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  1. Book: Development, differentiation, and disease of the luminal gastrointestinal tract

    Kaestner, Klaus H.

    (Progress in molecular biology and translational science ; 96)

    2010  

    Author's details ed. by Klaus H. Kaestner
    Series title Progress in molecular biology and translational science ; 96
    Collection
    Language English
    Size XIV, 277 S. : Ill., graph. Darst.
    Publisher Elsevier AP
    Publishing place Amsterdam u.a.
    Publishing country Netherlands
    Document type Book
    HBZ-ID HT016642515
    ISBN 978-0-12-381280-3 ; 0-12-381280-1
    Database Catalogue ZB MED Medicine, Health

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    In stock of ZB MED Cologne/Königswinter

    Shelf markLoan statusLocation
    Uc I Zs 357 -96- verfügbar in Königswinter Königswinter

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  2. Book: Development, differentiation, and disease of the para-alimentary tract

    Kaestner, Klaus H.

    (Progress in molecular biology and translational science ; 97)

    2010  

    Title variant Development, differentiation, and disease of the para alimentary tract
    Author's details ed. by Klaus H. Kaestner
    Series title Progress in molecular biology and translational science ; 97
    Collection
    Language English
    Size XII, 286 S. : Ill., graph. Darst.
    Publisher Elsevier AP
    Publishing place Amsterdam u.a.
    Publishing country Netherlands
    Document type Book
    HBZ-ID HT016642520
    ISBN 978-0-12-385233-5 ; 0-12-385233-1
    Database Catalogue ZB MED Medicine, Health

    Kategorien

    In stock of ZB MED Cologne/Königswinter

    Shelf markLoan statusLocation
    Uc I Zs 357 -97- verfügbar in Königswinter Königswinter

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  3. Article ; Online: All Good Things Come to an End: 5 Years at the Helm of CMGH.

    Kaestner, Klaus H / Pack, Michael

    Cellular and molecular gastroenterology and hepatology

    2024  

    Language English
    Publishing date 2024-04-15
    Publishing country United States
    Document type Editorial
    ZDB-ID 2819778-1
    ISSN 2352-345X ; 2352-345X
    ISSN (online) 2352-345X
    ISSN 2352-345X
    DOI 10.1016/j.jcmgh.2024.03.015
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  4. Article ; Online: The Role of Non-Coding RNAs in Liver Disease, Injury, and Regeneration.

    Rowe, Melissa M / Kaestner, Klaus H

    Cells

    2023  Volume 12, Issue 3

    Abstract: Non-coding RNAs (ncRNAs) have diverse functions in health and pathology in many tissues, including the liver. This review highlights important microRNAs (miRs), long non-coding RNAs (lncRNAs), and circular RNAs (circRNAs) in liver disease and ... ...

    Abstract Non-coding RNAs (ncRNAs) have diverse functions in health and pathology in many tissues, including the liver. This review highlights important microRNAs (miRs), long non-coding RNAs (lncRNAs), and circular RNAs (circRNAs) in liver disease and regeneration. Greater attention is given to more prevalent and well characterized RNAs, including: miR-122, miR-21, the let-7 family of miRs, miR-451a, miR-144, and MALAT1.
    MeSH term(s) Humans ; MicroRNAs/genetics ; RNA, Long Noncoding/genetics ; Liver Diseases/genetics ; RNA, Circular/genetics
    Chemical Substances MicroRNAs ; RNA, Long Noncoding ; RNA, Circular
    Language English
    Publishing date 2023-01-18
    Publishing country Switzerland
    Document type Journal Article ; Review ; Research Support, N.I.H., Extramural
    ZDB-ID 2661518-6
    ISSN 2073-4409 ; 2073-4409
    ISSN (online) 2073-4409
    ISSN 2073-4409
    DOI 10.3390/cells12030359
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  5. Article ; Online: Mammalian Intestinal Development and Differentiation-The State of the Art.

    Kolev, Hannah M / Kaestner, Klaus H

    Cellular and molecular gastroenterology and hepatology

    2023  Volume 16, Issue 5, Page(s) 809–821

    Abstract: The development of the mammalian intestine, from its earliest origins as a morphologically uniform sheet of endoderm cells during gastrulation into the complex organ system that is essential for the life of the organism, is a truly fascinating process. ... ...

    Abstract The development of the mammalian intestine, from its earliest origins as a morphologically uniform sheet of endoderm cells during gastrulation into the complex organ system that is essential for the life of the organism, is a truly fascinating process. During midgestation development, reciprocal interactions between endoderm-derived epithelium and mesoderm-derived mesenchyme enable villification, or the conversion of a radially symmetric pseudostratified epithelium into the functional subdivision of crypts and villi. Once a mature crypt-villus axis is established, proliferation and differentiation of new epithelial cells continue throughout life. Spatially localized signals including the wingless and Int-1, fibroblast growth factor, and Hippo systems, among others, ensure that new cells are being born continuously in the crypt. As cells exit the crypt compartment, a gradient of bone morphogenetic protein signaling limits proliferation to allow for the specification of multiple mature cell types. The first major differentiation decision is dependent on Notch signaling, which specifies epithelial cells into absorptive and secretory lineages. The secretory lineage is subdivided further into Paneth, goblet, tuft, and enteroendocrine cells via a complex network of transcription factors. Although some of the signaling molecules are produced by epithelial cells, critical components are derived from specialized crypt-adjacent mesenchymal cells termed telocytes, which are marked by Forkhead box l1, GLI Family Zinc Finger 1, and platelet-derived growth factor receptor α. The crucial nature of these processes is evidenced by the multitude of intestinal disorders such as colorectal cancer, short-bowel syndrome, and inflammatory bowel disease, which all reflect perturbations of the development and/or differentiation of the intestine.
    MeSH term(s) Animals ; Cell Differentiation ; Intestines ; Intestinal Mucosa/metabolism ; Enteroendocrine Cells ; Epithelial Cells ; Mammals
    Language English
    Publishing date 2023-07-26
    Publishing country United States
    Document type Journal Article ; Review ; Research Support, N.I.H., Extramural
    ZDB-ID 2819778-1
    ISSN 2352-345X ; 2352-345X
    ISSN (online) 2352-345X
    ISSN 2352-345X
    DOI 10.1016/j.jcmgh.2023.07.011
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  6. Article ; Online: The Intestinal Stem Cell Niche: A Central Role for Foxl1-Expressing Subepithelial Telocytes.

    Kaestner, Klaus H

    Cellular and molecular gastroenterology and hepatology

    2019  Volume 8, Issue 1, Page(s) 111–117

    Abstract: The columnar epithelium of the alimentary tract, extending from stomach to colon, is constantly renewed by proliferation of stem and progenitor cells, which give rise to the various differentiated cell types as required by the regional specification of ... ...

    Abstract The columnar epithelium of the alimentary tract, extending from stomach to colon, is constantly renewed by proliferation of stem and progenitor cells, which give rise to the various differentiated cell types as required by the regional specification of the gut tube. Proliferation occurs in specific zones, which in the intestine form crypts that reach into the underlying stroma. Cellular replication in the crypt is supported by an intestinal stem cell niche, the identity of which has long been controversial. Multiple recent studies have identified subepithelial telocytes, marked by expression of the winged helix transcription factor Foxl1 and the hedgehog signaling mediator Gli1, as the critical source of pro-proliferative Wnt signals to the stem/progenitor cell compartment. This review attempts to summarize and integrate these findings.
    MeSH term(s) Animals ; Cell Differentiation ; Cell Proliferation ; Forkhead Transcription Factors/metabolism ; Gene Expression Regulation ; Hedgehog Proteins ; Humans ; Intestinal Mucosa/cytology ; Intestinal Mucosa/metabolism ; Stem Cell Niche ; Stem Cells/cytology ; Stem Cells/metabolism ; Telocytes/cytology ; Telocytes/metabolism ; Wnt Signaling Pathway ; Zinc Finger Protein GLI1/metabolism
    Chemical Substances Forkhead Transcription Factors ; Hedgehog Proteins ; Zinc Finger Protein GLI1
    Language English
    Publishing date 2019-04-06
    Publishing country United States
    Document type Journal Article ; Research Support, N.I.H., Extramural ; Review
    ISSN 2352-345X
    ISSN (online) 2352-345X
    DOI 10.1016/j.jcmgh.2019.04.001
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  7. Article ; Online: Tracking Dysbiosis Where It Matters.

    Kaestner, Klaus H

    Cellular and molecular gastroenterology and hepatology

    2019  Volume 9, Issue 3, Page(s) 547–548

    MeSH term(s) Dysbiosis ; Humans ; Immunity, Innate ; Inflammatory Bowel Diseases ; Mucous Membrane ; Phagocytes
    Language English
    Publishing date 2019-12-19
    Publishing country United States
    Document type Editorial ; Comment
    ISSN 2352-345X
    ISSN (online) 2352-345X
    DOI 10.1016/j.jcmgh.2019.11.015
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  8. Article: Villification of the intestinal epithelium is driven by Foxl1.

    Zhu, Guoli / Lahori, Deeksha / Schug, Jonathan / Kaestner, Klaus H

    bioRxiv : the preprint server for biology

    2024  

    Abstract: The primitive gut tube of mammals initially forms as a simple cylinder consisting of the endoderm-derived, pseudostratified epithelium and the mesoderm-derived surrounding mesenchyme. During mid-gestation a dramatic transformation occurs in which the ... ...

    Abstract The primitive gut tube of mammals initially forms as a simple cylinder consisting of the endoderm-derived, pseudostratified epithelium and the mesoderm-derived surrounding mesenchyme. During mid-gestation a dramatic transformation occurs in which the epithelium is both restructured into its final cuboidal form and simultaneously folded and refolded to create intestinal villi and intervillus regions, the incipient crypts. Here we show that the mesenchymal winged helix transcription factor Foxl1, itself induced by epithelial hedgehog signaling, controls villification by activating BMP and PDGFRα as well as planar cell polarity genes in epithelial-adjacent telocyte progenitors, both directly and in a feed-forward loop with Foxo3.
    Language English
    Publishing date 2024-02-28
    Publishing country United States
    Document type Preprint
    DOI 10.1101/2024.02.27.582300
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  9. Article ; Online: Benchmarking algorithms for joint integration of unpaired and paired single-cell RNA-seq and ATAC-seq data.

    Lee, Michelle Y Y / Kaestner, Klaus H / Li, Mingyao

    Genome biology

    2023  Volume 24, Issue 1, Page(s) 244

    Abstract: Background: Single-cell RNA-sequencing (scRNA-seq) measures gene expression in single cells, while single-nucleus ATAC-sequencing (snATAC-seq) quantifies chromatin accessibility in single nuclei. These two data types provide complementary information ... ...

    Abstract Background: Single-cell RNA-sequencing (scRNA-seq) measures gene expression in single cells, while single-nucleus ATAC-sequencing (snATAC-seq) quantifies chromatin accessibility in single nuclei. These two data types provide complementary information for deciphering cell types and states. However, when analyzed individually, they sometimes produce conflicting results regarding cell type/state assignment. The power is compromised since the two modalities reflect the same underlying biology. Recently, it has become possible to measure both gene expression and chromatin accessibility from the same nucleus. Such paired data enable the direct modeling of the relationships between the two modalities. Given the availability of the vast amount of single-modality data, it is desirable to integrate the paired and unpaired single-modality datasets to gain a comprehensive view of the cellular complexity.
    Results: We benchmark nine existing single-cell multi-omic data integration methods. Specifically, we evaluate to what extent the multiome data provide additional guidance for analyzing the existing single-modality data, and whether these methods uncover peak-gene associations from single-modality data. Our results indicate that multiome data are helpful for annotating single-modality data. However, we emphasize that the availability of an adequate number of nuclei in the multiome dataset is crucial for achieving accurate cell type annotation. Insufficient representation of nuclei may compromise the reliability of the annotations. Additionally, when generating a multiome dataset, the number of cells is more important than sequencing depth for cell type annotation.
    Conclusions: Seurat v4 is the best currently available platform for integrating scRNA-seq, snATAC-seq, and multiome data even in the presence of complex batch effects.
    MeSH term(s) Chromatin Immunoprecipitation Sequencing/methods ; Benchmarking ; Reproducibility of Results ; Single-Cell Gene Expression Analysis ; Algorithms ; Chromatin/genetics ; Single-Cell Analysis/methods ; Sequence Analysis, RNA
    Chemical Substances Chromatin
    Language English
    Publishing date 2023-10-24
    Publishing country England
    Document type Journal Article ; Research Support, N.I.H., Extramural
    ZDB-ID 2040529-7
    ISSN 1474-760X ; 1474-760X
    ISSN (online) 1474-760X
    ISSN 1474-760X
    DOI 10.1186/s13059-023-03073-x
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  10. Article: Benchmarking algorithms for joint integration of unpaired and paired single-cell RNA-seq and ATAC-seq data.

    Lee, Michelle Y Y / Kaestner, Klaus H / Li, Mingyao

    bioRxiv : the preprint server for biology

    2023  

    Abstract: Single-cell RNA-sequencing (scRNA-seq) measures gene expression in single cells, while single-nucleus ATAC-sequencing (snATAC-seq) enables the quantification of chromatin accessibility in single nuclei. These two data types provide complementary ... ...

    Abstract Single-cell RNA-sequencing (scRNA-seq) measures gene expression in single cells, while single-nucleus ATAC-sequencing (snATAC-seq) enables the quantification of chromatin accessibility in single nuclei. These two data types provide complementary information for deciphering cell types/states. However, when analyzed individually, scRNA-seq and snATAC-seq data often produce conflicting results regarding cell type/state assignment. In addition, there is a loss of power as the two modalities reflect the same underlying cell types/states. Recently, it has become possible to measure both gene expression and chromatin accessibility from the same nucleus. Such paired data make it possible to directly model the relationships between the two modalities. However, given the availability of the vast amount of single-modality data, it is desirable to integrate the paired and unpaired single-modality data to gain a comprehensive view of the cellular complexity. Here, we benchmarked the performance of seven existing single-cell multi-omic data integration methods. Specifically, we evaluated whether these methods are able to uncover peak-gene associations from single-modality data, and to what extent the multiome data can provide additional guidance for the analysis of the existing single-modality data. Our results indicate that multiome data are helpful for annotating single-modality data, but the number of cells in the multiome data is critical to ensure a good cell type annotation. Additionally, when generating a multiome dataset, the number of cells is more important than sequencing depth for cell type annotation. Lastly, Seurat v4 is the best at integrating scRNA-seq, snATAC-seq, and multiome data even in the presence of complex batch effects.
    Language English
    Publishing date 2023-02-03
    Publishing country United States
    Document type Preprint
    DOI 10.1101/2023.02.01.526609
    Database MEDical Literature Analysis and Retrieval System OnLINE

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