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Article ; Online: The global proteome and ubiquitinome of bacterial and viral co-infected bronchial epithelial cells

Sura, Thomas / Surabhi, Surabhi / Maaß, Sandra / Hammerschmidt, Sven / Siemens, Nikolai / Becher, Dörte

Journal of Proteomics. 2022 Jan., v. 250 p.104387-

2022

Abstract: Viral infections facilitate bacterial trafficking to the lower respiratory tract resulting in bacterial-viral co-infections. Bacterial dissemination to the lower respiratory tract is enhanced by influenza A virus induced epithelial cell damage and ... ...

Abstract	Viral infections facilitate bacterial trafficking to the lower respiratory tract resulting in bacterial-viral co-infections. Bacterial dissemination to the lower respiratory tract is enhanced by influenza A virus induced epithelial cell damage and dysregulation of immune responses. Epithelial cells act as a line of defense and detect pathogens by a high variety of pattern recognition receptors. The post-translational modification ubiquitin is involved in almost every cellular process. Moreover, ubiquitination contributes to the regulation of host immune responses, influenza A virus uncoating and transport within host cells. We applied proteomics with a special focus on ubiquitination to assess the impact of single bacterial and viral as well as bacterial-viral co-infections on bronchial epithelial cells. We used Tandem Ubiquitin Binding Entities to enrich polyubiquitinated proteins and assess changes in the ubiquitinome. Infecting 16HBE cells with Streptococcus pyogenes led to an increased abundance of proteins related to mitochondrial translation and energy metabolism in proteome and ubiquitinome. In contrast, influenza A virus infection mainly altered the ubiquitinome. Co-infections had no additional impact on protein abundances or affected pathways. Changes in protein abundance and enriched pathways were assigned to imprints of both infecting pathogens. Viral and bacterial co-infections of the lower respiratory tract are a burden for health systems worldwide. Therefore, it is necessary to elucidate the complex interplay between the host and the infecting pathogens. Thus, we analyzed the proteome and the ubiquitinome of co-infected bronchial epithelial cells to elaborate a potential synergism of the two infecting organisms. The results presented in this work can be used as a starting point for further analyses.
Keywords	Influenza A virus ; Streptococcus pyogenes ; energy metabolism ; epithelial cells ; epithelium ; mitochondria ; mixed infection ; proteome ; proteomics ; respiratory system ; synergism ; ubiquitin ; ubiquitination ; Co-infection ; Staphylococcus aureus ; 16HBE
Language	English
Dates of publication	2022-01
Publishing place	Elsevier B.V.
Document type	Article ; Online
ZDB-ID	2400835-7
ISSN	1876-7737 ; 1874-3919
ISSN (online)	1876-7737
ISSN	1874-3919
DOI	10.1016/j.jprot.2021.104387
Database	NAL-Catalogue (AGRICOLA)

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Book ; Online: When Everything Changes Over Night

Saidy, Christina / Sura, Thomas

Teaching/Writing: The Journal of Writing Teacher Education

What We Learned from Teaching the Writing Practicum in the Era of Covid-19

2020

Abstract: In this article, two university-level writing teacher educators describe their experiences in the Spring 2020 as they abruptly moved their spring practica and first-year writing courses to emergency remote teaching online. The authors share takeaways and ...

Abstract	In this article, two university-level writing teacher educators describe their experiences in the Spring 2020 as they abruptly moved their spring practica and first-year writing courses to emergency remote teaching online. The authors share takeaways and guiding principles that emerged from the shift to emergency remote teaching that can be applied in similar contexts and beyond.
Keywords	writing ; composition ; writing practicum ; writing teacher education ; Rhetoric and Composition ; covid19
Publishing date	2020-07-07T10:36:49Z
Publisher	ScholarWorks at WMU
Publishing country	us
Document type	Book ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Streptococcus pneumoniae

Sura, Thomas / Gering, Vanessa / Cammann, Clemens / Hammerschmidt, Sven / Maaß, Sandra / Seifert, Ulrike / Becher, Dörte

Frontiers in cellular and infection microbiology

2022 Volume 12, Page(s) 817532

Abstract: Epithelial cells are an important line of defense within the lung. Disruption of the epithelial barrier by pathogens enables the systemic dissemination of bacteria or viruses within the host leading to severe diseases with fatal outcomes. Thus, the lung ... ...

Abstract	Epithelial cells are an important line of defense within the lung. Disruption of the epithelial barrier by pathogens enables the systemic dissemination of bacteria or viruses within the host leading to severe diseases with fatal outcomes. Thus, the lung epithelium can be damaged by seasonal and pandemic influenza A viruses. Influenza A virus infection induced dysregulation of the immune system is beneficial for the dissemination of bacteria to the lower respiratory tract, causing bacterial and viral co-infection. Host cells regulate protein homeostasis and the response to different perturbances, for instance provoked by infections, by post translational modification of proteins. Aside from protein phosphorylation, ubiquitination of proteins is an essential regulatory tool in virtually every cellular process such as protein homeostasis, host immune response, cell morphology, and in clearing of cytosolic pathogens. Here, we analyzed the proteome and ubiquitinome of A549 alveolar lung epithelial cells in response to infection by either
MeSH term(s)	A549 Cells ; Coinfection/microbiology ; Humans ; Influenza A Virus, H1N1 Subtype/physiology ; Influenza A virus ; Influenza, Human ; Streptococcus pneumoniae ; Ubiquitination
Language	English
Publishing date	2022-02-24
Publishing country	Switzerland
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2619676-1
ISSN	2235-2988 ; 2235-2988
ISSN (online)	2235-2988
ISSN	2235-2988
DOI	10.3389/fcimb.2022.817532
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Book ; Online ; Thesis: Mass spectrometry based analyses of posttranslational protein modification in bacterial and viral (co)-infection

Sura, Thomas [Verfasser] / Becher, Dörte [Akademischer Betreuer] / Becher, Dörte [Gutachter] / Pich, Andreas [Gutachter]

2023

Author's details	Thomas Sura ; Gutachter: Dörte Becher, Andreas Pich ; Betreuer: Dörte Becher
Keywords	Biowissenschaften, Biologie ; Life Science, Biology
Subject code	sg570
Language	English
Publisher	Universität Greifswald
Publishing place	Greifswald
Document type	Book ; Online ; Thesis
Database	Digital theses on the web

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Article: Migration of Acanthamoeba through Legionella biofilms is regulated by the bacterial Lqs‐LvbR network, effector proteins and the flagellum

Hochstrasser, Ramon / Michaelis, Sarah / Brülisauer, Sabrina / Sura, Thomas / Fan, Mingzhen / Maaß, Sandra / Becher, Dörte / Hilbi, Hubert

Environmental microbiology. 2022 Aug., v. 24, no. 8

2022

Abstract: The environmental bacterium Legionella pneumophila causes the pneumonia Legionnaires' disease. The opportunistic pathogen forms biofilms and employs the Icm/Dot type IV secretion system (T4SS) to replicate in amoebae and macrophages. A regulatory network ...

Abstract	The environmental bacterium Legionella pneumophila causes the pneumonia Legionnaires' disease. The opportunistic pathogen forms biofilms and employs the Icm/Dot type IV secretion system (T4SS) to replicate in amoebae and macrophages. A regulatory network comprising the Legionella quorum sensing (Lqs) system and the transcription factor LvbR controls bacterial motility, virulence and biofilm architecture. Here we show by comparative proteomics that in biofilms formed by the L. pneumophila ΔlqsR or ΔlvbR regulatory mutants the abundance of proteins encoded by a genomic ‘fitness island’, metabolic enzymes, effector proteins and flagellar components (e.g. FlaA) varies. ∆lqsR or ∆flaA mutants form ‘patchy’ biofilms like the parental strain JR32, while ∆lvbR forms a ‘mat‐like’ biofilm. Acanthamoeba castellanii amoebae migrated more slowly through biofilms of L. pneumophila lacking lqsR, lvbR, flaA, a functional Icm/Dot T4SS (∆icmT), or secreted effector proteins. Clusters of bacteria decorated amoebae in JR32, ∆lvbR or ∆icmT biofilms but not in ∆lqsR or ∆flaA biofilms. The amoeba‐adherent bacteria induced promoters implicated in motility (PfₗₐA) or virulence (PₛᵢdC, PᵣₐₗF). Taken together, the Lqs‐LvbR network (quorum sensing), FlaA (motility) and the Icm/Dot T4SS (virulence) regulate migration of A. castellanii through L. pneumophila biofilms, and – apart from the T4SS – govern bacterial cluster formation on the amoebae.
Keywords	Acanthamoeba castellanii ; Legionella pneumophila ; bacteria ; bacterial motility ; biofilm ; flagellum ; genomics ; macrophages ; opportunistic pathogens ; pneumonia ; proteomics ; secretion ; transcription factors ; virulence
Language	English
Dates of publication	2022-08
Size	p. 3672-3692.
Publishing place	John Wiley & Sons, Inc.
Document type	Article
Note	JOURNAL ARTICLE
ZDB-ID	2020213-1
ISSN	1462-2920 ; 1462-2912
ISSN (online)	1462-2920
ISSN	1462-2912
DOI	10.1111/1462-2920.16008
Database	NAL-Catalogue (AGRICOLA)

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Article ; Online: The global proteome and ubiquitinome of bacterial and viral co-infected bronchial epithelial cells.

Sura, Thomas / Surabhi, Surabhi / Maaß, Sandra / Hammerschmidt, Sven / Siemens, Nikolai / Becher, Dörte

Journal of proteomics

2021 Volume 250, Page(s) 104387

Abstract	Viral infections facilitate bacterial trafficking to the lower respiratory tract resulting in bacterial-viral co-infections. Bacterial dissemination to the lower respiratory tract is enhanced by influenza A virus induced epithelial cell damage and dysregulation of immune responses. Epithelial cells act as a line of defense and detect pathogens by a high variety of pattern recognition receptors. The post-translational modification ubiquitin is involved in almost every cellular process. Moreover, ubiquitination contributes to the regulation of host immune responses, influenza A virus uncoating and transport within host cells. We applied proteomics with a special focus on ubiquitination to assess the impact of single bacterial and viral as well as bacterial-viral co-infections on bronchial epithelial cells. We used Tandem Ubiquitin Binding Entities to enrich polyubiquitinated proteins and assess changes in the ubiquitinome. Infecting 16HBE cells with Streptococcus pyogenes led to an increased abundance of proteins related to mitochondrial translation and energy metabolism in proteome and ubiquitinome. In contrast, influenza A virus infection mainly altered the ubiquitinome. Co-infections had no additional impact on protein abundances or affected pathways. Changes in protein abundance and enriched pathways were assigned to imprints of both infecting pathogens. SIGNIFICANCE: Viral and bacterial co-infections of the lower respiratory tract are a burden for health systems worldwide. Therefore, it is necessary to elucidate the complex interplay between the host and the infecting pathogens. Thus, we analyzed the proteome and the ubiquitinome of co-infected bronchial epithelial cells to elaborate a potential synergism of the two infecting organisms. The results presented in this work can be used as a starting point for further analyses.
MeSH term(s)	Epithelial Cells/metabolism ; Host-Pathogen Interactions ; Proteome/metabolism ; Proteomics/methods ; Ubiquitin/metabolism ; Ubiquitination
Chemical Substances	Proteome ; Ubiquitin
Language	English
Publishing date	2021-09-30
Publishing country	Netherlands
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2400835-7
ISSN	1876-7737 ; 1874-3919
ISSN (online)	1876-7737
ISSN	1874-3919
DOI	10.1016/j.jprot.2021.104387
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: Surviving Serum: the Escherichia coli

Biran, Dvora / Sura, Thomas / Otto, Andreas / Yair, Yael / Becher, Dörte / Ron, Eliora Z

Infection and immunity

2021 Volume 89, Issue 10, Page(s) e0031621

Abstract: Extraintestinal pathogenic Escherichia coli (ExPEC) strains constitute a serious and emerging clinical problem, as they cause a variety of infections and are usually highly antibiotic resistant. Many ExPEC strains are capable of evading the bactericidal ... ...

Abstract	Extraintestinal pathogenic Escherichia coli (ExPEC) strains constitute a serious and emerging clinical problem, as they cause a variety of infections and are usually highly antibiotic resistant. Many ExPEC strains are capable of evading the bactericidal effects of serum and causing sepsis. One critical factor for the development of septicemia is the increased serum survival (
MeSH term(s)	Anti-Bacterial Agents/pharmacology ; Drug Resistance, Bacterial/genetics ; Escherichia coli Infections/drug therapy ; Escherichia coli Infections/microbiology ; Escherichia coli Proteins/genetics ; Extraintestinal Pathogenic Escherichia coli/drug effects ; Extraintestinal Pathogenic Escherichia coli/genetics ; Humans ; Sepsis/drug therapy ; Sepsis/microbiology ; Serum/microbiology
Chemical Substances	Anti-Bacterial Agents ; Escherichia coli Proteins ; Iss protein, E coli
Language	English
Publishing date	2021-06-28
Publishing country	United States
Document type	Journal Article
ZDB-ID	218698-6
ISSN	1098-5522 ; 0019-9567
ISSN (online)	1098-5522
ISSN	0019-9567
DOI	10.1128/IAI.00316-21
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: Migration of Acanthamoeba through Legionella biofilms is regulated by the bacterial Lqs-LvbR network, effector proteins and the flagellum.

Hochstrasser, Ramon / Michaelis, Sarah / Brülisauer, Sabrina / Sura, Thomas / Fan, Mingzhen / Maaß, Sandra / Becher, Dörte / Hilbi, Hubert

Environmental microbiology

2022 Volume 24, Issue 8, Page(s) 3672–3692

Abstract	The environmental bacterium Legionella pneumophila causes the pneumonia Legionnaires' disease. The opportunistic pathogen forms biofilms and employs the Icm/Dot type IV secretion system (T4SS) to replicate in amoebae and macrophages. A regulatory network comprising the Legionella quorum sensing (Lqs) system and the transcription factor LvbR controls bacterial motility, virulence and biofilm architecture. Here we show by comparative proteomics that in biofilms formed by the L. pneumophila ΔlqsR or ΔlvbR regulatory mutants the abundance of proteins encoded by a genomic 'fitness island', metabolic enzymes, effector proteins and flagellar components (e.g. FlaA) varies. ∆lqsR or ∆flaA mutants form 'patchy' biofilms like the parental strain JR32, while ∆lvbR forms a 'mat-like' biofilm. Acanthamoeba castellanii amoebae migrated more slowly through biofilms of L. pneumophila lacking lqsR, lvbR, flaA, a functional Icm/Dot T4SS (∆icmT), or secreted effector proteins. Clusters of bacteria decorated amoebae in JR32, ∆lvbR or ∆icmT biofilms but not in ∆lqsR or ∆flaA biofilms. The amoeba-adherent bacteria induced promoters implicated in motility (P
MeSH term(s)	Acanthamoeba castellanii ; Bacterial Proteins/metabolism ; Biofilms ; Flagella/genetics ; Flagella/metabolism ; Humans ; Legionella/metabolism ; Legionella pneumophila/genetics ; Legionnaires' Disease ; Quorum Sensing
Chemical Substances	Bacterial Proteins
Language	English
Publishing date	2022-05-25
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2020213-1
ISSN	1462-2920 ; 1462-2912
ISSN (online)	1462-2920
ISSN	1462-2912
DOI	10.1111/1462-2920.16008
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article: Optimized Proteomics Workflow for the Detection of Small Proteins

Bartel, Jürgen / Varadarajan, Adithi R / Sura, Thomas / Ahrens, Christian H / Maaß, Sandra / Becher, Dörte

Journal of proteome research. 2020 Aug. 19, v. 19, no. 10

2020

Abstract: Small open reading frame encoded proteins (SEPs) gained increasing interest during the last few years because of their broad range of important functions in both prokaryotes and eukaryotes. In bacteria, signaling, virulence, and regulation of enzyme ... ...

Abstract	Small open reading frame encoded proteins (SEPs) gained increasing interest during the last few years because of their broad range of important functions in both prokaryotes and eukaryotes. In bacteria, signaling, virulence, and regulation of enzyme activities have been associated with SEPs. Nonetheless, the number of SEPs detected in large-scale proteome studies is often low as classical methods are biased toward the identification of larger proteins. Here, we present a workflow that allows enhanced identification of small proteins compared to traditional protocols. For this aim, the steps of small protein enrichment, proteolytic digest, and database search were reviewed and adjusted to the special requirement of SEPs. Enrichment by the use of small-pore-sized solid-phase material increased the number of identified SEPs by a factor of 2, and utilization of alternative proteases to trypsin reduced the spectral counts for larger proteins. The application of the optimized protocol allowed the detection of 210 already annotated proteins up to 100 amino acids (aa) length, including 16 proteins below 51 aa in the Gram-positive model organism Bacillus subtilis. Moreover, 12% of all identified proteins were up to 100 aa, which is a significantly larger fraction than that reported in studies involving traditional proteomics workflows. Finally, the application of an integrated proteogenomics search database and extensive subsequent validation resulted in the confident identification of three novel, not yet annotated, SEPs, which are 21, 26, and 42 aa long.
Keywords	Bacillus subtilis ; amino acids ; bacteria ; databases ; enzyme activity ; eukaryotic cells ; models ; open reading frames ; prokaryotic cells ; proteins ; proteolysis ; proteome ; proteomics ; trypsin ; virulence
Language	English
Dates of publication	2020-0819
Size	p. 4004-4018.
Publishing place	American Chemical Society
Document type	Article
ZDB-ID	2078618-9
ISSN	1535-3907 ; 1535-3893
ISSN (online)	1535-3907
ISSN	1535-3893
DOI	10.1021/acs.jproteome.0c00286
Database	NAL-Catalogue (AGRICOLA)

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Article ; Online: Optimized Proteomics Workflow for the Detection of Small Proteins.

Bartel, Jürgen / Varadarajan, Adithi R / Sura, Thomas / Ahrens, Christian H / Maaß, Sandra / Becher, Dörte

Journal of proteome research

2020 Volume 19, Issue 10, Page(s) 4004–4018

Abstract	Small open reading frame encoded proteins (SEPs) gained increasing interest during the last few years because of their broad range of important functions in both prokaryotes and eukaryotes. In bacteria, signaling, virulence, and regulation of enzyme activities have been associated with SEPs. Nonetheless, the number of SEPs detected in large-scale proteome studies is often low as classical methods are biased toward the identification of larger proteins. Here, we present a workflow that allows enhanced identification of small proteins compared to traditional protocols. For this aim, the steps of small protein enrichment, proteolytic digest, and database search were reviewed and adjusted to the special requirement of SEPs. Enrichment by the use of small-pore-sized solid-phase material increased the number of identified SEPs by a factor of 2, and utilization of alternative proteases to trypsin reduced the spectral counts for larger proteins. The application of the optimized protocol allowed the detection of 210 already annotated proteins up to 100 amino acids (aa) length, including 16 proteins below 51 aa in the Gram-positive model organism
MeSH term(s)	Open Reading Frames ; Proteogenomics ; Proteome ; Proteomics ; Workflow
Chemical Substances	Proteome
Language	English
Publishing date	2020-09-02
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2078618-9
ISSN	1535-3907 ; 1535-3893
ISSN (online)	1535-3907
ISSN	1535-3893
DOI	10.1021/acs.jproteome.0c00286
Database	MEDical Literature Analysis and Retrieval System OnLINE

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