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  1. Article: ESSAY. Wie unpolitisch ist Wissenschaft

    Wyler, Emanuel

    Laborjournal

    2021  Volume 28, Issue 7/8, Page(s) 16

    Language German
    Document type Article
    ZDB-ID 1237282-1
    ISSN 1612-8354
    Database Current Contents Medicine

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    In stock of ZB MED Cologne/Königswinter

    Zs.A 4842: Show issues Location:
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    bis Jg. 1994: Bestellungen von Artikeln über das Online-Bestellformular
    Jg. 1995 - 2021: Lesesall (2.OG)
    ab Jg. 2022: Lesesaal (EG)

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  2. Book ; Online: Bulk and single-cell gene expression profiling of SARS-CoV-2 infected human cell lines identifies molecular targets for therapeutic intervention

    Wyler Emanuel, Franke Vedran

    2020  

    Abstract: Single cell RNA seq datasets used for analysis in the Bulk and single-cell gene expression profiling of SARS-CoV-2 infected human cell lines identifies molecular targets for therapeutic ... ...

    Abstract Single cell RNA seq datasets used for analysis in the Bulk and single-cell gene expression profiling of SARS-CoV-2 infected human cell lines identifies molecular targets for therapeutic intervention
    Keywords SARS-CoV ; SARS-CoV2 ; Single Cell Sequencing ; dropseq ; virus ; covid19
    Publishing date 2020-09-15
    Publishing country eu
    Document type Book ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

    Full text online

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  3. Article: Krankheitserreger mit Abwasser beobachten. Abwassermonitoring als zukünftiger Beitrag zur Prävention von Infektionskrankheiten

    Wyler, Emanuel / Landthaler, Markus

    KU-Gesundheitsmanagement

    2023  Volume 92, Issue 10, Page(s) 61

    Language German
    Document type Article
    ZDB-ID 2420760-3
    ISSN 1867-9269
    Database Current Contents Medicine

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    Un I Zs.336/1: Show issues Location:
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  4. Article ; Online: Grainyhead-like 2 Deficiency and Kidney Cyst Growth in a Mouse Model.

    Yurtdas, Zeliha Yesim / Kilic, Ergin / Boor, Peter / Wyler, Emanuel / Landthaler, Markus / Jung, Klaus / Schmidt-Ott, Kai M

    Journal of the American Society of Nephrology : JASN

    2024  

    Abstract: Background: The transcription factor Grainyhead-like 2 (GRHL2) plays a crucial role in maintaining the epithelial barrier properties of the renal collecting duct and is essential for osmoregulation. We noticed a reduction in GRHL2 expression in cysts ... ...

    Abstract Background: The transcription factor Grainyhead-like 2 (GRHL2) plays a crucial role in maintaining the epithelial barrier properties of the renal collecting duct and is essential for osmoregulation. We noticed a reduction in GRHL2 expression in cysts derived from the collecting ducts in kidneys affected by Autosomal Dominant Polycystic Kidney Disease (ADPKD). However, the specific role of GRHL2 in cystic kidney disease remains unknown.
    Methods: The functional role of the transcription factor Grhl2 in the context of cystic kidney disease was examined through analysis of its expression pattern in patient samples with ADPKD and generating a transgenic cystic kidney disease (TCKD) mouse model by overexpressing the human proto-oncogene c-MYC in kidney collecting ducts. Next, TCKD mice bred with collecting duct-specific Grhl2 knockout mice (Grhl2KO). The resulting TCKD-Grhl2KO mice and their littermates were examined by various types of histological and biochemical assays and gene profiling analysis via RNA-seq.
    Results: A comprehensive examination of kidney samples from patients with ADPKD revealed GRHL2 downregulation in collecting duct-derived cyst epithelia. Comparative analysis of TCKD and TCKD-Grhl2KO mice exhibited that the collecting duct-specific deletion of Grhl2 resulted in markedly aggravated cyst growth, worsened kidney dysfunction, and shortened life span. Furthermore, transcriptomic analyses indicated sequential downregulation of kidney epithelial cyst development regulators (Frem2, Muc1, Cdkn2c, Pkd2, and Tsc1) during cyst progression in kidneys of TCKD-Grhl2KO mice which included presumed direct Grhl2 target genes.
    Conclusions: These results suggest GRHL2 as a potential progression modifier, especially for cysts originating from collecting ducts.
    Language English
    Publishing date 2024-04-24
    Publishing country United States
    Document type Journal Article
    ZDB-ID 1085942-1
    ISSN 1533-3450 ; 1046-6673
    ISSN (online) 1533-3450
    ISSN 1046-6673
    DOI 10.1681/ASN.0000000000000353
    Database MEDical Literature Analysis and Retrieval System OnLINE

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    In stock of ZB MED Cologne/Königswinter

    Zs.A 3344: Show issues Location:
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    Jg. 1995 - 2021: Lesesall (2.OG)
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  5. Article: In Vitro Kinase-to-Phosphosite Database (iKiP-DB) Predicts Kinase Activity in Phosphoproteomic Datasets

    Mari, Tommaso / Mösbauer, Kirstin / Wyler, Emanuel / Landthaler, Markus / Drosten, Christian / Selbach, Matthias

    Journal of proteome research. 2022 May 24, v. 21, no. 6

    2022  

    Abstract: Phosphoproteomics routinely quantifies changes in the levels of thousands of phosphorylation sites, but functional analysis of such data remains a major challenge. While databases like PhosphoSitePlus contain information about many phosphorylation sites, ...

    Abstract Phosphoproteomics routinely quantifies changes in the levels of thousands of phosphorylation sites, but functional analysis of such data remains a major challenge. While databases like PhosphoSitePlus contain information about many phosphorylation sites, the vast majority of known sites is not assigned to any protein kinase. Assigning changes in the phosphoproteome to the activity of individual kinases therefore remains a key challenge. A recent large-scale study systematically identified in vitro substrates for most human protein kinases. Here, we reprocessed and filtered these data to generate an in vitro Kinase-to-Phosphosite database (iKiP-DB). We show that iKiP-DB can accurately predict changes in kinase activity in published phosphoproteomic data sets for both well-studied and poorly characterized kinases. We apply iKiP-DB to a newly generated phosphoproteomic analysis of SARS-CoV-2 infected human lung epithelial cells and provide evidence for coronavirus-induced changes in host cell kinase activity. In summary, we show that iKiP-DB is widely applicable to facilitate the functional analysis of phosphoproteomic data sets.
    Keywords Severe acute respiratory syndrome coronavirus 2 ; data collection ; databases ; epithelium ; humans ; lungs ; phosphoproteome ; phosphorylation ; protein kinases ; proteomics ; research
    Language English
    Dates of publication 2022-0524
    Size p. 1575-1587.
    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.2c00198
    Database NAL-Catalogue (AGRICOLA)

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    Zs.A 6189: Show issues Location:
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  6. Article ; Online: In Vitro Kinase-to-Phosphosite Database (iKiP-DB) Predicts Kinase Activity in Phosphoproteomic Datasets.

    Mari, Tommaso / Mösbauer, Kirstin / Wyler, Emanuel / Landthaler, Markus / Drosten, Christian / Selbach, Matthias

    Journal of proteome research

    2022  Volume 21, Issue 6, Page(s) 1575–1587

    Abstract: Phosphoproteomics routinely quantifies changes in the levels of thousands of phosphorylation sites, but functional analysis of such data remains a major challenge. While databases like PhosphoSitePlus contain information about many phosphorylation sites, ...

    Abstract Phosphoproteomics routinely quantifies changes in the levels of thousands of phosphorylation sites, but functional analysis of such data remains a major challenge. While databases like PhosphoSitePlus contain information about many phosphorylation sites, the vast majority of known sites is not assigned to any protein kinase. Assigning changes in the phosphoproteome to the activity of individual kinases therefore remains a key challenge. A recent large-scale study systematically identified in vitro substrates for most human protein kinases. Here, we reprocessed and filtered these data to generate an
    MeSH term(s) COVID-19 ; Humans ; Phosphoproteins/metabolism ; Phosphorylation ; Protein Kinases/genetics ; Protein Kinases/metabolism ; SARS-CoV-2
    Chemical Substances Phosphoproteins ; Protein Kinases (EC 2.7.-)
    Language English
    Publishing date 2022-05-24
    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.2c00198
    Database MEDical Literature Analysis and Retrieval System OnLINE

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    In stock of ZB MED Cologne/Königswinter

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  7. Article ; Online: Global analysis of contact-dependent human-to-mouse intercellular mRNA and lncRNA transfer in cell culture.

    Dasgupta, Sandipan / Dayagi, Daniella Y / Haimovich, Gal / Wyler, Emanuel / Olender, Tsviya / Singer, Robert H / Landthaler, Markus / Gerst, Jeffrey E

    eLife

    2023  Volume 12

    Abstract: Full-length mRNAs transfer between adjacent mammalian cells via direct cell-to-cell connections called tunneling nanotubes (TNTs). However, the extent of mRNA transfer at the transcriptome-wide level (the 'transferome') is unknown. Here, we analyzed the ... ...

    Abstract Full-length mRNAs transfer between adjacent mammalian cells via direct cell-to-cell connections called tunneling nanotubes (TNTs). However, the extent of mRNA transfer at the transcriptome-wide level (the 'transferome') is unknown. Here, we analyzed the transferome in an in vitro human-mouse cell co-culture model using RNA-sequencing. We found that mRNA transfer is non-selective, prevalent across the human transcriptome, and that the amount of transfer to mouse embryonic fibroblasts (MEFs) strongly correlates with the endogenous level of gene expression in donor human breast cancer cells. Typically,<1% of endogenous mRNAs undergo transfer. Non-selective, expression-dependent RNA transfer was further validated using synthetic reporters. RNA transfer appears contact-dependent via TNTs, as exemplified for several mRNAs. Notably, significant differential changes in the native MEF transcriptome were observed in response to co-culture, including the upregulation of multiple cancer and cancer-associated fibroblast-related genes and pathways. Together, these results lead us to suggest that TNT-mediated RNA transfer could be a phenomenon of physiological importance under both normal and pathogenic conditions.
    MeSH term(s) Humans ; Mice ; Animals ; RNA, Long Noncoding/genetics ; RNA, Messenger/genetics ; Fibroblasts ; Nanotubes ; Cell Culture Techniques ; Cell Communication/physiology ; Mammals
    Chemical Substances Tunneling Nanotubes ; RNA, Long Noncoding ; RNA, Messenger
    Language English
    Publishing date 2023-05-30
    Publishing country England
    Document type Journal Article
    ZDB-ID 2687154-3
    ISSN 2050-084X ; 2050-084X
    ISSN (online) 2050-084X
    ISSN 2050-084X
    DOI 10.7554/eLife.83584
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  8. Article ; Online: The Interactive Complex between Cytomegalovirus Kinase vCDK/pUL97 and Host Factors CDK7-Cyclin H Determines Individual Patterns of Transcription in Infected Cells.

    Schütz, Martin / Cordsmeier, Arne / Wangen, Christina / Horn, Anselm H C / Wyler, Emanuel / Ensser, Armin / Sticht, Heinrich / Marschall, Manfred

    International journal of molecular sciences

    2023  Volume 24, Issue 24

    Abstract: The infection of human cytomegalovirus (HCMV) is strongly determined by the host-cell interaction in a way that the efficiency of HCMV lytic replication is dependent on the regulatory interplay between viral and cellular proteins. In particular, the ... ...

    Abstract The infection of human cytomegalovirus (HCMV) is strongly determined by the host-cell interaction in a way that the efficiency of HCMV lytic replication is dependent on the regulatory interplay between viral and cellular proteins. In particular, the activities of protein kinases, such as cyclin-dependent kinases (CDKs) and the viral CDK ortholog (vCDK/pUL97), play an important role in both viral reproduction and virus-host interaction. Very recently, we reported on the complexes formed between vCDK/pUL97, human cyclin H, and CDK7. Major hallmarks of this interplay are the interaction between cyclin H and vCDK/pUL97, which is consistently detectable across various conditions and host cell types of infection, the decrease or increase in pUL97 kinase activity resulting from cyclin H knock-down or elevated levels, respectively, and significant trans-stimulation of human CDK7 activity by pUL97 in vitro. Due to the fact that even a ternary complex of vCDK/pUL97-cyclin H-CDK7 can be detected by coimmunoprecipitation and visualized by bioinformatic structural modeling, we postulated a putative impact of the respective kinase activities on the patterns of transcription in HCMV-infected cells. Here, we undertook a first vCDK/pUL97-specific transcriptomic analysis, which combined conditions of fully lytic HCMV replication with those under specific vCDK/pUL97 or CDK7 drug-mediated inhibition or transient cyclin H knockout. The novel results were further strengthened using bioinformatic modeling of the involved multi-protein complexes. Our data underline the importance of these kinase activities for the C-terminal domain (CTD) phosphorylation-driven activation of host RNA polymerase in HCMV-infected cells. The impact of the individual experimental conditions on differentially expressed gene profiles is described in detail and discussed.
    MeSH term(s) Humans ; Cyclins/metabolism ; Cytomegalovirus/genetics ; Cyclin H/metabolism ; Cyclin-Dependent Kinases/genetics ; Cyclin-Dependent Kinases/metabolism ; Phosphorylation ; Herpesviridae Infections
    Chemical Substances Cyclins ; Cyclin H ; Cyclin-Dependent Kinases (EC 2.7.11.22)
    Language English
    Publishing date 2023-12-13
    Publishing country Switzerland
    Document type Journal Article
    ZDB-ID 2019364-6
    ISSN 1422-0067 ; 1422-0067 ; 1661-6596
    ISSN (online) 1422-0067
    ISSN 1422-0067 ; 1661-6596
    DOI 10.3390/ijms242417421
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  9. Book ; Online ; Thesis: Tandem affinity purification combined with inducible shRNA expression as a tool to study the maturation of macromolecular assemblies

    Wyler, Emanuel

    2010  

    Author's details by Emanuel Wyler
    Language English
    Size Online-Ressource (120 S), Ill
    Publisher ETH
    Publishing place Zürich
    Document type Book ; Online ; Thesis
    Thesis / German Habilitation thesis Diss., Eidgenössische Technische Hochschule ETH Zürich, Nr. 19129--Zürich, 1912
    Database Former special subject collection: coastal and deep sea fishing

    Full text online

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  10. Article ; Online: Protocol to dissociate healthy and infected murine- and hamster-derived lung tissue for single-cell transcriptome analysis.

    Pennitz, Peter / Goekeri, Cengiz / Trimpert, Jakob / Wyler, Emanuel / Ebenig, Aileen / Weissfuss, Chantal / Mühlebach, Michael D / Witzenrath, Martin / Nouailles, Geraldine

    STAR protocols

    2022  Volume 4, Issue 1, Page(s) 101957

    Abstract: In infectious disease research, single-cell RNA sequencing allows dissection of host-pathogen interactions. As a prerequisite, we provide a protocol to transform solid and complex organs such as lungs into representative diverse, viable single-cell ... ...

    Abstract In infectious disease research, single-cell RNA sequencing allows dissection of host-pathogen interactions. As a prerequisite, we provide a protocol to transform solid and complex organs such as lungs into representative diverse, viable single-cell suspensions. Our protocol describes performance of vascular perfusion, pneumonectomy, enzymatic digestion, and mechanical dissociation of lung tissue, as well as red blood cell lysis and counting of isolated cells. A challenge remains, however, to further increase the proportion of pulmonary endothelial cells without compromising on viability. For complete details on the use and execution of this protocol, please refer to Nouailles et al. (2021),
    MeSH term(s) Cricetinae ; Animals ; Mice ; Endothelial Cells ; Single-Cell Gene Expression Analysis ; Cell Death ; Dissection ; Lung
    Language English
    Publishing date 2022-12-20
    Publishing country United States
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ISSN 2666-1667
    ISSN (online) 2666-1667
    DOI 10.1016/j.xpro.2022.101957
    Database MEDical Literature Analysis and Retrieval System OnLINE

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