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  1. Book: Chromosomal mutagenesis

    Pruett-Miller, Shondra M.

    (Methods in molecular biology ; 1239 ; Springer protocols)

    2015  

    Author's details ed. by Shondra M. Pruett-Miller
    Series title Methods in molecular biology ; 1239
    Springer protocols
    Collection
    Keywords Chromosomes ; Chromosomes/Research/Methodology ; Genetic Engineering ; Mutagenesis ; Mutagenesis/Methodology ; Endonucleasen ; CRISPR/Cas-Methode ; DNS ; Synthese ; Proteine ; Fluoreszenz ; RNS ; Genome Editing ; Zielgenauigkeit ; Mutagenese ; Mensch ; Stammzelle ; Zebrabärbling ; Knockout ; Spermium ; Konservierung ; Gefriertrocknung ; Dependoviren
    Subject Adeno-assoziierte Viren ; AAV ; Defekte Parvoviren ; Gefriertrocknen ; Lyophilisation ; Samenzelle ; Spermatozoon ; Spermien ; Spermatozoid ; Spermatozoe ; Samenfaden ; Mikrogamet ; Gen-Knockout ; Brachydanio rerio ; Danio rerio ; Zebrafisch ; Zebrabarbe ; Genomchirurgie ; Genom-Editierung ; Gene Editing ; Stem cell ; Menschen ; Homo sapiens ; Ribonucleinsäure ; Ribonukleinsäure ; RNA ; Ribonucleinsäuren ; Ribonukleinsäuren ; Eiweiss ; Protein ; Synthesis ; Desoxyribonucleinsäure ; DNA ; DNA-Molekül ; Desoxyribonukleinsäure ; CRISPR/Cas9-Methode ; Endonukleasen
    Language English
    Size XIV, 333 S. : Ill., graph. Darst., 23cm
    Edition 2. ed.
    Publisher Humana Press
    Publishing place New York u.a.
    Publishing country United States
    Document type Book
    HBZ-ID HT018512480
    ISBN 978-1493955411 ; 978-1-4939-1861-4 ; 9781493918621 ; 1493955411 ; 1-4939-1861-3 ; 1493918621
    Database Catalogue ZB MED Medicine, Health

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    In stock of ZB MED Cologne/Königswinter

    Shelf markLoan statusLocation
    Zs A 7042 -1239- verfügbar in Königswinter Königswinter

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  2. Article ; Online: Fragmid: A toolkit for rapid assembly and assessment of CRISPR technologies.

    Pruett-Miller, Shondra M

    Cell genomics

    2024  Volume 4, Issue 3, Page(s) 100525

    Abstract: The CRISPR toolbox continues to expand at a rapid pace, leaving researchers scrambling to assess the latest tools in their systems of interest. McGee et al. ...

    Abstract The CRISPR toolbox continues to expand at a rapid pace, leaving researchers scrambling to assess the latest tools in their systems of interest. McGee et al.
    MeSH term(s) Clustered Regularly Interspaced Short Palindromic Repeats/genetics
    Language English
    Publishing date 2024-01-30
    Publishing country United States
    Document type Journal Article
    ISSN 2666-979X
    ISSN (online) 2666-979X
    DOI 10.1016/j.xgen.2024.100525
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  3. Article ; Online: High-Throughput Analysis of CRISPR-Cas9 Editing Outcomes in Cell and Animal Models Using CRIS.py.

    Narina, Shilpa / Connelly, Jon P / Pruett-Miller, Shondra M

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

    2023  Volume 2631, Page(s) 155–182

    Abstract: Genome editing using the CRISPR-Cas9 platform creates precise modifications in cells and whole organisms. Although knockout (KO) mutations can occur at high frequencies, determining the editing rates in a pool of cells or selecting clones that contain ... ...

    Abstract Genome editing using the CRISPR-Cas9 platform creates precise modifications in cells and whole organisms. Although knockout (KO) mutations can occur at high frequencies, determining the editing rates in a pool of cells or selecting clones that contain only KO alleles can be a challenge. User-defined knock-in (KI) modifications are achieved at much lower rates, making the identification of correctly modified clones even more challenging. The high-throughput format of targeted next-generation sequencing (NGS) provides a platform allowing sequence information to be gathered from a one to thousands of samples. However, it also poses a challenge in terms of analyzing the large amount of data that is generated. In this chapter, we present and discuss CRIS.py, a simple and highly versatile Python-based program for analyzing NGS data for genome-editing outcomes. CRIS.py can be used to analyze sequencing results for any kind of modification or multiplex modifications specified by the user. Moreover, CRIS.py runs on all fastq files found in a directory, thereby concurrently analyzing all uniquely indexed samples. CRIS.py results are consolidated into two summary files, which allows users to sort and filter results and quickly identify the clones (or animals) of greatest interest.
    MeSH term(s) Animals ; CRISPR-Cas Systems/genetics ; Gene Editing/methods ; Mutation ; Models, Animal
    Language English
    Publishing date 2023-03-30
    Publishing country United States
    Document type Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
    ISSN 1940-6029
    ISSN (online) 1940-6029
    DOI 10.1007/978-1-0716-2990-1_6
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  4. Article ; Online: Assessing Off-Target Editing of CRISPR-Cas9 Systems.

    Pruett-Miller, Shondra M

    The CRISPR journal

    2020  Volume 3, Issue 6, Page(s) 430–432

    MeSH term(s) CRISPR-Cas Systems/genetics ; Clustered Regularly Interspaced Short Palindromic Repeats/genetics ; Gene Editing
    Language English
    Publishing date 2020-12-21
    Publishing country United States
    Document type Journal Article ; Comment
    ZDB-ID 3017891-5
    ISSN 2573-1602 ; 2573-1599
    ISSN (online) 2573-1602
    ISSN 2573-1599
    DOI 10.1089/crispr.2020.29116.smi
    Database MEDical Literature Analysis and Retrieval System OnLINE

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    In stock of ZB MED Cologne/Königswinter

    Zs.A 7195: Show issues Location:
    Je nach Verfügbarkeit (siehe Angabe bei Bestand)
    bis Jg. 2021: Bestellungen von Artikeln über das Online-Bestellformular
    ab Jg. 2022: Lesesaal (EG)
    Zs.MG 119: Show issues

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  5. Article ; Online: Cancer Screens: Better Together.

    Pruett-Miller, Shondra M

    The CRISPR journal

    2020  Volume 3, Issue 1, Page(s) 12–14

    MeSH term(s) CRISPR-Cas Systems ; Clustered Regularly Interspaced Short Palindromic Repeats ; Early Detection of Cancer ; Humans ; Neoplasms/genetics ; Oncogenes
    Language English
    Publishing date 2020-02-20
    Publishing country United States
    Document type Journal Article ; Comment
    ZDB-ID 3017891-5
    ISSN 2573-1602 ; 2573-1599
    ISSN (online) 2573-1602
    ISSN 2573-1599
    DOI 10.1089/crispr.2020.29084.spm
    Database MEDical Literature Analysis and Retrieval System OnLINE

    Full text online

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    In stock of ZB MED Cologne/Königswinter

    Zs.A 7195: Show issues Location:
    Je nach Verfügbarkeit (siehe Angabe bei Bestand)
    bis Jg. 2021: Bestellungen von Artikeln über das Online-Bestellformular
    ab Jg. 2022: Lesesaal (EG)
    Zs.MG 119: Show issues

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  6. Article ; Online: It's CRISPR Clear: Off-Target Study Misses the Mark.

    Pruett-Miller, Shondra M

    The CRISPR journal

    2018  Volume 1, Page(s) 130–131

    Language English
    Publishing date 2018-04-09
    Publishing country United States
    Document type Journal Article
    ISSN 2573-1602
    ISSN (online) 2573-1602
    DOI 10.1089/crispr.2018.29013.mil
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  7. Article ; Online: Short tandem repeat profiling via next-generation sequencing for cell line authentication.

    Chen, Yi-Hsien / Connelly, Jon P / Florian, Colin / Cui, Xiaoxia / Pruett-Miller, Shondra M

    Disease models & mechanisms

    2023  Volume 16, Issue 10

    Abstract: Cell lines are indispensable models for modern biomedical research. A large part of their usefulness derives from the ability of a cell line to proliferate over multiple passages (often indefinitely), allowing multiple experiments to be performed. ... ...

    Abstract Cell lines are indispensable models for modern biomedical research. A large part of their usefulness derives from the ability of a cell line to proliferate over multiple passages (often indefinitely), allowing multiple experiments to be performed. However, over time, cell line identity and purity can be compromised by human errors. Cross-contamination from other cell lines and complete misidentification are both possible. Routine cell line authentication is a necessary preventive measure and has become a requirement for many funding applications and publications. Short tandem repeat (STR) profiling is the most common method for cell line authentication and is usually carried out using standard polymerase chain reaction-capillary electrophoresis analysis (STR-CE). Here, we evaluated next-generation sequencing (NGS)-based STR profiling of human and mouse cell lines at 18 and 15 loci, respectively, in a high-throughput format. Using the Python program STRight, we demonstrate that NGS-based analysis (STR-NGS) is superior to standard STR-CE in terms of the ability to report the sequence context of repeat motifs, sensitivity and flexible multiplexing capability. STR-NGS is thus a valuable alternative for cell line authentication.
    MeSH term(s) Mice ; Animals ; Humans ; Cell Line Authentication ; Microsatellite Repeats/genetics ; Cell Line ; High-Throughput Nucleotide Sequencing
    Language English
    Publishing date 2023-10-23
    Publishing country England
    Document type Journal Article ; Research Support, Non-U.S. Gov't ; Research Support, N.I.H., Extramural
    ZDB-ID 2451104-3
    ISSN 1754-8411 ; 1754-8403
    ISSN (online) 1754-8411
    ISSN 1754-8403
    DOI 10.1242/dmm.050150
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  8. Book: Chromosomal mutagenesis

    Pruett-Miller, Shondra M

    (Methods in molecular biology, ; 1239 ; Springer protocols)

    2015  

    Author's details edited by Shondra M. Pruett-Miller
    Series title Methods in molecular biology, ; 1239
    Springer protocols
    MeSH term(s) Mutagenesis ; Chromosomes ; Genetic Engineering/methods
    Language English
    Size xiv, 333 pages :, illustrations
    Edition Second edition.
    Document type Book
    ISBN 9781493918614 ; 9781493918621 ; 1493918613 ; 1493918621
    Database Catalogue of the US National Library of Medicine (NLM)

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  9. Article ; Online: Preface. Chromosomal mutagenesis.

    Pruett-Miller, Shondra M

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

    2015  Volume 1239, Page(s) vii–ix

    MeSH term(s) Animals ; Chromosomes ; Humans ; Mutagenesis
    Language English
    Publishing date 2015
    Publishing country United States
    Document type Letter
    ISSN 1940-6029
    ISSN (online) 1940-6029
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  10. Article ; Online: Glutathione limits RUNX2 oxidation and degradation to regulate bone formation.

    Hu, Guoli / Yu, Yilin / Sharma, Deepika / Pruett-Miller, Shondra M / Ren, Yinshi / Zhang, Guo-Fang / Karner, Courtney M

    JCI insight

    2023  Volume 8, Issue 16

    Abstract: Reactive oxygen species (ROS) are natural products of mitochondrial oxidative metabolism and oxidative protein folding. ROS levels must be well controlled, since elevated ROS has been shown to have deleterious effects on osteoblasts. Moreover, excessive ... ...

    Abstract Reactive oxygen species (ROS) are natural products of mitochondrial oxidative metabolism and oxidative protein folding. ROS levels must be well controlled, since elevated ROS has been shown to have deleterious effects on osteoblasts. Moreover, excessive ROS is thought to underlie many of the skeletal phenotypes associated with aging and sex steroid deficiency in mice and humans. The mechanisms by which osteoblasts regulate ROS and how ROS inhibits osteoblasts are not well understood. Here, we demonstrate that de novo glutathione (GSH) biosynthesis is essential in neutralizing ROS and establish a proosteogenic reduction and oxidation reaction (REDOX) environment. Using a multifaceted approach, we demonstrate that reducing GSH biosynthesis led to acute degradation of RUNX2, impaired osteoblast differentiation, and reduced bone formation. Conversely, reducing ROS using catalase enhanced RUNX2 stability and promoted osteoblast differentiation and bone formation when GSH biosynthesis was limited. Highlighting the therapeutic implications of these findings, in utero antioxidant therapy stabilized RUNX2 and improved bone development in the Runx2+/- haplo-insufficient mouse model of human cleidocranial dysplasia. Thus, our data establish RUNX2 as a molecular sensor of the osteoblast REDOX environment and mechanistically clarify how ROS negatively impacts osteoblast differentiation and bone formation.
    MeSH term(s) Mice ; Humans ; Animals ; Osteogenesis/genetics ; Reactive Oxygen Species ; Core Binding Factor Alpha 1 Subunit/genetics ; Core Binding Factor Alpha 1 Subunit/metabolism ; Oxidation-Reduction ; Glutathione/metabolism
    Chemical Substances Reactive Oxygen Species ; Core Binding Factor Alpha 1 Subunit ; Glutathione (GAN16C9B8O) ; RUNX2 protein, human
    Language English
    Publishing date 2023-08-22
    Publishing country United States
    Document type Journal Article ; Research Support, Non-U.S. Gov't ; Research Support, N.I.H., Extramural
    ISSN 2379-3708
    ISSN (online) 2379-3708
    DOI 10.1172/jci.insight.166888
    Database MEDical Literature Analysis and Retrieval System OnLINE

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