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Article ; Online: Type 2 transglutaminase in the nucleus: the new epigenetic face of a cytoplasmic enzyme

Rossin, Federica / Ciccosanti, Fabiola / D'Eletto, Manuela / Occhigrossi, Luca / Fimia, Gian Maria / Piacentini, Mauro

Cell. Mol. Life Sci.. 2023 Feb., v. 80, no. 2 p.52-52

2023

Abstract: One of the major mysteries in science is how it is possible to pack the cellular chromatin with a total length of over 1 m, into a small sphere with a diameter of 5 mm "the nucleus", and even more difficult to envisage how to make it functional. Although ...

Abstract	One of the major mysteries in science is how it is possible to pack the cellular chromatin with a total length of over 1 m, into a small sphere with a diameter of 5 mm "the nucleus", and even more difficult to envisage how to make it functional. Although we know that compaction is achieved through the histones, however, the DNA needs to be accessible to the transcription machinery and this is allowed thanks to a variety of very complex epigenetic mechanisms. Either DNA (methylation) or post-translational modifications of histone proteins (acetylation, methylation, ubiquitination and sumoylation) play a crucial role in chromatin remodelling and consequently on gene expression. Recently the serotonylation and dopaminylation of the histone 3, catalyzed by the Transglutaminase type 2 (TG2), has been reported. These novel post-translational modifications catalyzed by a predominantly cytoplasmic enzyme opens a new avenue for future investigations on the enzyme function itself and for the possibility that other biological amines, substrate of TG2, can influence the genome regulation under peculiar cellular conditions. In this review we analyzed the nuclear TG2's biology by discussing both its post-translational modification of various transcription factors and the implications of its epigenetic new face. Finally, we will focus on the potential impact of these events in human diseases.
Keywords	DNA ; acetylation ; chromatin ; epigenetics ; gene expression ; genome ; histones ; humans ; methylation ; protein-glutamine gamma-glutamyltransferase ; sumoylation
Language	English
Dates of publication	2023-02
Size	p. 52.
Publishing place	Springer International Publishing
Document type	Article ; Online
Note	Review
ZDB-ID	1358415-7
ISSN	1420-9071 ; 1420-682X
ISSN (online)	1420-9071
ISSN	1420-682X
DOI	10.1007/s00018-023-04698-8
Database	NAL-Catalogue (AGRICOLA)

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Article ; Online: Type 2 transglutaminase in the nucleus: the new epigenetic face of a cytoplasmic enzyme.

Rossin, Federica / Ciccosanti, Fabiola / D'Eletto, Manuela / Occhigrossi, Luca / Fimia, Gian Maria / Piacentini, Mauro

Cellular and molecular life sciences : CMLS

2023 Volume 80, Issue 2, Page(s) 52

Abstract	One of the major mysteries in science is how it is possible to pack the cellular chromatin with a total length of over 1 m, into a small sphere with a diameter of 5 mm "the nucleus", and even more difficult to envisage how to make it functional. Although we know that compaction is achieved through the histones, however, the DNA needs to be accessible to the transcription machinery and this is allowed thanks to a variety of very complex epigenetic mechanisms. Either DNA (methylation) or post-translational modifications of histone proteins (acetylation, methylation, ubiquitination and sumoylation) play a crucial role in chromatin remodelling and consequently on gene expression. Recently the serotonylation and dopaminylation of the histone 3, catalyzed by the Transglutaminase type 2 (TG2), has been reported. These novel post-translational modifications catalyzed by a predominantly cytoplasmic enzyme opens a new avenue for future investigations on the enzyme function itself and for the possibility that other biological amines, substrate of TG2, can influence the genome regulation under peculiar cellular conditions. In this review we analyzed the nuclear TG2's biology by discussing both its post-translational modification of various transcription factors and the implications of its epigenetic new face. Finally, we will focus on the potential impact of these events in human diseases.
MeSH term(s)	Humans ; Acetylation ; Chromatin ; DNA/genetics ; DNA Methylation ; Epigenesis, Genetic ; Histones/metabolism ; Protein Processing, Post-Translational ; Transglutaminases/genetics ; Transglutaminases/metabolism ; Cytoplasm/enzymology ; Cytoplasm/genetics ; Cytoplasm/metabolism ; Cell Nucleus/enzymology ; Cell Nucleus/genetics ; Cell Nucleus/metabolism ; Chromatin Assembly and Disassembly/genetics ; Chromatin Assembly and Disassembly/physiology
Chemical Substances	Chromatin ; DNA (9007-49-2) ; Histones ; Transglutaminases (EC 2.3.2.13) ; TGM2 protein, human
Language	English
Publishing date	2023-01-25
Publishing country	Switzerland
Document type	Journal Article ; Review
ZDB-ID	1358415-7
ISSN	1420-9071 ; 1420-682X
ISSN (online)	1420-9071
ISSN	1420-682X
DOI	10.1007/s00018-023-04698-8
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: Analysis of Secreted Proteins from Prepubertal Ovarian Tissues Exposed In Vitro to Cisplatin and LH.

Marcozzi, Serena / Ciccosanti, Fabiola / Fimia, Gian Maria / Piacentini, Mauro / Caggiano, Cinzia / Sette, Claudio / De Felici, Massimo / Klinger, Francesca Gioia

Cells

2022 Volume 11, Issue 7

Abstract: It is well known that secreted and exosomal proteins are associated with a broad range of physiological processes involving tissue homeostasis and differentiation. In the present paper, our purpose was to characterize the proteome of the culture medium ... ...

Abstract	It is well known that secreted and exosomal proteins are associated with a broad range of physiological processes involving tissue homeostasis and differentiation. In the present paper, our purpose was to characterize the proteome of the culture medium in which the oocytes within the primordial/primary follicles underwent apoptosis induced by cisplatin (CIS) or were, for the most part, protected by LH against the drug. To this aim, prepubertal ovarian tissues were cultured under control and in the presence of CIS, LH, and CIS + LH. The culture media were harvested after 2, 12, and 24 h from chemotherapeutic drug treatment and analyzed by liquid chromatography-mass spectrometry (LC-MS). We found that apoptotic conditions generated by CIS in the cultured ovarian tissues and/or oocytes are reflected in distinct changes in the extracellular microenvironment in which they were cultured. These changes became evident mainly from 12 h onwards and were characterized by the inhibition or decreased release of a variety of compounds, such as the proteases Htra1 and Prss23, the antioxidants Prdx2 and Hbat1, the metabolic regulators Ldha and Pkm, and regulators of apoptotic pathways such as Tmsb4x. Altogether, these results confirm the biological relevance of the LH action on prepuberal ovaries and provide novel information about the proteins released by the ovarian tissues exposed to CIS and LH in the surrounding microenvironment. These data might represent a valuable resource for future studies aimed to clarify the effects and identify biomarkers of these compounds' action on the developing ovary.
MeSH term(s)	Animals ; Apoptosis ; Cisplatin/metabolism ; Cisplatin/pharmacology ; Female ; Oocytes/metabolism ; Ovarian Follicle/metabolism ; Ovary/metabolism
Chemical Substances	Cisplatin (Q20Q21Q62J)
Language	English
Publishing date	2022-04-03
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	2661518-6
ISSN	2073-4409 ; 2073-4409
ISSN (online)	2073-4409
ISSN	2073-4409
DOI	10.3390/cells11071208
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Article: Mitochondrial Interactome: A Focus on Antiviral Signaling Pathways.

Refolo, Giulia / Vescovo, Tiziana / Piacentini, Mauro / Fimia, Gian Maria / Ciccosanti, Fabiola

Frontiers in cell and developmental biology

2020 Volume 8, Page(s) 8

Abstract: In the last years, proteomics has represented a valuable approach to elucidate key aspects in the regulation of type I/III interferons (IFNs) and autophagy, two main processes involved in the response to viral infection, to unveil the molecular ... ...

Abstract	In the last years, proteomics has represented a valuable approach to elucidate key aspects in the regulation of type I/III interferons (IFNs) and autophagy, two main processes involved in the response to viral infection, to unveil the molecular strategies that viruses have evolved to counteract these processes. Besides their main metabolic roles, mitochondria are well recognized as pivotal organelles in controlling signaling pathways essential to restrain viral infections. In particular, a major role in antiviral defense is played by mitochondrial antiviral signaling (MAVS) protein, an adaptor protein that coordinates the activation of IFN inducing pathways and autophagy at the mitochondrial level. Here, we provide an overview of how mass spectrometry-based studies of protein-protein interactions and post-translational modifications (PTMs) have fostered our understanding of the molecular mechanisms that control the mitochondria-mediated antiviral immunity.
Language	English
Publishing date	2020-02-14
Publishing country	Switzerland
Document type	Journal Article ; Review
ZDB-ID	2737824-X
ISSN	2296-634X
ISSN	2296-634X
DOI	10.3389/fcell.2020.00008
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Article ; Online: A microRNA Arising from the Negative Strand of SARS-CoV-2 Genome Targets FOS to Reduce AP-1 Activity.

Greco, Francesco / Lorefice, Elisa / Carissimi, Claudia / Laudadio, Ilaria / Ciccosanti, Fabiola / Di Rienzo, Martina / Colavita, Francesca / Meschi, Silvia / Maggi, Fabrizio / Fimia, Gian Maria / Fulci, Valerio

Non-coding RNA

2023 Volume 9, Issue 3

Abstract: Virus-encoded microRNAs were first reported in the Epstein-Barr virus in 2004. Subsequently, a few hundred viral miRNAs have been identified, mainly in DNA viruses belonging to ... ...

Abstract	Virus-encoded microRNAs were first reported in the Epstein-Barr virus in 2004. Subsequently, a few hundred viral miRNAs have been identified, mainly in DNA viruses belonging to the
Language	English
Publishing date	2023-05-23
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	2813993-8
ISSN	2311-553X ; 2311-553X
ISSN (online)	2311-553X
ISSN	2311-553X
DOI	10.3390/ncrna9030033
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Article ; Online: AMBRA1 regulates mitophagy by interacting with ATAD3A and promoting PINK1 stability.

Di Rienzo, Martina / Romagnoli, Alessandra / Ciccosanti, Fabiola / Refolo, Giulia / Consalvi, Veronica / Arena, Giuseppe / Valente, Enza Maria / Piacentini, Mauro / Fimia, Gian Maria

Autophagy

2021 Volume 18, Issue 8, Page(s) 1752–1762

Abstract: PINK1 accumulation at the outer mitochondrial membrane (OMM) is a key event required to signal depolarized mitochondria to the autophagy machinery. How this early step is, in turn, modulated by autophagy proteins remains less characterized. Here, we show ...

Abstract	PINK1 accumulation at the outer mitochondrial membrane (OMM) is a key event required to signal depolarized mitochondria to the autophagy machinery. How this early step is, in turn, modulated by autophagy proteins remains less characterized. Here, we show that, upon mitochondrial depolarization, the proautophagic protein AMBRA1 is recruited to the OMM and interacts with PINK1 and ATAD3A, a transmembrane protein that mediates mitochondrial import and degradation of PINK1. Downregulation of AMBRA1 expression results in reduced levels of PINK1 due to its enhanced degradation by the mitochondrial protease LONP1, which leads to a decrease in PINK1-mediated ubiquitin phosphorylation and mitochondrial PRKN/PARKIN recruitment. Notably, ATAD3A silencing rescues defective PINK1 accumulation in AMBRA1-deficient cells upon mitochondrial damage. Overall, our findings underline an upstream contribution of AMBRA1 in the control of PINK1-PRKN mitophagy by interacting with ATAD3A and promoting PINK1 stability. This novel regulatory element may account for changes of PINK1 levels in neuropathological conditions.
MeSH term(s)	Adaptor Proteins, Signal Transducing ; Autophagy ; Carbonyl Cyanide m-Chlorophenyl Hydrazone/pharmacology ; Mitochondria/metabolism ; Mitophagy ; Protein Kinases/metabolism ; Ubiquitin-Protein Ligases/metabolism
Chemical Substances	AMBRA1 protein, human ; Adaptor Proteins, Signal Transducing ; Carbonyl Cyanide m-Chlorophenyl Hydrazone (555-60-2) ; Ubiquitin-Protein Ligases (EC 2.3.2.27) ; Protein Kinases (EC 2.7.-)
Language	English
Publishing date	2021-11-19
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2454135-7
ISSN	1554-8635 ; 1554-8627
ISSN (online)	1554-8635
ISSN	1554-8627
DOI	10.1080/15548627.2021.1997052
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Article: Peroxiredoxin 6 Modulates Insulin Secretion and Beta Cell Death

Pacifici, Francesca / Della-Morte, David / Capuani, Barbara / Coppola, Andrea / Scioli, Maria Giovanna / Donadel, Giulia / Andreadi, Aikaterini / Ciccosanti, Fabiola / Fimia, Gian Maria / Bellia, Alfonso / Orlandi, Augusto / Lauro, Davide

Frontiers in endocrinology

2022 Volume 13, Page(s) 842575

Abstract: In pancreatic beta cells, mitochondrial metabolism controls glucose-stimulated insulin secretion (GSIS) by ATP production, redox signaling, and calcium ( ... ...

Abstract	In pancreatic beta cells, mitochondrial metabolism controls glucose-stimulated insulin secretion (GSIS) by ATP production, redox signaling, and calcium (Ca
MeSH term(s)	Animals ; Apoptosis ; Insulin/metabolism ; Insulin Secretion ; Insulin-Secreting Cells/metabolism ; Mice ; Mitochondrial Dynamics ; Peroxiredoxin VI/genetics ; Peroxiredoxin VI/metabolism
Chemical Substances	Insulin ; Peroxiredoxin VI (EC 1.11.1.15) ; Prdx6 protein, mouse (EC 1.11.1.15)
Language	English
Publishing date	2022-03-18
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	2592084-4
ISSN	1664-2392
ISSN	1664-2392
DOI	10.3389/fendo.2022.842575
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Article ; Online: Proteomic analysis identifies deregulated metabolic and oxidative-associated proteins in Italian intrahepatic cholangiocarcinoma patients.

Cavalloni, Giuliana / Peraldo-Neia, Caterina / Massa, Annamaria / Bergamini, Carlo / Trentini, Alessandro / De Rosa, Giovanni / Daniele, Lorenzo / Ciccosanti, Fabiola / Cervellati, Carlo / Leone, Francesco / Aglietta, Massimo

BMC cancer

2021 Volume 21, Issue 1, Page(s) 865

Abstract: Background: Cholangiocarcinoma (CCA) is an aggressive disease with poor prognosis. A molecular classification based on mutational, methylation and transcriptomic features could allow identifying tailored therapies to improve CCA patient outcome. ... ...

Abstract	Background: Cholangiocarcinoma (CCA) is an aggressive disease with poor prognosis. A molecular classification based on mutational, methylation and transcriptomic features could allow identifying tailored therapies to improve CCA patient outcome. Proteomic remains partially unexplored; here, we analyzed the proteomic profile of five intrahepatic cholangiocarcinoma (ICC) derived from Italian patients undergone surgery and one normal bile duct cell line. Methods: Proteome profile was investigated by using 2D electrophoresis followed by Mass Spectrometry (MS). To validate proteomic data, the expression of four overexpressed proteins (CAT, SOD, PRDX6, DBI/ACBP) was evaluated by immunohistochemistry in an independent cohort of formalin fixed, paraffin-embedded (FFPE) ICC tissues. We also compared proteomic data with those obtained by transcriptomic profile evaluated by microarray analysis of the same tissues. Results: We identified 19 differentially expressed protein spots, which were further characterized by MS; 13 of them were up- and 6 were down-regulated in ICC. These proteins are mainly involved in redox processes (CAT, SODM, PRDX2, PRDX6), in metabolism (ACBP, ACY1, UCRI, FTCD, HCMS2), and cell structure and organization (TUB2, ACTB). CAT is overexpressed in 86% of patients, PRDX6 in 73%, SODM in 100%, and DBI/ACBP in 81% compared to normal adjacent tissues. A concordance of 50% between proteomic and transcriptomic data was observed. Conclusions: This study pointed out that the impairment of the metabolic and antioxidant systems, with a subsequent accumulation of free radicals, might be a key step in CCA development and progression.
MeSH term(s)	Bile Duct Neoplasms/genetics ; Bile Duct Neoplasms/metabolism ; Bile Duct Neoplasms/pathology ; Biomarkers, Tumor ; Cell Line, Tumor ; Cholangiocarcinoma/genetics ; Cholangiocarcinoma/metabolism ; Cholangiocarcinoma/pathology ; Electrophoresis, Gel, Two-Dimensional ; Energy Metabolism ; Gene Expression Profiling ; Humans ; Immunohistochemistry ; Mass Spectrometry/methods ; Oxidation-Reduction ; Proteome ; Proteomics/methods
Chemical Substances	Biomarkers, Tumor ; Proteome
Language	English
Publishing date	2021-07-28
Publishing country	England
Document type	Journal Article
ISSN	1471-2407
ISSN (online)	1471-2407
DOI	10.1186/s12885-021-08576-z
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Article ; Online: High Levels of TRIM5α Are Associated with Xenophagy in HIV-1-Infected Long-Term Nonprogressors.

Ciccosanti, Fabiola / Corazzari, Marco / Casetti, Rita / Amendola, Alessandra / Collalto, Diletta / Refolo, Giulia / Vergori, Alessandra / Taibi, Chiara / D'Offizi, Gianpiero / Antinori, Andrea / Agrati, Chiara / Fimia, Gian Maria / Ippolito, Giuseppe / Piacentini, Mauro / Nardacci, Roberta

Cells

2021 Volume 10, Issue 5

Abstract: Autophagy is a lysosomal-dependent degradative mechanism essential in maintaining cellular homeostasis, but it is also considered an ancient form of innate eukaryotic fighting against invading microorganisms. Mounting evidence has shown that HIV-1 is a ... ...

Abstract	Autophagy is a lysosomal-dependent degradative mechanism essential in maintaining cellular homeostasis, but it is also considered an ancient form of innate eukaryotic fighting against invading microorganisms. Mounting evidence has shown that HIV-1 is a critical target of autophagy that plays a role in HIV-1 replication and disease progression. In a special subset of HIV-1-infected patients that spontaneously and durably maintain extremely low viral replication, namely, long-term nonprogressors (LTNP), the resistance to HIV-1-induced pathogenesis is accompanied, in vivo, by a significant increase in the autophagic activity in peripheral blood mononuclear cells. Recently, a new player in the battle of autophagy against HIV-1 has been identified, namely, tripartite motif protein 5α (TRIM5α). In vitro data demonstrated that TRIM5α directly recognizes HIV-1 and targets it for autophagic destruction, thus protecting cells against HIV-1 infection. In this paper, we analyzed the involvement of this factor in the control of HIV-1 infection through autophagy, in vivo, in LTNP. The results obtained showed significantly higher levels of TRIM5α expression in cells from LTNP with respect to HIV-1-infected normal progressor patients. Interestingly, the colocalization of TRIM5α and HIV-1 proteins in autophagic vacuoles in LTNP cells suggested the participation of TRIM5α in the autophagy containment of HIV-1 in LTNP. Altogether, our results point to a protective role of TRIM5α in the successful control of the chronic viral infection in HIV-1-controllers through the autophagy mechanism. In our opinion, these findings could be relevant in fighting against HIV-1 disease, because autophagy inducers might be employed in combination with antiretroviral drugs.
MeSH term(s)	Adult ; Aged ; Autophagy ; Case-Control Studies ; Cohort Studies ; Female ; HIV Infections/immunology ; HIV Long-Term Survivors ; HIV-1 ; Humans ; Male ; Middle Aged ; Tripartite Motif Proteins/immunology ; Ubiquitin-Protein Ligases/immunology ; Virus Replication ; Young Adult
Chemical Substances	Tripartite Motif Proteins ; TRIM5 protein, human (EC 2.3.2.27) ; Ubiquitin-Protein Ligases (EC 2.3.2.27)
Language	English
Publishing date	2021-05-14
Publishing country	Switzerland
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2661518-6
ISSN	2073-4409 ; 2073-4409
ISSN (online)	2073-4409
ISSN	2073-4409
DOI	10.3390/cells10051207
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Article: Proteomic analysis identifies a signature of disease severity in the plasma of COVID-19 pneumonia patients associated to neutrophil, platelet and complement activation.

Ciccosanti, Fabiola / Antonioli, Manuela / Sacchi, Alessandra / Notari, Stefania / Farina, Anna / Beccacece, Alessia / Fusto, Marisa / Vergori, Alessandra / D'Offizi, Gianpiero / Taglietti, Fabrizio / Antinori, Andrea / Nicastri, Emanuele / Marchioni, Luisa / Palmieri, Fabrizio / Ippolito, Giuseppe / Piacentini, Mauro / Agrati, Chiara / Fimia, Gian Maria

Clinical proteomics

2022 Volume 19, Issue 1, Page(s) 38

Abstract: Most patients infected with SARS-CoV-2 display mild symptoms with good prognosis, while 20% of patients suffer from severe viral pneumonia and up to 5% may require intensive care unit (ICU) admission due to severe acute respiratory syndrome, which could ... ...

Abstract	Most patients infected with SARS-CoV-2 display mild symptoms with good prognosis, while 20% of patients suffer from severe viral pneumonia and up to 5% may require intensive care unit (ICU) admission due to severe acute respiratory syndrome, which could be accompanied by multiorgan failure.Plasma proteomics provide valuable and unbiased information about disease progression and therapeutic candidates. Recent proteomic studies have identified molecular changes in plasma of COVID-19 patients that implied significant dysregulation of several aspects of the inflammatory response accompanied by a general metabolic suppression. However, which of these plasma alterations are associated with disease severity remains only partly characterized.A known limitation of proteomic studies of plasma samples is the large difference in the macromolecule abundance, with concentration spanning at least 10 orders of magnitude. To improve the coverage of plasma contents, we performed a deep proteomic analysis of plasma from 10 COVID-19 patients with severe/fatal pneumonia compared to 10 COVID-19 patients with pneumonia who did not require ICU admission (non-ICU). To this aim, plasma samples were first depleted of the most abundant proteins, trypsin digested and peptides subjected to a high pH reversed-phase peptide fractionation before LC-MS analysis.These results highlighted an increase of proteins involved in neutrophil and platelet activity and acute phase response, which is significantly higher in severe/fatal COVID-19 patients when compared to non-ICU ones. Importantly, these changes are associated with a selective induction of complement cascade factors in severe/fatal COVID-19 patients. Data are available via ProteomeXchange with identifier PXD036491. Among these alterations, we confirmed by ELISA that higher levels of the neutrophil granule proteins DEFA3 and LCN2 are present in COVID-19 patients requiring ICU admission when compared to non-ICU and healthy donors.Altogether, our study provided an in-depth view of plasma proteome changes that occur in COVID-19 patients in relation to disease severity, which can be helpful to identify therapeutic strategies to improve the disease outcome.
Language	English
Publishing date	2022-11-08
Publishing country	England
Document type	Journal Article
ZDB-ID	2205154-5
ISSN	1542-6416
ISSN	1542-6416
DOI	10.1186/s12014-022-09377-7
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