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  1. AU="Schraivogel, Daniel"
  2. AU="Madkhali, Norah Abdullah Bazek"
  3. AU=Vural H
  4. AU="Matsuoka, Shiho"
  5. AU="Simon, Marcelo F"
  6. AU="Ahmad, W Haj" AU="Ahmad, W Haj"
  7. AU="Drillich, Ann"
  8. AU="Bennett, Hamilton"
  9. AU="Al Kaabi, Hoor"
  10. AU="Hecht, Harvey S"
  11. AU="Minsky, Bruce D"
  12. AU="Manzano, Joanna-Grace M"
  13. AU="Acín-Pérez, Rebeca"
  14. AU="Kamakura, Tsukasa"
  15. AU="Lee, Theodore K"
  16. AU="So, Marvin"

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Treffer 1 - 10 von insgesamt 22

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  1. Artikel ; Online: Cell sorters see things more clearly now.

    Schraivogel, Daniel / Steinmetz, Lars M

    Molecular systems biology

    2023  Band 19, Heft 3, Seite(n) e11254

    Abstract: Microscopy and fluorescence-activated cell sorting (FACS) are two of the most important tools for single-cell phenotyping in basic and biomedical research. Microscopy provides high-resolution snapshots of cell morphology and the inner workings of cells, ... ...

    Abstract Microscopy and fluorescence-activated cell sorting (FACS) are two of the most important tools for single-cell phenotyping in basic and biomedical research. Microscopy provides high-resolution snapshots of cell morphology and the inner workings of cells, while FACS isolates thousands of cells per second using simple parameters, such as the intensity of fluorescent protein labels. Recent technologies are now combining both methods to enable the fast isolation of cells with microscopic phenotypes of interest, thereby bridging a long-standing gap in the life sciences. In this Commentary, we discuss the technical advancements made by image-enabled cell sorting and highlight novel experimental strategies in functional genomics and single-cell research.
    Mesh-Begriff(e) Flow Cytometry ; Cell Separation ; Microscopy
    Sprache Englisch
    Erscheinungsdatum 2023-02-13
    Erscheinungsland England
    Dokumenttyp Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 2193510-5
    ISSN 1744-4292 ; 1744-4292
    ISSN (online) 1744-4292
    ISSN 1744-4292
    DOI 10.15252/msb.202211254
    Datenquelle MEDical Literature Analysis and Retrieval System OnLINE

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  2. Artikel ; Online: Pooled Genome-Scale CRISPR Screens in Single Cells.

    Schraivogel, Daniel / Steinmetz, Lars M / Parts, Leopold

    Annual review of genetics

    2023  Band 57, Seite(n) 223–244

    Abstract: Assigning functions to genes and learning how to control their expression are part of the foundation of cell biology and therapeutic development. An efficient and unbiased method to accomplish this is genetic screening, which historically required ... ...

    Abstract Assigning functions to genes and learning how to control their expression are part of the foundation of cell biology and therapeutic development. An efficient and unbiased method to accomplish this is genetic screening, which historically required laborious clone generation and phenotyping and is still limited by scale today. The rapid technological progress on modulating gene function with CRISPR-Cas and measuring it in individual cells has now relaxed the major experimental constraints and enabled pooled screening with complex readouts from single cells. Here, we review the principles and practical considerations for pooled single-cell CRISPR screening. We discuss perturbation strategies, experimental model systems, matching the perturbation to the individual cells, reading out cell phenotypes, and data analysis. Our focus is on single-cell RNA sequencing and cell sorting-based readouts, including image-enabled cell sorting. We expect this transformative approach to fuel biomedical research for the next several decades.
    Mesh-Begriff(e) CRISPR-Cas Systems/genetics ; Genome/genetics ; Genetic Testing/methods ; Phenotype
    Sprache Englisch
    Erscheinungsdatum 2023-08-10
    Erscheinungsland United States
    Dokumenttyp Journal Article ; Review ; Research Support, Non-U.S. Gov't
    ZDB-ID 207928-8
    ISSN 1545-2948 ; 0066-4170 ; 0066-4197
    ISSN (online) 1545-2948
    ISSN 0066-4170 ; 0066-4197
    DOI 10.1146/annurev-genet-072920-013842
    Datenquelle MEDical Literature Analysis and Retrieval System OnLINE

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  3. Artikel: Import routes and nuclear functions of Argonaute and other small RNA-silencing proteins.

    Schraivogel, Daniel / Meister, Gunter

    Trends in biochemical sciences

    2014  Band 39, Heft 9, Seite(n) 420–431

    Abstract: Small RNAs are important regulators of gene expression in many different organisms. Nuclear and cytoplasmic biogenesis enzymes generate functional small RNAs from double-stranded (ds) or single-stranded (ss) RNA precursors, and mature small RNAs are ... ...

    Abstract Small RNAs are important regulators of gene expression in many different organisms. Nuclear and cytoplasmic biogenesis enzymes generate functional small RNAs from double-stranded (ds) or single-stranded (ss) RNA precursors, and mature small RNAs are loaded into Argonaute proteins. In the cytoplasm, small RNAs guide Argonaute proteins to complementary RNAs leading to cleavage of these targets, translational silencing, or mRNA decay. In the nucleus Argonaute proteins engage in transcriptional silencing processes such as epigenetic silencing of repetitive elements at the chromatin level. During the past few years many novel functions of small RNA-guided gene silencing proteins in the nucleus have been reported. However, their specific import routes are largely unknown. In this review we summarize the current knowledge on nuclear transport routes that Argonaute and other RNA-silencing proteins take to carry out their various functions in the nucleus.
    Mesh-Begriff(e) Active Transport, Cell Nucleus ; Animals ; Argonaute Proteins/genetics ; Argonaute Proteins/metabolism ; Cell Nucleus/metabolism ; Gene Silencing ; Humans ; RNA, Small Interfering/genetics ; RNA, Small Interfering/metabolism ; RNA-Binding Proteins/genetics ; RNA-Binding Proteins/metabolism
    Chemische Substanzen Argonaute Proteins ; RNA, Small Interfering ; RNA-Binding Proteins
    Sprache Englisch
    Erscheinungsdatum 2014-09
    Erscheinungsland England
    Dokumenttyp Journal Article ; Research Support, Non-U.S. Gov't ; Review
    ZDB-ID 194216-5
    ISSN 1362-4326 ; 0968-0004 ; 0376-5067
    ISSN (online) 1362-4326
    ISSN 0968-0004 ; 0376-5067
    DOI 10.1016/j.tibs.2014.07.004
    Datenquelle MEDical Literature Analysis and Retrieval System OnLINE

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  4. Artikel: Import routes and nuclear functions of Argonaute and other small RNA-silencing proteins

    Schraivogel, Daniel / Gunter Meister

    Trends in biochemical sciences. 2014 Sept., v. 39

    2014  

    Abstract: Small RNAs are important regulators of gene expression in many different organisms. Nuclear and cytoplasmic biogenesis enzymes generate functional small RNAs from double-stranded (ds) or single-stranded (ss) RNA precursors, and mature small RNAs are ... ...

    Abstract Small RNAs are important regulators of gene expression in many different organisms. Nuclear and cytoplasmic biogenesis enzymes generate functional small RNAs from double-stranded (ds) or single-stranded (ss) RNA precursors, and mature small RNAs are loaded into Argonaute proteins. In the cytoplasm, small RNAs guide Argonaute proteins to complementary RNAs leading to cleavage of these targets, translational silencing, or mRNA decay. In the nucleus Argonaute proteins engage in transcriptional silencing processes such as epigenetic silencing of repetitive elements at the chromatin level. During the past few years many novel functions of small RNA-guided gene silencing proteins in the nucleus have been reported. However, their specific import routes are largely unknown. In this review we summarize the current knowledge on nuclear transport routes that Argonaute and other RNA-silencing proteins take to carry out their various functions in the nucleus.
    Schlagwörter RNA precursors ; biogenesis ; chromatin ; cytoplasm ; enzymes ; epigenetics ; gene expression ; gene silencing ; messenger RNA ; regulator genes ; transcription (genetics) ; translation (genetics)
    Sprache Englisch
    Erscheinungsverlauf 2014-09
    Umfang p. 420-431.
    Erscheinungsort Elsevier Ltd
    Dokumenttyp Artikel
    ZDB-ID 194220-7
    ISSN 0968-0004 ; 0376-5067
    ISSN 0968-0004 ; 0376-5067
    DOI 10.1016/j.tibs.2014.07.004
    Datenquelle NAL Katalog (AGRICOLA)

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  5. Artikel ; Online: Large scale microfluidic CRISPR screening for increased amylase secretion in yeast.

    Johansson, S Andreas / Dulermo, Thierry / Jann, Cosimo / Smith, Justin D / Pryszlak, Anna / Pignede, Georges / Schraivogel, Daniel / Colavizza, Didier / Desfougères, Thomas / Rave, Christophe / Farwick, Alexander / Merten, Christoph A / Roy, Kevin R / Wei, Wu / Steinmetz, Lars M

    Lab on a chip

    2023  Band 23, Heft 16, Seite(n) 3704–3715

    Abstract: Key to our ability to increase recombinant protein production through secretion is a better understanding of the pathways that interact to translate, process and export mature proteins to the surrounding environment, including the supporting cellular ... ...

    Abstract Key to our ability to increase recombinant protein production through secretion is a better understanding of the pathways that interact to translate, process and export mature proteins to the surrounding environment, including the supporting cellular machinery that supplies necessary energy and building blocks. By combining droplet microfluidic screening with large-scale CRISPR libraries that perturb the expression of the majority of coding and non-coding genes in
    Mesh-Begriff(e) Saccharomyces cerevisiae/genetics ; Saccharomyces cerevisiae/metabolism ; Saccharomyces cerevisiae Proteins/genetics ; Saccharomyces cerevisiae Proteins/metabolism ; Amylases/metabolism ; Microfluidics ; alpha-Amylases/genetics ; alpha-Amylases/metabolism
    Chemische Substanzen Saccharomyces cerevisiae Proteins ; Amylases (EC 3.2.1.-) ; alpha-Amylases (EC 3.2.1.1)
    Sprache Englisch
    Erscheinungsdatum 2023-08-08
    Erscheinungsland England
    Dokumenttyp Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 2056646-3
    ISSN 1473-0189 ; 1473-0197
    ISSN (online) 1473-0189
    ISSN 1473-0197
    DOI 10.1039/d3lc00111c
    Datenquelle MEDical Literature Analysis and Retrieval System OnLINE

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  6. Artikel ; Online: Mislocalization of pathogenic RBM20 variants in dilated cardiomyopathy is caused by loss-of-interaction with Transportin-3.

    Kornienko, Julia / Rodríguez-Martínez, Marta / Fenzl, Kai / Hinze, Florian / Schraivogel, Daniel / Grosch, Markus / Tunaj, Brigit / Lindenhofer, Dominik / Schraft, Laura / Kueblbeck, Moritz / Smith, Eric / Mao, Chad / Brown, Emily / Owens, Anjali / Saguner, Ardan M / Meder, Benjamin / Parikh, Victoria / Gotthardt, Michael / Steinmetz, Lars M

    Nature communications

    2023  Band 14, Heft 1, Seite(n) 4312

    Abstract: Severe forms of dilated cardiomyopathy (DCM) are associated with point mutations in the alternative splicing regulator RBM20 that are frequently located in the arginine/serine-rich domain (RS-domain). Such mutations can cause defective splicing and ... ...

    Abstract Severe forms of dilated cardiomyopathy (DCM) are associated with point mutations in the alternative splicing regulator RBM20 that are frequently located in the arginine/serine-rich domain (RS-domain). Such mutations can cause defective splicing and cytoplasmic mislocalization, which leads to the formation of detrimental cytoplasmic granules. Successful development of personalized therapies requires identifying the direct mechanisms of pathogenic RBM20 variants. Here, we decipher the molecular mechanism of RBM20 mislocalization and its specific role in DCM pathogenesis. We demonstrate that mislocalized RBM20 RS-domain variants retain their splice regulatory activity, which reveals that aberrant cellular localization is the main driver of their pathological phenotype. A genome-wide CRISPR knockout screen combined with image-enabled cell sorting identified Transportin-3 (TNPO3) as the main nuclear importer of RBM20. We show that the direct RBM20-TNPO3 interaction involves the RS-domain, and is disrupted by pathogenic variants. Relocalization of pathogenic RBM20 variants to the nucleus restores alternative splicing and dissolves cytoplasmic granules in cell culture and animal models. These findings provide proof-of-principle for developing therapeutic strategies to restore RBM20's nuclear localization in RBM20-DCM patients.
    Mesh-Begriff(e) Animals ; Cardiomyopathy, Dilated/genetics ; Cardiomyopathy, Dilated/pathology ; RNA Splicing/genetics ; Alternative Splicing/genetics ; Mutation ; Karyopherins/genetics
    Chemische Substanzen Karyopherins
    Sprache Englisch
    Erscheinungsdatum 2023-07-18
    Erscheinungsland England
    Dokumenttyp Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 2553671-0
    ISSN 2041-1723 ; 2041-1723
    ISSN (online) 2041-1723
    ISSN 2041-1723
    DOI 10.1038/s41467-023-39965-6
    Datenquelle MEDical Literature Analysis and Retrieval System OnLINE

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  7. Artikel ; Online: High-speed fluorescence image-enabled cell sorting.

    Schraivogel, Daniel / Kuhn, Terra M / Rauscher, Benedikt / Rodríguez-Martínez, Marta / Paulsen, Malte / Owsley, Keegan / Middlebrook, Aaron / Tischer, Christian / Ramasz, Beáta / Ordoñez-Rueda, Diana / Dees, Martina / Cuylen-Haering, Sara / Diebold, Eric / Steinmetz, Lars M

    Science (New York, N.Y.)

    2022  Band 375, Heft 6578, Seite(n) 315–320

    Abstract: Fast and selective isolation of single cells with unique spatial and morphological traits remains a technical challenge. Here, we address this by establishing high-speed image-enabled cell sorting (ICS), which records multicolor fluorescence images and ... ...

    Abstract Fast and selective isolation of single cells with unique spatial and morphological traits remains a technical challenge. Here, we address this by establishing high-speed image-enabled cell sorting (ICS), which records multicolor fluorescence images and sorts cells based on measurements from image data at speeds up to 15,000 events per second. We show that ICS quantifies cell morphology and localization of labeled proteins and increases the resolution of cell cycle analyses by separating mitotic stages. We combine ICS with CRISPR-pooled screens to identify regulators of the nuclear factor κB (NF-κB) pathway, enabling the completion of genome-wide image-based screens in about 9 hours of run time. By assessing complex cellular phenotypes, ICS substantially expands the phenotypic space accessible to cell-sorting applications and pooled genetic screening.
    Mesh-Begriff(e) Active Transport, Cell Nucleus ; Animals ; CRISPR-Cas Systems ; Cell Nucleus/metabolism ; Cell Shape ; Flow Cytometry ; Genetic Techniques ; Genome ; Genome, Human ; Humans ; Microscopy, Fluorescence ; Mitosis ; NF-kappa B/metabolism ; Optical Imaging ; Organelles/ultrastructure ; Phenotype ; Transcription Factor RelA/metabolism
    Chemische Substanzen NF-kappa B ; RELA protein, human ; Transcription Factor RelA
    Sprache Englisch
    Erscheinungsdatum 2022-01-20
    Erscheinungsland United States
    Dokumenttyp Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 128410-1
    ISSN 1095-9203 ; 0036-8075
    ISSN (online) 1095-9203
    ISSN 0036-8075
    DOI 10.1126/science.abj3013
    Datenquelle MEDical Literature Analysis and Retrieval System OnLINE

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  8. Artikel ; Online: Single-cell analyses reveal SARS-CoV-2 interference with intrinsic immune response in the human gut.

    Triana, Sergio / Metz-Zumaran, Camila / Ramirez, Carlos / Kee, Carmon / Doldan, Patricio / Shahraz, Mohammed / Schraivogel, Daniel / Gschwind, Andreas R / Sharma, Ashwini K / Steinmetz, Lars M / Herrmann, Carl / Alexandrov, Theodore / Boulant, Steeve / Stanifer, Megan L

    Molecular systems biology

    2021  Band 17, Heft 4, Seite(n) e10232

    Abstract: Exacerbated pro-inflammatory immune response contributes to COVID-19 pathology. However, despite the mounting evidence about SARS-CoV-2 infecting the human gut, little is known about the antiviral programs triggered in this organ. To address this gap, we ...

    Abstract Exacerbated pro-inflammatory immune response contributes to COVID-19 pathology. However, despite the mounting evidence about SARS-CoV-2 infecting the human gut, little is known about the antiviral programs triggered in this organ. To address this gap, we performed single-cell transcriptomics of SARS-CoV-2-infected intestinal organoids. We identified a subpopulation of enterocytes as the prime target of SARS-CoV-2 and, interestingly, found the lack of positive correlation between susceptibility to infection and the expression of ACE2. Infected cells activated strong pro-inflammatory programs and produced interferon, while expression of interferon-stimulated genes was limited to bystander cells due to SARS-CoV-2 suppressing the autocrine action of interferon. These findings reveal that SARS-CoV-2 curtails the immune response and highlights the gut as a pro-inflammatory reservoir that should be considered to fully understand SARS-CoV-2 pathogenesis.
    Mesh-Begriff(e) COVID-19/virology ; Gastrointestinal Microbiome ; Humans ; In Situ Hybridization, Fluorescence ; Intestines/immunology ; Organoids/metabolism ; SARS-CoV-2/physiology ; Sequence Analysis, RNA ; Single-Cell Analysis
    Sprache Englisch
    Erscheinungsdatum 2021-04-27
    Erscheinungsland England
    Dokumenttyp Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 2193510-5
    ISSN 1744-4292 ; 1744-4292
    ISSN (online) 1744-4292
    ISSN 1744-4292
    DOI 10.15252/msb.202110232
    Datenquelle MEDical Literature Analysis and Retrieval System OnLINE

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  9. Buch ; Online ; Dissertation / Habilitation: miR-9/9* regulate the tumor suppressor CAMTA1 in glioblastoma stem cells - Part I. Nuclear transport of Argonaute and TNRC6 proteins - Part II

    Schraivogel, Daniel [Verfasser] / Meister, Gunter [Akademischer Betreuer]

    2015  

    Verfasserangabe Daniel Schraivogel. Betreuer: Gunter Meister
    Schlagwörter Biowissenschaften, Biologie ; Life Science, Biology
    Thema/Rubrik (Code) sg570
    Sprache Englisch
    Verlag Universitätsbibliothek Regensburg
    Erscheinungsort Regensburg
    Dokumenttyp Buch ; Online ; Dissertation / Habilitation
    Datenquelle Digitale Dissertationen im Internet

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  10. Artikel ; Online: Targeted Perturb-seq enables genome-scale genetic screens in single cells.

    Schraivogel, Daniel / Gschwind, Andreas R / Milbank, Jennifer H / Leonce, Daniel R / Jakob, Petra / Mathur, Lukas / Korbel, Jan O / Merten, Christoph A / Velten, Lars / Steinmetz, Lars M

    Nature methods

    2020  Band 17, Heft 6, Seite(n) 629–635

    Abstract: The transcriptome contains rich information on molecular, cellular and organismal phenotypes. However, experimental and statistical limitations constrain sensitivity and throughput of genetic screening with single-cell transcriptomics readout. To ... ...

    Abstract The transcriptome contains rich information on molecular, cellular and organismal phenotypes. However, experimental and statistical limitations constrain sensitivity and throughput of genetic screening with single-cell transcriptomics readout. To overcome these limitations, we introduce targeted Perturb-seq (TAP-seq), a sensitive, inexpensive and platform-independent method focusing single-cell RNA-seq coverage on genes of interest, thereby increasing the sensitivity and scale of genetic screens by orders of magnitude. TAP-seq permits routine analysis of thousands of CRISPR-mediated perturbations within a single experiment, detects weak effects and lowly expressed genes, and decreases sequencing requirements by up to 50-fold. We apply TAP-seq to generate perturbation-based enhancer-target gene maps for 1,778 enhancers within 2.5% of the human genome. We thereby show that enhancer-target association is jointly determined by three-dimensional contact frequency and epigenetic states, allowing accurate prediction of enhancer targets throughout the genome. In addition, we demonstrate that TAP-seq can identify cell subtypes with only 100 sequencing reads per cell.
    Mesh-Begriff(e) Clustered Regularly Interspaced Short Palindromic Repeats/genetics ; Genome, Human ; Humans ; RNA-Seq/methods ; Single-Cell Analysis/methods ; Transcriptome/genetics
    Sprache Englisch
    Erscheinungsdatum 2020-06-01
    Erscheinungsland United States
    Dokumenttyp Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 2169522-2
    ISSN 1548-7105 ; 1548-7091
    ISSN (online) 1548-7105
    ISSN 1548-7091
    DOI 10.1038/s41592-020-0837-5
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