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  • The Limp-2/scarb2 Binding Motif On Acid Beta-glucosidase Basic And Applied Implications For Gaucher Disease And Associated Neurodegenerative Diseases

    Article thumbnail: The Limp-2/scarb2 Binding Motif On Acid Beta-glucosidase Basic And Applied Implications For Gaucher Disease And Associated Neurodegenerative Diseases
    Type:
    Article
    Description/Abstract:
    Background: Acid -glucosidase is trafficked to the lysosome by LIMP-2. Results: A unique 11-amino acid sequence on acid -glucosidase was critical for its LIMP-2-dependent targeting to the lysosome. Conclusion: This sequence is essential for oligosaccharide-independent targeting of synthesized acid -glucosidase to the lysosome. Significance: Modification of this sequence has basic/therapeutic implications for Gaucher disease and its comorbidities (e.g. Parkinson disease).
    Creator/Author:
    Grabowski, Gregory A.; Haffey, Wendy D.; Greis, Kenneth D., and Llou, Benjamin
    Submitter:
    Kenneth Greis
    Date Uploaded:
    03/03/2017
    Date Modified:
    04/07/2017
    Date Created:
    2014-09
    License:
    All rights reserved

  • Systematic evaluation of data-independent acquisition for sensitive and reproducible proteomics—a prototype design for a single injection assay

    Article thumbnail: Systematic evaluation of data-independent acquisition for sensitive and reproducible proteomics—a prototype design for a single injection assay
    Type:
    Article
    Description/Abstract:
    Data-independent acquisition (DIA)-based proteomics has become increasingly complicated in recent years because of the vast number of workflows described, coupled with a lack of studies indicating a rational framework for selecting effective settings to use. To address this issue and provide a resource for the proteomics community, we compared 12 DIA methods that assay tryptic peptides using various mass-isolation windows. Our findings indicate that the most sensitive single injection LC-DIA method uses 6 m/z isolation windows to analyze the densely populated tryptic peptide range from 450 to 730 m/z, which allowed quantification of 4465 Escherichia coli peptides. In contrast, using the sequential windowed acquisition of all theoretical fragmentions (SWATH) approach with 26 m/z isolation windows across the entire 400–1200 m/z range, allowed quantification of only 3309 peptides. This reduced sensitivity with 26 m/z windows is caused by an increase in co-eluting compounds with similar precursor values detected in the same tandemMS spectra, which lowers the signal-to-noise of peptide fragment-ion chromatograms and reduces the amount of low abundance peptides that can be quantified from 410 to 920 m/z. Above 920 m/z, more peptides were quantified with 26 m/z windows because of substantial peptide 13C isotope distributions that parse peptide ions into separate isolation windows. Because reproducible quantification has been a long-standing aimof quantitative proteomics, and is a socalled trait of DIA, we sought to determine whether precursor-level chromatograms used in some methods rather than their fragment-level counterparts have similar precision. Our data show that extracted fragment-ion chromatograms are the reason DIA provides superior reproducibility. Copyright © 2015 John Wiley & Sons, Ltd.
    Creator/Author:
    Haffey, Wendy D.; Norris, Jeremy L.; McCullumsmith, Robert E.; Heaven, Michael R.; Cobbs, Archie L.; Funk, Adam J., and Greis, Kenneth D.
    Submitter:
    Kenneth Greis
    Date Uploaded:
    03/03/2017
    Date Modified:
    04/07/2017
    Date Created:
    2016-01
    License:
    All rights reserved

  • Cardiac Metabolic Pathways Affected in the Mouse Model of Barth Syndrome

    Article thumbnail: Cardiac Metabolic Pathways Affected in the Mouse Model of Barth Syndrome
    Type:
    Article
    Description/Abstract:
    Cardiolipin (CL) is a mitochondrial phospholipid essential for electron transport chain (ETC) integrity. CL-deficiency in humans is caused by mutations in the tafazzin (Taz) gene and results in a multisystem pediatric disorder, Barth syndrome (BTHS). It has been reported that tafazzin deficiency destabilizes mitochondrial respiratory chain complexes and affects supercomplex assembly. The aim of this study was to investigate the impact of Taz-knockdown on the mitochondrial proteomic landscape and metabolic processes, such as stability of respiratory chain supercomplexes and their interactions with fatty acid oxidation enzymes in cardiac muscle. Proteomic analysis demonstrated reduction of several polypeptides of the mitochondrial respiratory chain, including Rieske and cytochrome c1 subunits of complex III, NADH dehydrogenase alpha subunit 5 of complex I and the catalytic core-forming subunit of F0F1-ATP synthase. Taz gene knockdown resulted in upregulation of enzymes of folate and amino acid metabolic pathways in heart mitochondria, demonstrating that Tazdeficiency causes substantive metabolic remodeling in cardiac muscle. Mitochondrial respiratory chain supercomplexes are destabilized in CL-depleted mitochondria from Taz knockdown hearts resulting in disruption of the interactions between ETC and the fatty acid oxidation enzymes, very long-chain acyl-CoA dehydrogenase and long-chain 3-hydroxyacylCoA dehydrogenase, potentially affecting the metabolic channeling of reducing equivalents between these two metabolic pathways. Mitochondria-bound myoglobin was significantly reduced in Taz-knockdown hearts, potentially disrupting intracellular oxygen delivery to the oxidative phosphorylation system. Our results identify the critical pathways affected by the Taz-deficiency in mitochondria and establish a future framework for development of therapeutic options for BTHS.
    Creator/Author:
    Haffey, Wendy D.; Mandala, Satish K.; Purevjav, Enkhsalkhan; Huang, Yan; Javadov, Sabzali; Greis, Kenneth D.; Powers, Corey; Strauss, Arnold W.; Towbin, Jeffrey A., and Khuchua, Zaza
    Submitter:
    Kenneth Greis
    Date Uploaded:
    03/03/2017
    Date Modified:
    04/07/2017
    Date Created:
    2015-06
    License:
    All rights reserved