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  1. Article ; Online: Global analysis of gene expression mediated by OX1 orexin receptor signaling in a hypothalamic cell line.

    Eric Koesema / Thomas Kodadek

    PLoS ONE, Vol 12, Iss 11, p e

    2017  Volume 0188082

    Abstract: The orexins and their cognate G-protein coupled receptors have been widely studied due to their associations with various behaviors and cellular processes. However, the detailed downstream signaling cascades that mediate these effects are not completely ... ...

    Abstract The orexins and their cognate G-protein coupled receptors have been widely studied due to their associations with various behaviors and cellular processes. However, the detailed downstream signaling cascades that mediate these effects are not completely understood. We report the generation of a neuronal model cell line that stably expresses the OX1 orexin receptor (OX1) and an RNA-Seq analysis of changes in gene expression seen upon receptor activation. Upon treatment with orexin, several families of related transcription factors are transcriptionally regulated, including the early growth response genes (Egr), the Kruppel-like factors (Klf), and the Nr4a subgroup of nuclear hormone receptors. Furthermore, some of the transcriptional effects observed have also been seen in data from in vivo sleep deprivation microarray studies, supporting the physiological relevance of the data set. Additionally, inhibition of one of the most highly regulated genes, serum and glucocorticoid-regulated kinase 1 (Sgk1), resulted in the diminished orexin-dependent induction of a subset of genes. These results provide new insight into the molecular signaling events that occur during OX1 signaling and support a role for orexin signaling in the stimulation of wakefulness during sleep deprivation studies.
    Keywords Medicine ; R ; Science ; Q
    Subject code 570 ; 572
    Language English
    Publishing date 2017-01-01T00:00:00Z
    Publisher Public Library of Science (PLoS)
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  2. Article ; Online: And then there were two

    Lorraine F Clark / Thomas Kodadek

    eLife, Vol

    2015  Volume 4

    Abstract: A second enzyme that removes acetyl groups from lysine residues in E. coli been discovered and represents the founding member of a new enzyme family. ...

    Abstract A second enzyme that removes acetyl groups from lysine residues in E. coli been discovered and represents the founding member of a new enzyme family.
    Keywords proteome microarray ; protein lysine deacetylase ; clip-chip strategy ; Medicine ; R ; Science ; Q ; Biology (General) ; QH301-705.5
    Language English
    Publishing date 2015-12-01T00:00:00Z
    Publisher eLife Sciences Publications Ltd
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  3. Article: Establishment of a suite of assays that support the discovery of proteasome stimulators

    Trader, Darci J / Paige Dickson / Scott Simanski / Thomas Kodadek

    Biochimica et biophysica acta. 2017 Apr., v. 1861, no. 4

    2017  

    Abstract: The proteasome catalyzes the degradation of many mis-folded proteins, which are otherwise cytotoxic. There is interest in the discovery of proteasome agonists, but previous efforts to do so have been disappointing.The cleavage of small fluorogenic ... ...

    Abstract The proteasome catalyzes the degradation of many mis-folded proteins, which are otherwise cytotoxic. There is interest in the discovery of proteasome agonists, but previous efforts to do so have been disappointing.The cleavage of small fluorogenic peptides is used routinely as an assay to screen for proteasome modulators. We have developed follow-on assays that employ more physiologically relevant substrates.To demonstrate the efficacy of this workflow, the NIH Clinical Collection (NCC) was screened. While many compounds stimulated proteasome-mediated proteolysis of the pro-fluorogenic peptide substrates, most failed to evince activity in assays with larger peptide or protein substrates. We also show that two molecules claimed previously to be proteasome agonists, oleuropein and betulinic acid, indeed accelerate hydrolysis of the fluorogenic substrate, but have no effect on the turnover of a mis-folded protein in vitro or in cellulo. However, two small molecules from the NCC, MK-866 and AM-404, stimulate the proteasome-mediated turnover of a mis-folded protein in living cells by 3- to 4-fold.Assays that monitor the proteasome-mediated degradation of larger peptides and proteins can distinguish bona fide agonists from compounds only able to stimulate the cleavage of short, non-physiologically relevant peptides.A suite of assays has been established that allows the discovery of bona fide proteasome agonists. AM-404 and MK-866 can be useful tools for cell culture experiments, and can serve as scaffolds to generate more potent 20S stimulators.
    Keywords agonists ; betulinic acid ; cell culture ; cytotoxicity ; hydrolysis ; oleuropein ; peptides ; proteasome endopeptidase complex ; proteins ; proteolysis
    Language English
    Dates of publication 2017-04
    Size p. 892-899.
    Publishing place Elsevier B.V.
    Document type Article
    ZDB-ID 840755-1
    ISSN 0304-4165
    ISSN 0304-4165
    DOI 10.1016/j.bbagen.2017.01.003
    Database NAL-Catalogue (AGRICOLA)

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  4. Article ; Online: BRD4 Phosphorylation Regulates HPV E2-Mediated Viral Transcription, Origin Replication, and Cellular MMP-9 Expression

    Shwu-Yuan Wu / Dawn Sijin Nin / A-Young Lee / Scott Simanski / Thomas Kodadek / Cheng-Ming Chiang

    Cell Reports, Vol 16, Iss 6, Pp 1733-

    2016  Volume 1748

    Abstract: Post-translational modification can modulate protein conformation and alter binding partner recruitment within gene regulatory regions. Here, we report that bromodomain-containing protein 4 (BRD4), a transcription co-factor and chromatin regulator, uses ... ...

    Abstract Post-translational modification can modulate protein conformation and alter binding partner recruitment within gene regulatory regions. Here, we report that bromodomain-containing protein 4 (BRD4), a transcription co-factor and chromatin regulator, uses a phosphorylation-induced switch mechanism to recruit E2 protein encoded by cancer-associated human papillomavirus (HPV) to viral early gene and cellular matrix metalloproteinase-9 (MMP-9) promoters. Enhanced MMP-9 expression, induced upon keratinocyte differentiation, occurs via BRD4-dependent recruitment of active AP-1 and NF-κB to their target sequences. This is triggered by replacement of AP-1 family members JunB and JunD by c-Jun and by re-localization of NF-κB from the cytoplasm to the nucleus. In addition, BRD4 phosphorylation is critical for E2- and origin-dependent HPV DNA replication. A class of phospho-BRD4-targeting compounds, distinct from the BET bromodomain inhibitors, effectively blocks BRD4 phosphorylation-specific functions in transcription and factor recruitment.
    Keywords Biology (General) ; QH301-705.5
    Subject code 570
    Language English
    Publishing date 2016-08-01T00:00:00Z
    Publisher Elsevier
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  5. Article: Discovery of biomarkers for systemic lupus erythematosus using a library of synthetic autoantigen surrogates

    Quan, Jiexia / Akshai Lakhanpal / David R. Karp / Dwight C. German / M.Muralidhar Reddy / Nancy J. Olsen / Quan-Zhen Li / Sayed Zaman / Thomas Kodadek

    Journal of Immunological Methods. 2014 Jan. 15, v. 402

    2014  

    Abstract: Antibodies to a wide range of self-antigens, including those directed against nucleic acids or nucleic acid-binding proteins are the essential biomarkers for diseases such as systemic lupus erythematosus (SLE). Highly complex libraries of nonamers ... ...

    Abstract Antibodies to a wide range of self-antigens, including those directed against nucleic acids or nucleic acid-binding proteins are the essential biomarkers for diseases such as systemic lupus erythematosus (SLE). Highly complex libraries of nonamers consisting of N-substituted glycines (peptoids) were screened for compounds that bound IgG from patients with SLE and earlier, incomplete autoimmune syndromes. Peptoids were identified that could identify subjects with SLE and related syndromes with a high sensitivity (70%) and specificity (97.5%). Immobilized peptoids were used to isolate IgG from both healthy subjects and SLE patients that reacted with known RNA-binding proteins. In the case of SLE patients, the peptoid-purified IgG reacted with several autoantigens, suggesting that the peptoids are capable of interacting with multiple, structurally similar molecules. These results show that the measurement of IgG binding to peptoids can identify subjects with high levels of pathogenic autoantibodies.
    Keywords autoantibodies ; autoantigens ; biomarkers ; immunoglobulin G ; lupus erythematosus ; nucleic acids ; patients ; RNA-binding proteins
    Language English
    Dates of publication 2014-0115
    Size p. 23-34.
    Publishing place Elsevier B.V.
    Document type Article
    ZDB-ID 120142-6
    ISSN 1872-7905 ; 0022-1759
    ISSN (online) 1872-7905
    ISSN 0022-1759
    DOI 10.1016/j.jim.2013.11.004
    Database NAL-Catalogue (AGRICOLA)

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    Zs.A 795: Show issues Location:
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  6. Article: Selection of a potential diagnostic biomarker for HIV infection from a random library of non-biological synthetic peptoid oligomers

    Gearhart, Tricia L / Charles R. Rinaldo / Chris D. Pilcher / Donald S. Burke / Ernesto T.A. Marques / Kazi Islam / Mark E. Schurdak / Raymond Yurko / Ronald C. Montelaro / Thomas Kodadek / Yongseok Park

    Journal of Immunological Methods. 2016 Aug., v. 435

    2016  

    Abstract: Non-biological synthetic oligomers can serve as ligands for antibodies. We hypothesized that a random combinatorial library of synthetic poly-N-substituted glycine oligomers, or peptoids, could represent a random “shape library” in antigen space, and ...

    Abstract Non-biological synthetic oligomers can serve as ligands for antibodies. We hypothesized that a random combinatorial library of synthetic poly-N-substituted glycine oligomers, or peptoids, could represent a random “shape library” in antigen space, and that some of these peptoids would be recognized by the antigen-binding pocket of disease-specific antibodies. We synthesized and screened a one bead one compound combinatorial library of peptoids, in which each bead displayed an 8-mer peptoid with ten possible different amines at each position (108 theoretical variants). By screening one million peptoid/beads we found 112 (approximately 1 in 10,000) that preferentially bound immunoglobulins from human sera known to be positive for anti-HIV antibodies. Reactive peptoids were then re-synthesized and rigorously evaluated in plate-based ELISAs. Four peptoids showed very good, and one showed excellent, properties for establishing a sero-diagnosis of HIV. These results demonstrate the feasibility of constructing sero-diagnostic assays for infectious diseases from libraries of random molecular shapes. In this study we sought a proof-of-principle that we could identify a potential diagnostic antibody ligand biomarker for an infectious disease in a random combinatorial library of 100 million peptoids. We believe that this is the first evidence that it is possible to develop sero-diagnostic assays – for any infectious disease – based on screening random libraries of non-biological molecular shapes.
    Keywords amines ; antigens ; biomarkers ; enzyme-linked immunosorbent assay ; HIV infections ; Human immunodeficiency virus ; humans ; immunoglobulins ; ligands ; screening ; serodiagnosis ; viral antibodies
    Language English
    Dates of publication 2016-08
    Size p. 85-89.
    Publishing place Elsevier B.V.
    Document type Article
    ZDB-ID 120142-6
    ISSN 1872-7905 ; 0022-1759
    ISSN (online) 1872-7905
    ISSN 0022-1759
    DOI 10.1016/j.jim.2016.05.001
    Database NAL-Catalogue (AGRICOLA)

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    In stock of ZB MED Cologne/Königswinter

    Zs.A 795: Show issues Location:
    Je nach Verfügbarkeit (siehe Angabe bei Bestand)
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    Jg. 1995 - 2021: Lesesall (1.OG)
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