A5064721834- Amyloidosis: Diagnosis, Treatment, Outcomes
- Multiple Myeloma Research and Treatments
- Chronic Lymphocytic Leukemia Research
- Adipose Tissue and Metabolism
- Monoclonal and Polyclonal Antibodies Research
- Lymphoma Diagnosis and Treatment
- Parathyroid Disorders and Treatments
- Glycosylation and Glycoproteins Research
- Advanced Proteomics Techniques and Applications
- Muscle metabolism and nutrition
- Renal Diseases and Glomerulopathies
- Mass Spectrometry Techniques and Applications
- Drug Transport and Resistance Mechanisms
- Extracellular vesicles in disease
- Genomics and Rare Diseases
- Peptidase Inhibition and Analysis
- Pancreatitis Pathology and Treatment
- Diet and metabolism studies
- Cardiomyopathy and Myosin Studies
- T-cell and B-cell Immunology
- Muscle Physiology and Disorders
- Neuroendocrine Tumor Research Advances
- Metabolomics and Mass Spectrometry Studies
- Immune Cell Function and Interaction
- Chemokine receptors and signaling
Mayo Clinic in Florida
2016-2025
Mayo Clinic
2016-2025
WinnMed
2017-2025
Mayo Clinic in Arizona
2016-2025
University of Minnesota Rochester
2015-2024
Quantitative BioSciences
2022-2024
Abiomed (United States)
2024
Siddhartha Medical College
2023
National Kidney Foundation
2023
VA Boston Healthcare System
2023
Thousands of novel transcripts have been identified using deep transcriptome sequencing. This discovery large and 'hidden' rejuvenates the demand for methods that can rapidly distinguish between coding noncoding RNA. Here, we present a alignment-free method, Coding Potential Assessment Tool (CPAT), which recognizes from pool candidates. To this end, CPAT uses logistic regression model built with four sequence features: open reading frame size, coverage, Fickett TESTCODE statistic hexamer...
Tandem mass spectrometry-based shotgun proteomics has become a widespread technology for analyzing complex protein mixtures. A number of database searching algorithms have been developed to assign peptide sequences tandem spectra. Assembling the identifications proteins, however, is challenging issue because many peptides are shared among multiple proteins. IDPicker an open-source assembly tool that derives minimum list from filtered specified False Discovery Rate. Here, we update increase...
The identification of biomarkers to noninvasively detect prediabetes/diabetes will facilitate interventions designed prevent or delay progression frank diabetes and its attendant complications. purpose this study was characterize the human salivary proteome in type-2 identify potential diabetes. Whole saliva from control diabetic individuals characterized by multidimensional liquid chromatography/tandem mass spectrometry (2D-LC-MS/MS). Label-free quantification used differentially abundant...
Abstract Background Stored biological samples with pathology information and medical records are invaluable resources for translational research. However, RNAs extracted from the archived clinical tissues often substantially degraded. RNA degradation distorts RNA-seq read coverage in a gene-specific manner, has profound influences on whole-genome gene expression profiling. Result We developed transcript integrity number (TIN) to measure degradation. When applied 3 independent datasets, we...
Regular exercise promotes whole-body health and prevents disease, but the underlying molecular mechanisms are incompletely understood
Nucleic acid-sensing Toll-like receptors (TLR) 3, 7/8, and 9 are key innate immune sensors whose activities must be tightly regulated to prevent systemic autoimmune or autoinflammatory disease virus-associated immunopathology. Here, we report a systematic scanning-alanine mutagenesis screen of all cytosolic luminal residues the TLR chaperone protein UNC93B1, which identified both negative positive regulatory regions affecting TLR3, TLR7, TLR9 responses. We subsequently two families harboring...
We have employed recently developed blind modification search techniques to generate the most comprehensive map of post-translational modifications (PTMs) in human lens constructed date. Three aged lenses, two which had moderate cataract, and one young control were analyzed using multidimensional liquid chromatography mass spectrometry. In total, 491 sites proteins identified. There 155 vivo PTM crystallins: 77 previously reported 78 newly detected sites. Several these undetected by...
Examination of abdominal subcutaneous fat aspirates is a practical, sensitive and specific method for the diagnosis systemic amyloidosis. Here we describe development implementation clinical assay using mass spectrometry-based proteomics to type amyloidosis in aspirates. First, validated comparing amyloid-positive (n=43) -negative (n=26) The classified with 88% sensitivity 96% specificity. We then implemented as test, analyzed 366 4-year period part routine care. had 90%, diverse amyloid...
A monoclonal gammopathy is defined by the detection a immunoglobulin (M-protein). In clinical practice, M-protein detected protein gel electrophoresis (PEL) and immunofixation (IFE). We theorized that molecular mass could be used instead of electrophoretic patterns to identify quantify because each light heavy chain has unique amino acid sequence thus whose increased concentration distinguished from normal polyclonal background. addition, we surmised top-down MS isotype constant region with...
Electrophoretic separation of serum and urine proteins has played a central role in diagnosing monitoring plasma cell disorders. Despite limitations resolution analytical sensitivity, plus the necessity for adjunct methods, protein gel electrophoresis immunofixation (IFE) remain front-line tests.We developed MALDI mass spectrometry-based assay that was simple to perform, automatable, analytically sensitive, applicable analyzing wide variety monoclonal (M-proteins) encountered clinically....
Omega-3 polyunsaturated fatty acids (n3-PUFA) are recognized for their anti-inflammatory effects and may be beneficial in the context of sarcopenia. We determined influence n3-PUFA on muscle mitochondrial physiology protein metabolism older adults. Twelve young (18-35 years) (65-85 men women were studied at baseline. Older adults again following supplementation (3.9g/day, 16 weeks). Muscle biopsies used to evaluate respiratory capacity (high resolution respirometry) oxidant emissions...
Fibrillary glomerulonephritis (FGN) is a rare disease with unknown pathogenesis and poor prognosis. Until now, the diagnosis of this has required demonstration glomerular deposition randomly oriented fibrils by electron microscopy that are Congo red negative stain antisera to Igs. We recently discovered novel proteomic tissue biomarker for FGN, namely, DNAJB9.In work, we developed DNAJB9 immunohistochemistry tested its sensitivity specificity FGN. This testing was performed on renal biopsy...
Abstract Extracellular vesicles (EVs) isolated from mesenchymal stem/stromal cells (MSCs) contribute to recovery of damaged tissue. We have previously shown that porcine MSC-derived EVs transport mRNA and miRNA capable modulating cellular pathways in recipient cells. To identify candidate factors the therapeutic effects EVs, we characterized their protein cargo using proteomics. Porcine MSCs were cultured abdominal fat, for expression typical MSC EV markers. LC-MS/MS proteomic analysis was...
Systemic anaplastic large cell lymphomas (ALCLs) are classified into ALK-positive and ALK-negative types. We recently reported that ALCLs genetically heterogenous. The largest subset, representing 30% of cases, had rearrangements the DUSP22 locus. These cases favorable outcomes similar to ALCL, superior other ALCLs. Here, we examined morphologic features these in more detail. First, conducted blinded review hematoxylin eosin slides 108 from our previous study, scoring for presence 3...