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  1. Article ; Online: Dissociation of Tissues for Single-Cell Analysis.

    Potter, Andrew S / Steven Potter, S

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

    2019  Volume 1926, Page(s) 55–62

    Abstract: It is now a routine to carry out single-cell RNA-Seq to define the gene expression patterns of thousands of cells, thereby revolutionizing many areas of research. Projects are underway to use these techniques to create an atlas of the expressed genes in ... ...

    Abstract It is now a routine to carry out single-cell RNA-Seq to define the gene expression patterns of thousands of cells, thereby revolutionizing many areas of research. Projects are underway to use these techniques to create an atlas of the expressed genes in all cell types of the human body. Here we describe cold-active protease methods for single-cell dissociation of organs and tissues that better preserve the in vivo gene expression patterns.
    MeSH term(s) Gene Expression Profiling/methods ; Humans ; Sequence Analysis, RNA/methods ; Single-Cell Analysis/methods
    Language English
    Publishing date 2019-02-11
    Publishing country United States
    Document type Journal Article ; Research Support, N.I.H., Extramural
    ISSN 1940-6029
    ISSN (online) 1940-6029
    DOI 10.1007/978-1-4939-9021-4_5
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  2. Article ; Online: SP8 regulates signaling centers during craniofacial development.

    Kasberg, Abigail D / Brunskill, Eric W / Steven Potter, S

    Developmental biology

    2013  Volume 381, Issue 2, Page(s) 312–323

    Abstract: Much of the bone, cartilage and smooth muscle of the vertebrate face is derived from neural crest (NC) cells. During craniofacial development, the anterior neural ridge (ANR) and olfactory pit (OP) signaling centers are responsible for driving the ... ...

    Abstract Much of the bone, cartilage and smooth muscle of the vertebrate face is derived from neural crest (NC) cells. During craniofacial development, the anterior neural ridge (ANR) and olfactory pit (OP) signaling centers are responsible for driving the outgrowth, survival, and differentiation of NC populated facial prominences, primarily via FGF. While much is known about the functional importance of signaling centers, relatively little is understood of how these signaling centers are made and maintained. In this report we describe a dramatic craniofacial malformation in mice mutant for the zinc finger transcription factor gene Sp8. At E14.5 they show facial prominences that are reduced in size and underdeveloped, giving an almost faceless phenotype. At later times they show severe midline defects, excencephaly, hyperterlorism, cleft palate, and a striking loss of many NC and paraxial mesoderm derived cranial bones. Sp8 expression was primarily restricted to the ANR and OP regions during craniofacial development. Analysis of an extensive series of conditional Sp8 mutants confirmed the critical role of Sp8 in signaling centers, and not directly in the NC and paraxial mesoderm cells. The NC cells of the Sp8 mutants showed increased levels of apoptosis and decreased cell proliferation, thereby explaining the reduced sizes of the facial prominences. Perturbed gene expression in the Sp8 mutants was examined by laser capture microdissection coupled with microarrays, as well as in situ hybridization and immunostaining. The most dramatic differences included striking reductions in Fgf8 and Fgf17 expression in the ANR and OP signaling centers. We were also able to achieve genetic and pharmaceutical partial rescue of the Sp8 mutant phenotype by reducing Sonic Hedgehog (SHH) signaling. These results show that Sp8 primarily functions to promote Fgf expression in the ANR and OP signaling centers that drive the survival, proliferation, and differentiation of the NC and paraxial mesoderm that make the face.
    MeSH term(s) Animals ; Apoptosis ; Cartilage/embryology ; Cartilage/metabolism ; Cartilage/pathology ; Cell Proliferation ; Craniofacial Abnormalities/embryology ; Craniofacial Abnormalities/genetics ; DNA-Binding Proteins/genetics ; DNA-Binding Proteins/metabolism ; Embryo, Mammalian/abnormalities ; Embryo, Mammalian/pathology ; Face/abnormalities ; Face/embryology ; Female ; Fibroblast Growth Factor 8/genetics ; Fibroblast Growth Factor 8/metabolism ; Fibroblast Growth Factors/genetics ; Fibroblast Growth Factors/metabolism ; Gene Expression Regulation, Developmental ; Hedgehog Proteins/genetics ; Hedgehog Proteins/metabolism ; Mesoderm/embryology ; Mesoderm/metabolism ; Mesoderm/pathology ; Mice ; Mice, Transgenic ; Mutation ; Neural Crest/embryology ; Neural Crest/metabolism ; Neural Crest/pathology ; Phenotype ; Pregnancy ; Signal Transduction ; Transcription Factors/genetics ; Transcription Factors/metabolism
    Chemical Substances DNA-Binding Proteins ; Fgf17 protein, mouse ; Fgf8 protein, mouse ; Hedgehog Proteins ; Shh protein, mouse ; Sp8 protein, mouse ; Transcription Factors ; Fibroblast Growth Factor 8 (148997-75-5) ; Fibroblast Growth Factors (62031-54-3)
    Language English
    Publishing date 2013-07-18
    Publishing country United States
    Document type Journal Article ; Research Support, N.I.H., Extramural
    ZDB-ID 1114-9
    ISSN 1095-564X ; 0012-1606
    ISSN (online) 1095-564X
    ISSN 0012-1606
    DOI 10.1016/j.ydbio.2013.07.007
    Database MEDical Literature Analysis and Retrieval System OnLINE

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    In stock of ZB MED Cologne/Königswinter

    Zs.B 508: Show issues Location:
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    bis Jg. 2021: Bestellungen von Artikeln über das Online-Bestellformular
    ab Jg. 2022: Lesesaal (EG)

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  3. Article ; Online: Single cell transcriptomic analysis of HPV16-infected epithelium identifies a keratinocyte subpopulation implicated in cancer.

    Bedard, Mary C / Chihanga, Tafadzwa / Carlile, Adrean / Jackson, Robert / Brusadelli, Marion G / Lee, Denis / VonHandorf, Andrew / Rochman, Mark / Dexheimer, Phillip J / Chalmers, Jeffrey / Nuovo, Gerard / Lehn, Maria / Williams, David E J / Kulkarni, Aditi / Carey, Molly / Jackson, Amanda / Billingsley, Caroline / Tang, Alice / Zender, Chad /
    Patil, Yash / Wise-Draper, Trisha M / Herzog, Thomas J / Ferris, Robert L / Kendler, Ady / Aronow, Bruce J / Kofron, Matthew / Rothenberg, Marc E / Weirauch, Matthew T / Van Doorslaer, Koenraad / Wikenheiser-Brokamp, Kathryn A / Lambert, Paul F / Adam, Mike / Steven Potter, S / Wells, Susanne I

    Nature communications

    2023  Volume 14, Issue 1, Page(s) 1975

    Abstract: Persistent HPV16 infection is a major cause of the global cancer burden. The viral life cycle is dependent on the differentiation program of stratified squamous epithelium, but the landscape of keratinocyte subpopulations which support distinct phases of ...

    Abstract Persistent HPV16 infection is a major cause of the global cancer burden. The viral life cycle is dependent on the differentiation program of stratified squamous epithelium, but the landscape of keratinocyte subpopulations which support distinct phases of the viral life cycle has yet to be elucidated. Here, single cell RNA sequencing of HPV16 infected compared to uninfected organoids identifies twelve distinct keratinocyte populations, with a subset mapped to reconstruct their respective 3D geography in stratified squamous epithelium. Instead of conventional terminally differentiated cells, an HPV-reprogrammed keratinocyte subpopulation (HIDDEN cells) forms the surface compartment and requires overexpression of the ELF3/ESE-1 transcription factor. HIDDEN cells are detected throughout stages of human carcinogenesis including primary human cervical intraepithelial neoplasias and HPV positive head and neck cancers, and a possible role in promoting viral carcinogenesis is supported by TCGA analyses. Single cell transcriptome information on HPV-infected versus uninfected epithelium will enable broader studies of the role of individual keratinocyte subpopulations in tumor virus infection and cancer evolution.
    MeSH term(s) Female ; Humans ; Human papillomavirus 16/genetics ; Human papillomavirus 16/metabolism ; Transcriptome ; Papillomavirus Infections ; Epithelium/metabolism ; Keratinocytes/metabolism ; Carcinogenesis/genetics ; Carcinoma, Squamous Cell/genetics ; Oncogene Proteins, Viral/genetics
    Chemical Substances Oncogene Proteins, Viral
    Language English
    Publishing date 2023-04-08
    Publishing country England
    Document type Journal Article ; Research Support, Non-U.S. Gov't ; Research Support, N.I.H., Extramural
    ZDB-ID 2553671-0
    ISSN 2041-1723 ; 2041-1723
    ISSN (online) 2041-1723
    ISSN 2041-1723
    DOI 10.1038/s41467-023-37377-0
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  4. Article: Gene expression in early ischemic renal injury: clues towards pathogenesis, biomarker discovery, and novel therapeutics.

    Devarajan, Prasad / Mishra, Jaya / Supavekin, Suroj / Patterson, Larry T / Steven Potter, S

    Molecular genetics and metabolism

    2003  Volume 80, Issue 4, Page(s) 365–376

    Abstract: Acute renal failure (ARF) represents a common and serious problem in clinical medicine. Renal ischemia-reperfusion injury (IRI) is the major cause of ARF in the native and transplanted kidney. Several decades of research have provided successful ... ...

    Abstract Acute renal failure (ARF) represents a common and serious problem in clinical medicine. Renal ischemia-reperfusion injury (IRI) is the major cause of ARF in the native and transplanted kidney. Several decades of research have provided successful therapeutic approaches in animal models, but translational efforts in humans have yielded disappointing results. The major reasons for this include a lack of early markers for ARF (and hence a delay in initiating therapy), and the multi-factorial nature of the disease. This review focuses on the use of cDNA microarrays to elucidate the molecular genetic mechanisms underlying tubule cell apoptosis, and to identify novel biomarkers for early renal IRI. Also presented is a comparative temporal analysis of cDNA microarray results from mature kidneys following IRI and during normal nephrogenesis. Molecular genetic evidence for the notion that regeneration recapitulates development in the kidney, and that injured tubule cells possess the capacity to de-differentiate to the earliest stages of development, is presented. The implications of these findings to the ability of the kidney to repair itself and potential strategies for accelerating recovery are briefly discussed.
    MeSH term(s) Acute Kidney Injury/genetics ; Acute Kidney Injury/pathology ; Acute Kidney Injury/therapy ; Animals ; Apoptosis/genetics ; Biomarkers ; Gene Expression ; Humans ; Kidney/blood supply ; Kidney/growth & development ; Kidney/physiology ; Kidney Diseases/genetics ; Kidney Diseases/pathology ; Kidney Diseases/therapy ; Regeneration/genetics ; Reperfusion Injury/genetics ; Reperfusion Injury/pathology ; Reperfusion Injury/therapy
    Chemical Substances Biomarkers
    Language English
    Publishing date 2003-11-20
    Publishing country United States
    Document type Journal Article ; Research Support, Non-U.S. Gov't ; Research Support, U.S. Gov't, P.H.S. ; Review
    ZDB-ID 1418518-0
    ISSN 1096-7206 ; 1096-7192
    ISSN (online) 1096-7206
    ISSN 1096-7192
    DOI 10.1016/j.ymgme.2003.09.012
    Database MEDical Literature Analysis and Retrieval System OnLINE

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    In stock of ZB MED Cologne/Königswinter

    Zs.A 617: 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)

    Order via subito

    This service is chargeable due to the Delivery terms set by subito. Orders including an article and supplementary material will be classified as separate orders. In these cases, fees will be demanded for each order.

  5. Article: SP8 regulates signaling centers during craniofacial development

    Kasberg, Abigail D. / Brunskill, Eric W. / Steven Potter, S.

    Developmental biology

    Volume v. 381,, Issue no. 2

    Abstract: Much of the bone, cartilage and smooth muscle of the vertebrate face is derived from neural crest (NC) cells. During craniofacial development, the anterior neural ridge (ANR) and olfactory pit (OP) signaling centers are responsible for driving the ... ...

    Abstract Much of the bone, cartilage and smooth muscle of the vertebrate face is derived from neural crest (NC) cells. During craniofacial development, the anterior neural ridge (ANR) and olfactory pit (OP) signaling centers are responsible for driving the outgrowth, survival, and differentiation of NC populated facial prominences, primarily via FGF. While much is known about the functional importance of signaling centers, relatively little is understood of how these signaling centers are made and maintained. In this report we describe a dramatic craniofacial malformation in mice mutant for the zinc finger transcription factor gene Sp8. At E14.5 they show facial prominences that are reduced in size and underdeveloped, giving an almost faceless phenotype. At later times they show severe midline defects, excencephaly, hyperterlorism, cleft palate, and a striking loss of many NC and paraxial mesoderm derived cranial bones. Sp8 expression was primarily restricted to the ANR and OP regions during craniofacial development. Analysis of an extensive series of conditional Sp8 mutants confirmed the critical role of Sp8 in signaling centers, and not directly in the NC and paraxial mesoderm cells. The NC cells of the Sp8 mutants showed increased levels of apoptosis and decreased cell proliferation, thereby explaining the reduced sizes of the facial prominences. Perturbed gene expression in the Sp8 mutants was examined by laser capture microdissection coupled with microarrays, as well as in situ hybridization and immunostaining. The most dramatic differences included striking reductions in Fgf8 and Fgf17 expression in the ANR and OP signaling centers. We were also able to achieve genetic and pharmaceutical partial rescue of the Sp8 mutant phenotype by reducing Sonic Hedgehog (SHH) signaling. These results show that Sp8 primarily functions to promote Fgf expression in the ANR and OP signaling centers that drive the survival, proliferation, and differentiation of the NC and paraxial mesoderm that make the face.
    Keywords face ; smooth muscle ; cartilage ; cleft palate ; apoptosis ; genes ; in situ hybridization ; transcription factors ; phenotype ; abnormal development ; mutants ; mice ; cell proliferation ; microarray technology ; bones ; neural crest ; gene expression ; zinc finger motif
    Language English
    Document type Article
    ISSN 0012-1606
    Database AGRIS - International Information System for the Agricultural Sciences and Technology

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  6. Article: RNA-Seq defines novel genes, RNA processing patterns and enhancer maps for the early stages of nephrogenesis: Hox supergenes

    Brunskill, Eric W. / Steven Potter, S.

    Developmental biology

    Volume v. 368,, Issue no. 1

    Abstract: During kidney development the cap mesenchyme progenitor cells both self renew and differentiate into nephrons. The balance between renewal and differentiation determines the final nephron count, which is of considerable medical importance. An important ... ...

    Abstract During kidney development the cap mesenchyme progenitor cells both self renew and differentiate into nephrons. The balance between renewal and differentiation determines the final nephron count, which is of considerable medical importance. An important goal is to create a precise genetic definition of the early differentiation of cap mesenchyme progenitors. We used RNA-Seq to transcriptional profile the cap mesenchyme progenitors and their first epithelial derivative, the renal vesicles. The results provide a global view of the changing gene expression program during this key period, defining expression levels for all transcription factors, growth factors, and receptors. The RNA-Seq was performed using two different biochemistries, with one examining only polyadenylated RNA and the other total RNA. This allowed the analysis of noncanonical transcripts, which for many genes were more abundant than standard exonic RNAs. Since a large fraction of enhancers are now known to be transcribed the results also provide global maps of potential enhancers. Further, the RNA-Seq data defined hundreds of novel splice patterns and large numbers of new genes. Particularly striking was the extensive sense/antisense transcription and changing RNA processing complexities of the Hox clusters.
    Keywords messenger RNA ; stem cells ; genes ; nephrons ; transcription factors ; gene expression ; receptors ; transcription (genetics) ; growth factors
    Language English
    Document type Article
    ISSN 0012-1606
    Database AGRIS - International Information System for the Agricultural Sciences and Technology

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