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Browsing by Subject "Proteomics"
Now showing items 1-20 of 30
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A chemical glycoproteomics platform reveals O-GlcNAcylation of mitochondrial voltage-dependent anion channel 2.
(Cell Rep, 2013-10-31)Protein modification by O-linked β-N-acetylglucosamine (O-GlcNAc) is a critical cell signaling modality, but identifying signal-specific O-GlcNAcylation events remains a significant experimental challenge. Here, we describe ... -
A Covalent Modification Technique for Protein-Ligand Binding Analysis Using Mass Spectrometry-Based Proteomics Platforms
(2009)Currently there is a dearth of analytical techniques for studying protein-ligand interactions on the proteomic scale. Existing techniques, which rely on various calorimetry or spectroscopy methods, are limited in ... -
A flexible statistical model for alignment of label-free proteomics data--incorporating ion mobility and product ion information.
(BMC Bioinformatics, 2013-12-16)BACKGROUND: The goal of many proteomics experiments is to determine the abundance of proteins in biological samples, and the variation thereof in various physiological conditions. High-throughput quantitative proteomics, ... -
Analysis of oxygen/glucose-deprivation-induced changes in SUMO3 conjugation using SILAC-based quantitative proteomics.
(Journal of proteome research, 2012-02)Transient cerebral ischemia dramatically activates small ubiquitin-like modifier (SUMO2/3) conjugation. In cells exposed to 6 h of transient oxygen/glucose deprivation (OGD), a model of ischemia, SUMOylation increases profoundly ... -
Application of the Stability of Proteins from Rates of Oxidation Technique to the Analysis of Mouse Models of Aging and Parkinson's Disease
(2017)Recently, several mass spectrometry-based proteomics techniques have been developed for the large-scale analysis of thermodynamic measurements of protein stability. This has created the possibility of characterizing disease ... -
Biomarkers and proteomic analysis of osteoarthritis.
(Matrix Biol, 2014-10)Our friend and colleague, Dr. Dick Heinegård, contributed greatly to the understanding of joint tissue biochemistry, the discovery and validation of arthritis-related biomarkers and the establishment of methodology for proteomic ... -
Cathelicidin-related antimicrobial peptide mediates skeletal muscle degeneration caused by injury and Duchenne muscular dystrophy in mice.
(Journal of cachexia, sarcopenia and muscle, 2022-12)<h4>Background</h4>Cathelicidin, an antimicrobial peptide, plays a key role in regulating bacterial killing and innate immunity; however, its role in skeletal muscle function is unknown. We investigated the potential role ... -
Characterization of the ubiquitin-modified proteome regulated by transient forebrain ischemia.
(Journal of cerebral blood flow and metabolism : official journal of the International Society of Cerebral Blood Flow and Metabolism, 2014-03)Ubiquitylation is a posttranslational protein modification that modulates various cellular processes of key significance, including protein degradation and DNA damage repair. In animals subjected to transient cerebral ischemia, ... -
Chlamydia trachomatis Infection Leads to Defined Alterations to the Lipid Droplet Proteome in Epithelial Cells.
(PLoS One, 2015)The obligate intracellular bacterium Chlamydia trachomatis is a major human pathogen and a main cause of genital and ocular diseases. During its intracellular cycle, C. trachomatis replicates inside a membrane-bound vacuole ... -
Computational Processing of Omics Data: Implications for Analysis
(2013)In this work, I present four studies across the range of 'omics data types - a Genome- Wide Association Study for gene-by-sex interaction of obesity traits, computational models for transcription start site classification, ... -
Development and Application of Large-Scale Protein Folding Stability Analysis in Drug Target Identification and Disease Biomarker Discovery
(2020)In the past decade, several mass spectrometry-based proteomic techniques have been developed for the large-scale analysis of protein folding stabilities. The main focus of this dissertation is to develop and apply these ... -
Development and Application of a quantitative Mass spectrometry based Platform for Thermodynamic Analysis of Protein interaction Networks
(2013)The identification and quantification of protein-protein interactions in large scale is critical to understanding biological processes at a systems level. Current approaches for the analysis of protein -protein interactions ... -
Development and Application of Complementary Protein Stability Profiling Techniques for Protein Target Identification and Biomarker Discovery
(2022)Protein stability profiling techniques, including stability of proteins from rates of oxidation (SPROX), thermal proteome profiling (TPP), and limited proteolysis (LiP), have created a new toolbox for making protein folding ... -
Development and Application of Mass Spectrometry-Based Approaches for Thermodynamic Analysis of Protein-Ligand Binding Interactions
(2017)The characterization of protein stability changes and protein-ligand interactions on the proteomic scale is important for understanding the biology of cellular processes. The identification and quantification of protein-ligand ... -
Development of Data Analysis Methods and Applications for Proteome-Wide SPROX Measurements
(2017)Protein-ligand interactions can be detected and quantified using protein folding stability measurements. Thus, protein folding stability changes are closely linked to protein function and are an important biophysical measurement. ... -
Elucidating the Molecular Architecture of Cartilage by Proteomics
(2015)Articular cartilage is a highly specialized avascular tissue and consists of chondrocytes and two major components, a collagen-rich framework and highly abundant proteoglycans. The chondrocyte morphology and extracellular ... -
Elucidating the Molecular Composition of Cartilage by Proteomics.
(J Proteome Res, 2016-02-05)Articular cartilage consists of chondrocytes and two major components, a collagen-rich framework and highly abundant proteoglycans. Most prior studies defining the zonal distribution of cartilage have extracted proteins ... -
Host-Based Diagnostics for Acute Respiratory Infections.
(Clinical therapeutics, 2019-10)PURPOSE:The inappropriate use of antimicrobials, especially in acute respiratory infections (ARIs), is largely driven by difficulty distinguishing bacterial, viral, and noninfectious etiologies of illness. A new frontier ... -
Investigation Into Molecular Mechanisms of Substrate Recognition for Chlamydial Protease-Like Activity Factor (CPAF)
(2015)The obligate intracellular pathogen, Chlamydia trachomatis, is becoming an ever greater public health threat worldwide. Despite aggressive public health awareness campaigns and treatment with antibiotics, chlamydial infections ... -
Mass Spectrometry-Based Strategies for Multiplexed Analyses of Protein-Ligand Binding Interactions
(2011)The detection and quantitation of protein-ligand binding interactions is important not only for understanding biological functions but also for the characterization of novel protein ligands. Because protein ligands can ...
