bivalent mRNA vaccination and JN.1-wave breakthrough infection sera compared to JN.1 and XBB.1.5. Interestingly, BA.2.87.1 is more resistant to neutralization by XBB.1.5-monovalent-vaccinated hamster sera than BA.2.86/JN.1 and XBB.1.5, but efficiently neutralized by a class III monoclonal antibody S309, which largely fails to neutralize BA.2.86/JN.1. Importantly, BA.2.87.1 exhibits higher levels of infectivity, cell-cell fusion activity, and furin cleavage efficiency than BA.2.86/JN.1. Antigenically, we found that BA.2.87.1 is closer to the ancestral BA.2 compared to other recently emerged Omicron subvariants including BA.2.86/JN.1 and XBB.1.5. Altogether, these results highlight immune escape properties as well as biology of new variants and underscore the importance of continuous surveillance and informed decision-making in the development of effective vaccines. Importance: This study investigates the recently emerged SARS-CoV-2 variants, BA.2.87.1 and JN.1, in comparison to earlier variants and the parental D614G. Varied infectivity and cell-cell fusion activity among these variants suggest potential disparities in their ability to infect target cells and possibly pathogenesis. BA.2.87.1 exhibits lower nAb escape from bivalent mRNA vaccinee and BA.2.86/JN.1-infected sera than JN.1 but is relatively resistance to XBB.1.5-vaccinated hamster sera, revealing distinct properties in immune reason and underscoring the significance of continuing surveillance of variants and reformulation of vaccines. Antigenic differences between BA.2.87.1 and other earlier variants yield critical information not only for antibody evasion but also for viral evolution. In conclusion, this study furnishes timely insights into the spike biology and immune escape of the emerging variants BA.2.87.1 and JN.1, thus guiding effective vaccine development and informing public health interventions.
Language	English
Publishing date	2024-04-09
Publishing country	United States
Document type	Journal Article
ZDB-ID	2557172-2
ISSN	2150-7511 ; 2161-2129
ISSN (online)	2150-7511
ISSN	2161-2129
DOI	10.1128/mbio.00751-24
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Article: Distinct Patterns of SARS-CoV-2 BA.2.87.1 and JN.1 Variants in Immune Evasion, Antigenicity and Cell-Cell Fusion.

Li, Pei / Liu, Yajie / Faraone, Julia / Hsu, Cheng Chih / Chamblee, Michelle / Zheng, Yi-Min / Carlin, Claire / Bednash, Joseph S / Horowitz, Jeffrey C / Mallampalli, Rama K / Saif, Linda J / Oltz, Eugene M / Jones, Daniel / Li, Jianrong / Gumina, Richard J / Liu, Shan-Lu

bioRxiv : the preprint server for biology

2024

Abstract	The rapid evolution of SARS-CoV-2 variants presents a constant challenge to the global vaccination effort. In this study, we conducted a comprehensive investigation into two newly emerged variants, BA.2.87.1 and JN.1, focusing on their neutralization resistance, infectivity, antigenicity, cell-cell fusion, and spike processing. Neutralizing antibody (nAb) titers were assessed in diverse cohorts, including individuals who received a bivalent mRNA vaccine booster, patients infected during the BA.2.86/JN.1-wave, and hamsters vaccinated with XBB.1.5-monovalent vaccine. We found that BA.2.87.1 shows much less nAb escape from WT-BA.4/5 bivalent mRNA vaccination and JN.1-wave breakthrough infection sera compared to JN.1 and XBB.1.5. Interestingly. BA.2.87.1 is more resistant to neutralization by XBB.15-monovalent-vaccinated hamster sera than BA.2.86/JN.1 and XBB.1.5, but efficiently neutralized by a class III monoclonal antibody S309, which largely fails to neutralize BA.2.86/JN.1. Importantly, BA.2.87.1 exhibits higher levels of infectivity, cell-cell fusion activity, and furin cleavage efficiency than BA.2.86/JN.1. Antigenically, we found that BA.2.87.1 is closer to the ancestral BA.2 compared to other recently emerged Omicron subvariants including BA.2.86/JN.1 and XBB.1.5. Altogether, these results highlight immune escape properties as well as biology of new variants and underscore the importance of continuous surveillance and informed decision-making in the development of effective vaccines.
Language	English
Publishing date	2024-03-11
Publishing country	United States
Document type	Preprint
DOI	10.1101/2024.03.11.583978
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Article ; Online: The deubiquitinase STAMBP modulates cytokine secretion through the NLRP3 inflammasome.

Bednash, Joseph S / Johns, Finny / Patel, Niharika / Smail, Taylor R / Londino, James D / Mallampalli, Rama K

Cellular signalling

2020 Volume 79, Page(s) 109859

Abstract: The NACHT, LRR and PYD domains-containing protein 3 (NLRP3) inflammasome is a multimeric, cytoplasmic, protein complex that regulates maturation and secretion of interleukin (IL)-1β, a potent pro-inflammatory cytokine. Critical to host defense against ... ...

Abstract	The NACHT, LRR and PYD domains-containing protein 3 (NLRP3) inflammasome is a multimeric, cytoplasmic, protein complex that regulates maturation and secretion of interleukin (IL)-1β, a potent pro-inflammatory cytokine. Critical to host defense against pathogens, IL-1β amplifies early innate immune responses by activating transcription of numerous other cytokines and chemokines. Excessive IL-1β is associated with poor outcomes in inflammatory illnesses, such as sepsis and the acute respiratory distress syndrome (ARDS). Tight regulation of this signaling axis is vital, but little is known about mechanisms to limit excessive inflammasome activity. Here we identify the deubiquitinase STAM-binding protein (STAMBP) as a negative regulator of the NLRP3 inflammasome. In monocytes, knockout of STAMBP by CRISPR/Cas9 gene editing increased expression of numerous cytokines and chemokines in response to Toll-like receptor (TLR) agonists or bacterial lipopolysaccharide (LPS). This exaggerated inflammatory response was dependent on IL-1β signaling, and STAMBP knockout directly increased release of IL-1β with TLR ligation. While STAMBP does not modulate NLRP3 protein abundance, cellular depletion of the deubiquitinase increased NLRP3 K63 chain polyubiquitination resulting in increased NLRP3 inflammasome activation. These findings describe a unique mechanism of non-degradative ubiquitination of NLRP3 by STAMBP to limit excessive inflammasome activation and to reduce injurious IL-1β signaling.
MeSH term(s)	Endosomal Sorting Complexes Required for Transport/immunology ; HEK293 Cells ; Humans ; Inflammasomes/immunology ; Interleukin-1beta/immunology ; NLR Family, Pyrin Domain-Containing 3 Protein/immunology ; Signal Transduction/immunology ; THP-1 Cells ; Ubiquitin Thiolesterase/immunology ; Ubiquitination/immunology
Chemical Substances	Endosomal Sorting Complexes Required for Transport ; IL1B protein, human ; Inflammasomes ; Interleukin-1beta ; NLR Family, Pyrin Domain-Containing 3 Protein ; NLRP3 protein, human ; STAMBP protein, human ; Ubiquitin Thiolesterase (EC 3.4.19.12)
Language	English
Publishing date	2020-11-27
Publishing country	England
Document type	Journal Article ; Research Support, N.I.H., Extramural
ZDB-ID	1002702-6
ISSN	1873-3913 ; 0898-6568
ISSN (online)	1873-3913
ISSN	0898-6568
DOI	10.1016/j.cellsig.2020.109859
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Article: A role for Toll-like receptor 3 in lung vascular remodeling associated with SARS-CoV-2 infection.

Farkas, Daniela / Bogamuwa, Srimathi / Piper, Bryce / Newcomb, Geoffrey / Gunturu, Pranav / Bednash, Joseph S / Londino, James D / Elhance, Ajit / Nho, Richard / Mejia, Oscar Rosas / Yount, Jacob S / Horowitz, Jeffrey C / Goncharova, Elena A / Mallampalli, Rama K / Robinson, Richard T / Farkas, Laszlo

bioRxiv : the preprint server for biology

2023

Abstract: Cardiovascular sequelae of severe acute respiratory syndrome (SARS) coronavirus-2 (CoV-2) disease 2019 (COVID-19) contribute to the complications of the disease. One potential complication is lung vascular remodeling, but the exact cause is still unknown. ...

Abstract	Cardiovascular sequelae of severe acute respiratory syndrome (SARS) coronavirus-2 (CoV-2) disease 2019 (COVID-19) contribute to the complications of the disease. One potential complication is lung vascular remodeling, but the exact cause is still unknown. We hypothesized that endothelial TLR3 insufficiency contributes to lung vascular remodeling induced by SARS-CoV-2. In the lungs of COVID-19 patients and SARS-CoV-2 infected Syrian hamsters, we discovered thickening of the pulmonary artery media and microvascular rarefaction, which were associated with decreased TLR3 expression in lung tissue and pulmonary artery endothelial cells (ECs).
Language	English
Publishing date	2023-01-25
Publishing country	United States
Document type	Preprint
DOI	10.1101/2023.01.25.524586
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