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  1. Article ; Online: Retraction for Bai and Kerppola, "Opposing Roles of FoxP1 and Nfat3 in Transcriptional Control of Cardiomyocyte Hypertrophy".

    Bai, Shoumei / Kerppola, Tom K

    Molecular and cellular biology

    2020  Volume 41, Issue 1

    Language English
    Publishing date 2020-12-21
    Publishing country United States
    Document type Journal Article ; Retraction of Publication
    ZDB-ID 779397-2
    ISSN 1098-5549 ; 0270-7306
    ISSN (online) 1098-5549
    ISSN 0270-7306
    DOI 10.1128/MCB.00544-20
    Database MEDical Literature Analysis and Retrieval System OnLINE

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    In stock of ZB MED Cologne/Königswinter

    Zs.A 1666: Show issues Location:
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  2. Article ; Online: Simultaneous visualization of multiple protein interactions using multicolor bimolecular fluorescence complementation (BiFC) analysis.

    Kerppola, Tom K

    Cold Spring Harbor protocols

    2013  Volume 2013, Issue 9, Page(s) 892–895

    Abstract: This multicolor bimolecular fluorescence complementation procedure is designed for the analysis of alternative protein interactions in cultured mammalian cells, but it can be readily adapted to any cell type or aerobically grown organism that can be ... ...

    Abstract This multicolor bimolecular fluorescence complementation procedure is designed for the analysis of alternative protein interactions in cultured mammalian cells, but it can be readily adapted to any cell type or aerobically grown organism that can be genetically modified to express the fusion proteins.
    MeSH term(s) Cells, Cultured ; Color ; Cytological Techniques/methods ; Luminescent Proteins/genetics ; Luminescent Proteins/metabolism ; Protein Interaction Mapping/methods ; Recombinant Fusion Proteins/genetics ; Recombinant Fusion Proteins/metabolism ; Spectrometry, Fluorescence/methods ; Staining and Labeling/methods
    Chemical Substances Luminescent Proteins ; Recombinant Fusion Proteins
    Language English
    Publishing date 2013-09-01
    Publishing country United States
    Document type Journal Article
    ISSN 1559-6095
    ISSN (online) 1559-6095
    DOI 10.1101/pdb.prot077172
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  3. Article ; Online: Design of fusion proteins for bimolecular fluorescence complementation (BiFC).

    Kerppola, Tom K

    Cold Spring Harbor protocols

    2013  Volume 2013, Issue 8, Page(s) 714–718

    Abstract: Bimolecular fluorescence complementation (BiFC) analysis enables direct visualization of protein interactions in living cells. It is based on the facilitated association of two nonfluorescent fragments of a fluorescent protein fused to putative ... ...

    Abstract Bimolecular fluorescence complementation (BiFC) analysis enables direct visualization of protein interactions in living cells. It is based on the facilitated association of two nonfluorescent fragments of a fluorescent protein fused to putative interaction partners. The intrinsic fluorescence of the active complex enables detection of protein interactions with high sensitivity, fine spatial resolution, and minimal perturbation of the cells. As discussed in more detail here, BiFC analysis requires careful consideration of the design and expression of the fusion proteins for the results to be interpretable.
    MeSH term(s) Cytological Techniques/methods ; Microscopy, Fluorescence/methods ; Optical Imaging/methods ; Protein Binding ; Proteins/metabolism ; Recombinant Fusion Proteins/genetics ; Recombinant Fusion Proteins/metabolism ; Staining and Labeling/methods
    Chemical Substances Proteins ; Recombinant Fusion Proteins
    Language English
    Publishing date 2013-08-01
    Publishing country United States
    Document type Journal Article
    ISSN 1559-6095
    ISSN (online) 1559-6095
    DOI 10.1101/pdb.top076489
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  4. Article ; Online: Bimolecular fluorescence complementation (BiFC) analysis of protein interactions in live cells.

    Kerppola, Tom K

    Cold Spring Harbor protocols

    2013  Volume 2013, Issue 8, Page(s) 727–731

    Abstract: Bimolecular fluorescence complementation (BiFC) analysis enables direct visualization of protein interactions and modifications in living cells. It is based on the facilitated association of two nonfluorescent fragments of a fluorescent protein fused to ... ...

    Abstract Bimolecular fluorescence complementation (BiFC) analysis enables direct visualization of protein interactions and modifications in living cells. It is based on the facilitated association of two nonfluorescent fragments of a fluorescent protein fused to putative interaction partners. The intrinsic fluorescence of the active complex enables detection of protein interactions with high sensitivity, fine spatial resolution, and minimal perturbation of the cells. This protocol outlines methods to analyze protein interactions in cultured mammalian cells using BiFC, but can be readily adapted to any cell type or aerobically grown organism that can be genetically modified to express the fusion proteins.
    MeSH term(s) Animals ; Cells, Cultured ; Cytological Techniques/methods ; Humans ; Mammals ; Microscopy, Fluorescence/methods ; Optical Imaging/methods ; Protein Binding ; Proteins/metabolism ; Recombinant Fusion Proteins/genetics ; Recombinant Fusion Proteins/metabolism ; Staining and Labeling/methods
    Chemical Substances Proteins ; Recombinant Fusion Proteins
    Language English
    Publishing date 2013-08-01
    Publishing country United States
    Document type Journal Article
    ISSN 1559-6095
    ISSN (online) 1559-6095
    DOI 10.1101/pdb.prot076497
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  5. Article ; Online: Multicolor bimolecular fluorescence complementation (BiFC) analysis of protein interactions with alternative partners.

    Kerppola, Tom K

    Cold Spring Harbor protocols

    2013  Volume 2013, Issue 9, Page(s) 798–803

    Abstract: Many proteins can interact with several alternative partners. The multicolor bimolecular fluorescence complementation (BiFC) assay enables simultaneous visualization of multiple protein interactions in the same cell. This assay, introduced here, is based ...

    Abstract Many proteins can interact with several alternative partners. The multicolor bimolecular fluorescence complementation (BiFC) assay enables simultaneous visualization of multiple protein interactions in the same cell. This assay, introduced here, is based on the fusion of fragments of fluorescent proteins that form spectrally distinct BiFC complexes to different interaction partners. These complexes can thereby be spectrally resolved and the relative amounts of complexes formed with different interaction partners can be determined. The multicolor BiFC assay enables comparison of the subcellular distributions of complexes formed with different interaction partners and allows analysis of the competition between mutually exclusive interaction partners for binding a shared partner present at limiting concentration.
    MeSH term(s) Cytological Techniques/methods ; Luminescent Proteins/genetics ; Luminescent Proteins/metabolism ; Protein Interaction Mapping/methods ; Recombinant Fusion Proteins/genetics ; Recombinant Fusion Proteins/metabolism ; Spectrometry, Fluorescence/methods ; Staining and Labeling/methods
    Chemical Substances Luminescent Proteins ; Recombinant Fusion Proteins
    Language English
    Publishing date 2013-09-01
    Publishing country United States
    Document type Journal Article
    ISSN 1559-6095
    ISSN (online) 1559-6095
    DOI 10.1101/pdb.top077164
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  6. Article ; Online: Visualization of ubiquitin conjugates using ubiquitin-mediated fluorescence complementation analysis.

    Kerppola, Tom K

    Cold Spring Harbor protocols

    2013  Volume 2013, Issue 10, Page(s) 949–954

    Abstract: Ubiquitin-family peptide conjugation regulates the functions and stabilities of many proteins. Numerous cellular proteins are modified by covalent conjugation of ubiquitin-family peptides to specific lysine residues. These modifications provide a ... ...

    Abstract Ubiquitin-family peptide conjugation regulates the functions and stabilities of many proteins. Numerous cellular proteins are modified by covalent conjugation of ubiquitin-family peptides to specific lysine residues. These modifications provide a flexible means for regulating the properties of the substrate proteins. Because ubiquitin can be conjugated to substrate proteins at many different sites and in many topological configurations, these modifications have the potential to confer a wide range of functional states to the modified proteins. Ubiquitin conjugation is typically detected by immunoprecipitation of a putative substrate protein followed by immunoblotting to detect ubiquitin conjugated to the substrate. However, this assay cannot be used to detect ubiquitin conjugates in live cells. It is also difficult to determine the subcellular distribution of a specific ubiquitin conjugate using this approach. To visualize ubiquitin conjugates in live cells, we have developed the ubiquitin-mediated fluorescence complementation assay, which is based on the association of fragments of fluorescent proteins when ubiquitin fused to one fragment is conjugated to a substrate protein fused to a complementary fragment. This protocol focuses on the visualization of ubiquitin conjugated in cultured mammalian cells, but it can be adapted to any cell type or aerobically grown organism that can be genetically modified to express the fusion proteins.
    MeSH term(s) Animals ; Cell Line ; Cytological Techniques/methods ; Fluorometry/methods ; Humans ; Staining and Labeling/methods ; Ubiquitin/analysis
    Chemical Substances Ubiquitin
    Language English
    Publishing date 2013-10-01
    Publishing country United States
    Document type Journal Article
    ISSN 1559-6095
    ISSN (online) 1559-6095
    DOI 10.1101/pdb.prot078170
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  7. Article ; Online: Visualization of the Genomic Loci That Are Bound by Specific Multiprotein Complexes by Bimolecular Fluorescence Complementation Analysis on Drosophila Polytene Chromosomes.

    Deng, Huai / Kerppola, Tom K

    Methods in enzymology

    2017  Volume 589, Page(s) 429–455

    Abstract: We have developed a procedure that enables visualization of the genomic loci that are bound by complexes formed by a specific combination of chromatin-binding proteins. This procedure is based on imaging bimolecular fluorescence complementation (BiFC) ... ...

    Abstract We have developed a procedure that enables visualization of the genomic loci that are bound by complexes formed by a specific combination of chromatin-binding proteins. This procedure is based on imaging bimolecular fluorescence complementation (BiFC) complexes on Drosophila polytene chromosomes. BiFC complexes are formed by the facilitated association of two fluorescent protein fragments that are fused to proteins that interact with, or are in close proximity to, each other. The intensity of BiFC complex fluorescence at individual genomic loci is greatly enhanced by the parallel alignment of hundreds of chromatids within the polytene chromosomes. The loci that are bound by the complexes are mapped by comparing the locations of BiFC complex fluorescence with the stereotypical banding patterns of the chromosomes. We describe strategies for the design, expression, and validation of fusion proteins for the analysis of BiFC complex binding on polytene chromosomes. We detail protocols for the preparation of polytene chromosome spreads that have been optimized for the purpose of BiFC complex visualization. Finally, we provide guidance for the interpretation of results from studies of BiFC complex binding on polytene chromosomes and for comparison of the genomic loci that are bound by BiFC complexes with those that are bound by subunits of the corresponding endogenous complexes. The visualization of BiFC complex binding on polytene chromosomes provides a unique method to visualize multiprotein complex binding at specific loci, throughout the genome, in individual cells.
    MeSH term(s) Animals ; Drosophila/cytology ; Drosophila/genetics ; Drosophila/metabolism ; Drosophila Proteins/analysis ; Drosophila Proteins/metabolism ; Genetic Loci ; Luminescent Proteins/analysis ; Luminescent Proteins/metabolism ; Microscopy, Fluorescence/methods ; Multiprotein Complexes/analysis ; Multiprotein Complexes/metabolism ; Optical Imaging/methods ; Polytene Chromosomes/metabolism ; Polytene Chromosomes/ultrastructure ; Recombinant Fusion Proteins/analysis ; Recombinant Fusion Proteins/metabolism
    Chemical Substances Drosophila Proteins ; Luminescent Proteins ; Multiprotein Complexes ; Recombinant Fusion Proteins
    Language English
    Publishing date 2017-03-11
    Publishing country United States
    Document type Journal Article
    ISSN 1557-7988 ; 0076-6879
    ISSN (online) 1557-7988
    ISSN 0076-6879
    DOI 10.1016/bs.mie.2017.02.003
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  8. Article ; Online: Polycomb group complexes--many combinations, many functions.

    Kerppola, Tom K

    Trends in cell biology

    2009  Volume 19, Issue 12, Page(s) 692–704

    Abstract: Polycomb Group (PcG) proteins are transcription regulatory proteins that control the expression of a variety of genes from early embryogenesis through birth to adulthood. PcG proteins form several complexes that are thought to collaborate to repress gene ...

    Abstract Polycomb Group (PcG) proteins are transcription regulatory proteins that control the expression of a variety of genes from early embryogenesis through birth to adulthood. PcG proteins form several complexes that are thought to collaborate to repress gene transcription. Individual PcG proteins have unique characteristics, and mutations in genes encoding different PcG proteins cause distinct phenotypes. Histone modifications have important roles in some PcG protein functions, but they are not universally required. The mechanisms of gene-specific recruitment, transcription repression, and selective derepression of genes by vertebrate PcG proteins are incompletely understood. Future studies of this enigmatic group of developmental regulators are certain to produce unanticipated discoveries.
    MeSH term(s) Animals ; Gene Expression Regulation ; Histones/metabolism ; Humans ; Polycomb-Group Proteins ; Protein Binding ; Repressor Proteins/metabolism ; Transcription, Genetic/genetics
    Chemical Substances Histones ; Polycomb-Group Proteins ; Repressor Proteins
    Language English
    Publishing date 2009-11-04
    Publishing country England
    Document type Journal Article ; Research Support, N.I.H., Extramural ; Review
    ZDB-ID 30122-x
    ISSN 1879-3088 ; 0962-8924
    ISSN (online) 1879-3088
    ISSN 0962-8924
    DOI 10.1016/j.tcb.2009.10.001
    Database MEDical Literature Analysis and Retrieval System OnLINE

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    In stock of ZB MED Cologne/Königswinter

    Zs.MG 25: Show issues
    Zs.MO 113: Show issues
    Zs.A 3410: Show issues Location:
    Je nach Verfügbarkeit (siehe Angabe bei Bestand)
    bis Jg. 1994: Bestellungen von Artikeln über das Online-Bestellformular
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  9. Article ; Online: Visualization of molecular interactions using bimolecular fluorescence complementation analysis: characteristics of protein fragment complementation.

    Kerppola, Tom K

    Chemical Society reviews

    2009  Volume 38, Issue 10, Page(s) 2876–2886

    Abstract: Investigations of the molecular processes that sustain life must include studies of these processes in their normal cellular environment. The bimolecular fluorescence complementation (BiFC) assay provides an approach for the visualization of protein ... ...

    Abstract Investigations of the molecular processes that sustain life must include studies of these processes in their normal cellular environment. The bimolecular fluorescence complementation (BiFC) assay provides an approach for the visualization of protein interactions and modifications in living cells. This assay is based on the facilitated association of complementary fragments of a fluorescent protein that are fused to interaction partners. Complex formation by the interaction partners tethers the fluorescent protein fragments in proximity to each other, which can facilitate their association. The BiFC assay enables sensitive visualization of protein complexes with high spatial resolution. The temporal resolution of BiFC analysis is limited by the time required for fluorophore formation, as well as the stabilization of complexes by association of the fluorescent protein fragments. Many modifications and enhancements to the BiFC assay have been developed. The multicolor BiFC assay enables simultaneous visualization of multiple protein complexes in the same cell, and can be used to investigate competition among mutually exclusive interaction partners for complex formation in cells. The ubiquitin-mediated fluorescence complementation (UbFC) assay enables visualization of covalent ubiquitin family peptide conjugation to substrate proteins in cells. The BiFC assay can also be used to visualize protein binding to specific chromatin domains, as well as other molecular scaffolds in cells. BiFC analysis therefore provides a powerful approach for the visualization of a variety of processes that affect molecular proximity in living cells. The visualization of macromolecular interactions and modifications is of great importance owing to the central roles of proteins, nucleic acids and other macromolecular complexes in the regulation of cellular functions. This tutorial review describes the BiFC assay, and discusses the advantages and disadvantages of this experimental approach. The review will be of interest to scientists interested in the investigation of macromolecular interactions or modifications who need exquisite sensitivity for the detection of their complexes or conjugates of interest.
    MeSH term(s) Bacterial Proteins/genetics ; Bacterial Proteins/metabolism ; Basic-Leucine Zipper Transcription Factors/metabolism ; Cell Physiological Phenomena/physiology ; Fluorescence ; Microscopy, Fluorescence/methods ; Plant Proteins/metabolism ; Protein Binding/drug effects ; Protein Interaction Mapping/methods ; Protein Multimerization ; Proteomics ; Spectrometry, Fluorescence/methods ; Spectrometry, Fluorescence/statistics & numerical data ; Transfection ; Two-Hybrid System Techniques
    Chemical Substances Bacterial Proteins ; Basic-Leucine Zipper Transcription Factors ; Plant Proteins
    Language English
    Publishing date 2009-09-04
    Publishing country England
    Document type Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't ; Review
    ZDB-ID 1472875-8
    ISSN 1460-4744 ; 0306-0012
    ISSN (online) 1460-4744
    ISSN 0306-0012
    DOI 10.1039/b909638h
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  10. Article ; Online: Overcoming uncertainty through advances in fluorescence imaging of molecular processes in cells.

    Kerppola, Tom K

    Methods (San Diego, Calif.)

    2008  Volume 45, Issue 3, Page(s) 183–184

    MeSH term(s) Animals ; Cell Physiological Phenomena ; Fluorescence ; Fluorometry/statistics & numerical data ; Fluorometry/trends ; Humans ; Molecular Biology/instrumentation ; Molecular Biology/trends ; Research/instrumentation ; Research/trends ; Sensitivity and Specificity
    Language English
    Publishing date 2008-05-07
    Publishing country United States
    Document type Introductory Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 1066584-5
    ISSN 1095-9130 ; 1046-2023
    ISSN (online) 1095-9130
    ISSN 1046-2023
    DOI 10.1016/j.ymeth.2008.07.005
    Database MEDical Literature Analysis and Retrieval System OnLINE

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    In stock of ZB MED Cologne/Königswinter

    Zs.A 3239: Show issues Location:
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