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  1. Book ; Online ; Thesis: DNA methylierungsbasierte Verbesserung der Klassifikation sinunasaler Tumore

    Glöß, Stefanie [Verfasser]

    2024  

    Author's details Stefanie Glöß
    Keywords Medizin, Gesundheit ; Medicine, Health
    Subject code sg610
    Language German
    Publisher Medizinische Fakultät Charité - Universitätsmedizin Berlin
    Publishing place Berlin
    Document type Book ; Online ; Thesis
    Database Digital theses on the web

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  2. Book ; Online ; Thesis: Detektion und Charakterisierung Polyphosphatspeichernder Bakterien in Gewässersedimenten = Detection and characterization of polyphosphate accumulating bacteria in lake sediments

    Glöß, Stefanie [Verfasser]

    2010  

    Author's details von Stefanie Glöß
    Keywords Geowissenschaften ; Earth Sciences
    Subject code sg550
    Language German
    Document type Book ; Online ; Thesis
    Database Digital theses on the web

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  3. Book ; Thesis: Detektion und Charakterisierung Polyphosphatspeichernder Bakterien in Gewässersedimenten

    Glöß, Stefanie / Grossart, Hans-Peter / Simon, Meinhard

    Detection and characterization of polyphosphate accumulating bacteria in lake sediments

    2010  

    Abstract: Das Vorkommen von Polyphosphat (Poly-P) in den obersten Sedimentschichten verschiedener Gewässer wurde untersucht. Parallel erfolgte eine molekularbiologische Charakterisierung der Bakteriengemeinschaften auf unterschiedlichem phylogenetischem Niveau ... ...

    Author's details von Stefanie Glöß
    Abstract Das Vorkommen von Polyphosphat (Poly-P) in den obersten Sedimentschichten verschiedener Gewässer wurde untersucht. Parallel erfolgte eine molekularbiologische Charakterisierung der Bakteriengemeinschaften auf unterschiedlichem phylogenetischem Niveau durch 16S rDNA Klonbibliotheken, DGGE und CARD-FISH. Ergänzende Untersuchungen wurden mittels Inkubationsexperimenten durchgeführt. Es zeigte sich in allen Proben eine große Diversität, in keinem Fall koinzidierte jedoch ein gehäuftes Vorkommen einer bestimmten Großgruppe mit einem hohen Poly-P Gehalt. Da die bisher eingesetzten Methoden zur Charakterisierung der Bakteriengemeinschaft in Hinblick auf Poly-P speichernden Bakterien (PAO) nicht den erhofften Erfolg brachten, wurde in der vorliegenden Arbeit die Laser-Mikrodissektion für Umweltproben etabliert. Bakterien mit Poly-P Granula wurden gezielt aus Sediment- und Belebtschlammproben separiert und phylogenetisch charakterisiert. Erste Ergebnisse zeigen eine hohe Diversität von bekannten aber auch bisher unbekannten Poly-P speichernden Bakterien in den untersuchten Proben. <dt.>

    This thesis investigated the occurrence of polyphosphate (poly-P) in different lake sediments in combination with a molecular characterization of the bacterial communitiy structure on different phylogenetic levels applying 16S rRNA gene clone libraries, DGGE and CARD-FISH. The inducibility of poly-P synthesis in the uppermost sediment layers and stimulation of growth of Poly-P accumulating bacteria (PAO) were studied in laboratory experiments. A high bacterial diversity was found in all studied samples but no significant correlations occurred between poly-P contents and the presence of specific microbial groups. Since analysis of microbial communities using 16S rRNA gene sequencing and FISH did not reveal PAO in the poly-P rich lake sediments a laser microdissection method has been established for the separation of poly-P positive bacterial cells (visualized by DAPI staining under a fluorescence microscope) from lake sediment and activated sludge samples. Coupled with a phylogenetic characterization of the selected bacteria a high diversity of known and unknown PAO were identified across all samples. <engl.>
    Language German
    Size XII, 109, [55] Bl., Ill., graph. Darst.
    Document type Book ; Thesis
    Thesis / German Habilitation thesis Univ., Diss.--Oldenburg, 2010
    Note Enth. auch 3 ZS-Artikel
    Database Library catalogue of the German National Library of Science and Technology (TIB), Hannover

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  4. Book ; Online ; Thesis: Detektion und Charakterisierung Polyphosphatspeichernder Bakterien in Gewässersedimenten

    Glöß, Stefanie / Grossart, Hans-Peter / Simon, Meinhard

    Detection and characterization of polyphosphate accumulating bacteria in lake sediments

    2010  

    Abstract: Das Vorkommen von Polyphosphat (Poly-P) in den obersten Sedimentschichten verschiedener Gewässer wurde untersucht. Parallel erfolgte eine molekularbiologische Charakterisierung der Bakteriengemeinschaften auf unterschiedlichem phylogenetischem Niveau ... ...

    Author's details Stefanie Glöß
    Abstract Das Vorkommen von Polyphosphat (Poly-P) in den obersten Sedimentschichten verschiedener Gewässer wurde untersucht. Parallel erfolgte eine molekularbiologische Charakterisierung der Bakteriengemeinschaften auf unterschiedlichem phylogenetischem Niveau durch 16S rDNA Klonbibliotheken, DGGE und CARD-FISH. Ergänzende Untersuchungen wurden mittels Inkubationsexperimenten durchgeführt. Es zeigte sich in allen Proben eine große Diversität, in keinem Fall koinzidierte jedoch ein gehäuftes Vorkommen einer bestimmten Großgruppe mit einem hohen Poly-P Gehalt. Da die bisher eingesetzten Methoden zur Charakterisierung der Bakteriengemeinschaft in Hinblick auf Poly-P speichernden Bakterien (PAO) nicht den erhofften Erfolg brachten, wurde in der vorliegenden Arbeit die Laser-Mikrodissektion für Umweltproben etabliert. Bakterien mit Poly-P Granula wurden gezielt aus Sediment- und Belebtschlammproben separiert und phylogenetisch charakterisiert. Erste Ergebnisse zeigen eine hohe Diversität von bekannten aber auch bisher unbekannten Poly-P speichernden Bakterien in den untersuchten Proben. <dt.>
    Language German
    Size Online-Ressource (PDF-Datei: XII, 109, [55] S., 3,9 MB)
    Document type Book ; Online ; Thesis
    Thesis / German Habilitation thesis Univ., Diss.--Oldenburg, 2010
    Database Former special subject collection: coastal and deep sea fishing

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  5. Book ; Online ; Thesis: Detektion und Charakterisierung Polyphosphatspeichernder Bakterien in Gewässersedimenten

    Glöß, Stefanie / Grossart, Hans-Peter / Simon, Meinhard

    Detection and characterization of polyphosphate accumulating bacteria in lake sediments

    2010  

    Abstract: Das Vorkommen von Polyphosphat (Poly-P) in den obersten Sedimentschichten verschiedener Gewässer wurde untersucht. Parallel erfolgte eine molekularbiologische Charakterisierung der Bakteriengemeinschaften auf unterschiedlichem phylogenetischem Niveau ... ...

    Author's details Stefanie Glöß
    Abstract Das Vorkommen von Polyphosphat (Poly-P) in den obersten Sedimentschichten verschiedener Gewässer wurde untersucht. Parallel erfolgte eine molekularbiologische Charakterisierung der Bakteriengemeinschaften auf unterschiedlichem phylogenetischem Niveau durch 16S rDNA Klonbibliotheken, DGGE und CARD-FISH. Ergänzende Untersuchungen wurden mittels Inkubationsexperimenten durchgeführt. Es zeigte sich in allen Proben eine große Diversität, in keinem Fall koinzidierte jedoch ein gehäuftes Vorkommen einer bestimmten Großgruppe mit einem hohen Poly-P Gehalt. Da die bisher eingesetzten Methoden zur Charakterisierung der Bakteriengemeinschaft in Hinblick auf Poly-P speichernden Bakterien (PAO) nicht den erhofften Erfolg brachten, wurde in der vorliegenden Arbeit die Laser-Mikrodissektion für Umweltproben etabliert. Bakterien mit Poly-P Granula wurden gezielt aus Sediment- und Belebtschlammproben separiert und phylogenetisch charakterisiert. Erste Ergebnisse zeigen eine hohe Diversität von bekannten aber auch bisher unbekannten Poly-P speichernden Bakterien in den untersuchten Proben. <dt.>
    Language German
    Size Online-Ressource (PDF-Datei: XII, 109, [55] S., 3,9 MB)
    Document type Book ; Online ; Thesis
    Thesis / German Habilitation thesis Univ., Diss.--Oldenburg, 2010
    Database Library catalogue of the German National Library of Science and Technology (TIB), Hannover

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  6. Article ; Online: IDH2 R172 Mutations Across Poorly Differentiated Sinonasal Tract Malignancies: Forty Molecularly Homogenous and Histologically Variable Cases With Favorable Outcome.

    Glöss, Stefanie / Jurmeister, Philipp / Thieme, Anne / Schmid, Simone / Cai, Wei Y / Serrette, Rene N / Perner, Sven / Ribbat-Idel, Julika / Pagenstecher, Axel / Bläker, Hendrik / Keber, Ursula / Stadelmann, Christine / Zechel, Sabrina / Johann, Pascal D / Hasselblatt, Martin / Paulus, Werner / Thomas, Christian / Dohmen, Hildegard / Baumhoer, Daniel /
    Frank, Stephan / Agaimy, Abbas / Schüller, Ulrich / Vasudevaraja, Varshini / Snuderl, Matija / Liu, Cheng Z / Pfister, David G / Jungbluth, Achim A / Ghossein, Ronald A / Xu, Bin / Capper, David / Dogan, Snjezana

    The American journal of surgical pathology

    2021  Volume 45, Issue 9, Page(s) 1190–1204

    Abstract: IDH2 R172 mutations occur in sinonasal undifferentiated carcinoma (SNUC), large-cell neuroendocrine carcinoma (LCNEC), sinonasal adenocarcinomas, and olfactory neuroblastoma (ONB). We performed a clinical, pathologic, and genetic/epigenetic analysis of a ...

    Abstract IDH2 R172 mutations occur in sinonasal undifferentiated carcinoma (SNUC), large-cell neuroendocrine carcinoma (LCNEC), sinonasal adenocarcinomas, and olfactory neuroblastoma (ONB). We performed a clinical, pathologic, and genetic/epigenetic analysis of a large IDH2-mutated sinonasal tumor cohort to explore their distinct features. A total 165 sinonasal/skull base tumors included 40 IDH2 mutants studied by light microscopy, immunohistochemistry, and genome-wide DNA methylation, and 125 IDH2 wild-type tumors used for comparison. Methylation profiles were analyzed by unsupervised hierarchical clustering, t-distributed stochastic neighbor embedding dimensionality reduction and assessed for copy number alterations (CNA). Thirty-nine histologically assessable cases included 25 (64.1%) SNUC, 8 (20.5%) LCNEC, 2 (5.1%) poorly differentiated adenocarcinomas, 1 (2.7%) ONB, and 3 (7.7%) IDH2-mutated tumors with ONB features. All cases were high-grade showing necrosis (82.4%), prominent nucleoli (88.9%), and median 21 mitoses/10 HPFs. AE1/AE3 and/or CAM 5.2 were positive in all and insulinoma-associated protein 1 (INSM1) in 80% cases. All IDH2 mutants formed one distinct group by t-distributed stochastic neighbor embedding dimensionality reduction separating from all IDH2 wild-type tumors. There was no correlation between methylation clusters and histopathologic diagnoses. Recurrent CNA included 1q gain (79.3%), 17p loss (75.9%), and 17q gain (58.6%). No CNA differences were observed between SNUC and LCNEC. IDH2 mutants showed better disease-specific survival than SMARCB1-deficient (P=0.027) and IDH2 wild-type carcinomas overall (P=0.042). IDH2-mutated sinonasal tumors are remarkably homogeneous at the molecular level and distinct from IDH2 wild-type sinonasal malignancies. Biology of IDH2-mutated sinonasal tumors might be primarily defined by their unique molecular fingerprint rather than by their respective histopathologic diagnoses.
    MeSH term(s) Adult ; Aged ; Aged, 80 and over ; Carcinoma/genetics ; Carcinoma/pathology ; Female ; Humans ; Isocitrate Dehydrogenase/genetics ; Male ; Middle Aged ; Mutation ; Neuroblastoma/genetics ; Neuroblastoma/pathology ; Paranasal Sinus Neoplasms/genetics ; Paranasal Sinus Neoplasms/pathology
    Chemical Substances IDH2 protein, human (EC 1.1.1.41) ; Isocitrate Dehydrogenase (EC 1.1.1.41)
    Language English
    Publishing date 2021-07-14
    Publishing country United States
    Document type Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
    ZDB-ID 752964-8
    ISSN 1532-0979 ; 0147-5185
    ISSN (online) 1532-0979
    ISSN 0147-5185
    DOI 10.1097/PAS.0000000000001697
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  7. Article: Use of Laser Microdissection for Phylogenetic Characterization of Polyphosphate-Accumulating Bacteria

    Gloess, Stefanie / Grossart, Hans-Peter / Allgaier, Martin / Ratering, Stefan / Hupfer, Michael

    Applied and environmental microbiology. 2008 July 1, v. 74, no. 13

    2008  

    Abstract: Our novel approach for taxonomic identification of uncultured bacteria harboring specific physiological features in complex environmental samples combines cell collection by laser microdissection and subsequent DNA analysis. The newly developed approach ... ...

    Abstract Our novel approach for taxonomic identification of uncultured bacteria harboring specific physiological features in complex environmental samples combines cell collection by laser microdissection and subsequent DNA analysis. The newly developed approach was successfully tested for collection and phylogenetic characterization of polyphosphate-accumulating bacteria in activated sludge and lake sediment.
    Keywords DNA ; activated sludge ; bacteria ; lakes ; lasers ; phylogeny
    Language English
    Dates of publication 2008-0701
    Size p. 4231-4235.
    Publishing place American Society for Microbiology
    Document type Article
    Note Includes references
    ZDB-ID 223011-2
    ISSN 1098-5336 ; 0099-2240
    ISSN (online) 1098-5336
    ISSN 0099-2240
    DOI 10.1128/AEM.02545-07
    Database NAL-Catalogue (AGRICOLA)

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    Z 2498: Show issues

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  8. Article ; Online: Use of laser microdissection for phylogenetic characterization of polyphosphate-accumulating bacteria.

    Gloess, Stefanie / Grossart, Hans-Peter / Allgaier, Martin / Ratering, Stefan / Hupfer, Michael

    Applied and environmental microbiology

    2008  Volume 74, Issue 13, Page(s) 4231–4235

    Abstract: Our novel approach for taxonomic identification of uncultured bacteria harboring specific physiological features in complex environmental samples combines cell collection by laser microdissection and subsequent DNA analysis. The newly developed approach ... ...

    Abstract Our novel approach for taxonomic identification of uncultured bacteria harboring specific physiological features in complex environmental samples combines cell collection by laser microdissection and subsequent DNA analysis. The newly developed approach was successfully tested for collection and phylogenetic characterization of polyphosphate-accumulating bacteria in activated sludge and lake sediment.
    MeSH term(s) Bacteria/classification ; Bacteria/genetics ; Bacteria/metabolism ; Dissection ; Fresh Water/microbiology ; Genes, rRNA ; Geologic Sediments/microbiology ; Lasers ; Microscopy ; Molecular Sequence Data ; Phylogeny ; Polyphosphates/metabolism ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; Sewage/microbiology
    Chemical Substances Polyphosphates ; RNA, Ribosomal, 16S ; Sewage
    Language English
    Publishing date 2008-05-02
    Publishing country United States
    Document type Journal Article
    ZDB-ID 223011-2
    ISSN 1098-5336 ; 0099-2240
    ISSN (online) 1098-5336
    ISSN 0099-2240
    DOI 10.1128/AEM.02545-07
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  9. Article ; Online: DNA methylation-based classification of sinonasal tumors.

    Jurmeister, Philipp / Glöß, Stefanie / Roller, Renée / Leitheiser, Maximilian / Schmid, Simone / Mochmann, Liliana H / Payá Capilla, Emma / Fritz, Rebecca / Dittmayer, Carsten / Friedrich, Corinna / Thieme, Anne / Keyl, Philipp / Jarosch, Armin / Schallenberg, Simon / Bläker, Hendrik / Hoffmann, Inga / Vollbrecht, Claudia / Lehmann, Annika / Hummel, Michael /
    Heim, Daniel / Haji, Mohamed / Harter, Patrick / Englert, Benjamin / Frank, Stephan / Hench, Jürgen / Paulus, Werner / Hasselblatt, Martin / Hartmann, Wolfgang / Dohmen, Hildegard / Keber, Ursula / Jank, Paul / Denkert, Carsten / Stadelmann, Christine / Bremmer, Felix / Richter, Annika / Wefers, Annika / Ribbat-Idel, Julika / Perner, Sven / Idel, Christian / Chiariotti, Lorenzo / Della Monica, Rosa / Marinelli, Alfredo / Schüller, Ulrich / Bockmayr, Michael / Liu, Jacklyn / Lund, Valerie J / Forster, Martin / Lechner, Matt / Lorenzo-Guerra, Sara L / Hermsen, Mario / Johann, Pascal D / Agaimy, Abbas / Seegerer, Philipp / Koch, Arend / Heppner, Frank / Pfister, Stefan M / Jones, David T W / Sill, Martin / von Deimling, Andreas / Snuderl, Matija / Müller, Klaus-Robert / Forgó, Erna / Howitt, Brooke E / Mertins, Philipp / Klauschen, Frederick / Capper, David

    Nature communications

    2022  Volume 13, Issue 1, Page(s) 7148

    Abstract: The diagnosis of sinonasal tumors is challenging due to a heterogeneous spectrum of various differential diagnoses as well as poorly defined, disputed entities such as sinonasal undifferentiated carcinomas (SNUCs). In this study, we apply a machine ... ...

    Abstract The diagnosis of sinonasal tumors is challenging due to a heterogeneous spectrum of various differential diagnoses as well as poorly defined, disputed entities such as sinonasal undifferentiated carcinomas (SNUCs). In this study, we apply a machine learning algorithm based on DNA methylation patterns to classify sinonasal tumors with clinical-grade reliability. We further show that sinonasal tumors with SNUC morphology are not as undifferentiated as their current terminology suggests but rather reassigned to four distinct molecular classes defined by epigenetic, mutational and proteomic profiles. This includes two classes with neuroendocrine differentiation, characterized by IDH2 or SMARCA4/ARID1A mutations with an overall favorable clinical course, one class composed of highly aggressive SMARCB1-deficient carcinomas and another class with tumors that represent potentially previously misclassified adenoid cystic carcinomas. Our findings can aid in improving the diagnostic classification of sinonasal tumors and could help to change the current perception of SNUCs.
    MeSH term(s) Humans ; DNA Methylation/genetics ; Proteomics ; Reproducibility of Results ; Carcinoma ; DNA Helicases/genetics ; Nuclear Proteins/genetics ; Transcription Factors
    Chemical Substances SMARCA4 protein, human (EC 3.6.1.-) ; DNA Helicases (EC 3.6.4.-) ; Nuclear Proteins ; Transcription Factors
    Language English
    Publishing date 2022-11-28
    Publishing country England
    Document type Journal Article
    ZDB-ID 2553671-0
    ISSN 2041-1723 ; 2041-1723
    ISSN (online) 2041-1723
    ISSN 2041-1723
    DOI 10.1038/s41467-022-34815-3
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  10. Article ; Online: Correction to: DNA methylation-based reclassification of olfactory neuroblastoma.

    Capper, David / Engel, Nils W / Stichel, Damian / Lechner, Matt / Glöss, Stefanie / Schmid, Simone / Kölsche, Christian / Schrimpf, Daniel / Niesen, Judith / Wefers, Annika K / Jones, David T W / Sill, Martin / Weigert, Oliver / Ligon, Keith L / Olar, Adriana / Koch, Arend / Forster, Martin / Moran, Sebastian / Tirado, Oscar M /
    Sáinz-Jaspeado, Miguel / Mora, Jaume / Esteller, Manel / Alonso, Javier / Del Muro, Xavier Garcia / Paulus, Werner / Felsberg, Jörg / Reifenberger, Guido / Glatzel, Markus / Frank, Stephan / Monoranu, Camelia M / Lund, Valerie J / von Deimling, Andreas / Pfister, Stefan / Buslei, Rolf / Ribbat-Idel, Julika / Perner, Sven / Gudziol, Volker / Meinhardt, Matthias / Schüller, Ulrich

    Acta neuropathologica

    2018  Volume 136, Issue 3, Page(s) 505

    Abstract: In the original publication, the second name of the twentieth author was incorrect. It should read as 'Miguel Sáinz-Jaspeado'. The original publication of the article has been updated to reflect the change. This correction was authored by Ulrich Schüller ...

    Abstract In the original publication, the second name of the twentieth author was incorrect. It should read as 'Miguel Sáinz-Jaspeado'. The original publication of the article has been updated to reflect the change. This correction was authored by Ulrich Schüller on behalf of all authors of the original publication.
    Language English
    Publishing date 2018-08-09
    Publishing country Germany
    Document type Journal Article ; Published Erratum
    ZDB-ID 1079-0
    ISSN 1432-0533 ; 0001-6322
    ISSN (online) 1432-0533
    ISSN 0001-6322
    DOI 10.1007/s00401-018-1887-y
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