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Dive into the research topics where Kent W. Seeley is active.

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Featured researches published by Kent W. Seeley.


Journal of Proteomics | 2012

Investigation of local primary structure effects on peroxynitrite-mediated tyrosine nitration using targeted mass spectrometry

Kent W. Seeley; Stanley M. Stevens

Protein-tyrosine nitration (PTN) is a posttranslational modification resulting from cellular nitrosative stress that has been implicated in a wide variety of disease states. Determination of factors that influence selectivity of PTN remains a major challenge due to several issues including low biological levels of PTN, proximity of target sites on a single analyte, and analytical limitations for site-specific quantification of the nitration modification. We report a systematic approach that addresses relevant contributing factors to PTN with particular focus on determining the effect of changing proximal amino acid side chain structure on tyrosine nitration yield. A trend was observed in which nitration yield tends to be greater when the tyrosine residue is surrounded by basic and/or uncharged polar residues compared to nitration levels observed when hydrophobic and acidic residues are proximal to the tyrosine residue. Moreover, an electric dipole effect was observed where a higher degree of charge asymmetry surrounding the tyrosine residue correlates with an increased tyrosine nitration yield in certain cases. The reported data are expected to facilitate site-specific prediction and validation of PTN, especially in cases of potential target residues that share a similar solvent exposure environment and contain elements of known higher-order structure.


Analytical and Bioanalytical Chemistry | 2010

Evaluation of microwave-assisted enzymatic digestion and tandem mass spectrometry for the identification of protein residues from an inorganic solid matrix: implications in archaeological research.

Stanley M. Stevens; Steve Wolverton; Barney J. Venables; Andrew Barker; Kent W. Seeley; Prem Adhikari

A method based on microwave-assisted enzymatic digestion and liquid chromatography–tandem mass spectrometry analysis is presented for the identification of proteins incorporated within solid matrices using protein standards bound to experimental cooking pottery as a validation model. The implementation of microwave irradiation allowed for a significant decrease in overall analysis time in addition to select enhancement of peptide recovery as determined by label-free relative quantitation. We envision that the reported methodology will provide new avenues for scientific discovery in areas such as archaeology and forensics. Results of this series of experiments are part of an ongoing project directed at developing a comprehensive methodology for extracting proteinaceous residues from archaeological pottery.


Microbiological Research | 2015

Klebsiella pneumoniae O antigen loss alters the outer membrane protein composition and the selective packaging of proteins into secreted outer membrane vesicles.

Bethaney K. Cahill; Kent W. Seeley; Dedra Gutel; Terri N. Ellis

Klebsiella pneumoniae is a nosocomial pathogen which naturally secretes lipopolysaccharide (LPS) and cell envelope associated proteins into the environment through the production of outer membrane vesicles (OMVs). The loss of the LPS O antigen has been demonstrated in other bacterial species to significantly alter the composition of OMVs. Therefore, this study aimed to comprehensively analyze the impact of O antigen loss on the sub-proteomes of both the outer membrane and secreted OMVs from K. pneumoniae. As determined by LC-MS/MS, OMVs were highly enriched with outer membrane proteins involved in cell wall, membrane, and envelope biogenesis as compared to the source cellular outer membrane. Deletion of wbbO, the enzyme responsible for O antigen attachment to LPS, decreased but did not eliminate this enrichment effect. Additionally, loss of O antigen resulted in OMVs with increased numbers of proteins involved in post-translational modification, protein turnover, and chaperones as compared to secreted vesicles from the wild type. This alteration of OMV composition may be a compensatory mechanism to deal with envelope stress. This comprehensive analysis confirms the highly distinct protein composition of OMVs as compared to their source membrane, and provides evidence for a selective sorting mechanism that involves LPS polysaccharides. These data support the hypothesis that modifications to LPS alters both the mechanics of protein sorting and the contents of secreted OMVs and significantly impacts the protein composition of the outer membrane.


Journal of Ethnopharmacology | 2015

Identification and quantitative analysis of cellular proteins affected by treatment with withaferin a using a SILAC-based proteomics approach

Malathi Narayan; Kent W. Seeley; Umesh K. Jinwal

ETHNOPHARMACOLOGICAL RELEVANCEnWithaferin A (WA) is a major bioactive compound isolated from the medicinal plant Withania somnifera Dunal, also known as Ashwagandha. A number of published reports suggest various uses for WA including its function as an anti-inflammatory and anti-angiogenic drug molecule. The effects of WA at the molecular level in a cellular environment are not well understood. Knowledge of the molecular mechanism of action of WA could enhance its therapeutic value and may reveal novel pathways it may modulate.nnnMATERIALS AND METHODSnIn order to identify and characterize proteins affected by treatment with WA, we used SILAC- based proteomics analysis on a mouse microglial cell line (N9), which replicates phenotypic characteristics of primary microglial cells.nnnRESULTSnUsing stable isotope labeling of amino acids in cell culture (SILAC) and mass spectrometry (MS), a total of 2300 unique protein groups were identified from three biological replicates, with significant expression changes in 32 non-redundant proteins. The top biological functions associated with these differentially expressed proteins include cell death and survival, free radical scavenging, and carbohydrate metabolism. Specifically, several heat shock proteins (Hsps) were found to be upregulated, which suggests that the chaperonic machinery might be regulated by WA. Furthermore, our study revealed several novel protein molecules that were not previously reported to be affected by WA. Among them, annexin A1, a key anti-inflammatory molecule in microglial cells was found to be downregulated. Hsc70, Hsp90α and Hsp105 were found to be upregulated. We also found sequestosome1/p62 (p62) to be upregulated. We performed Ingenuity Pathway Analysis (IPA) and found a number of pathways that were affected by WA treatment.nnnCONCLUSIONSnSILAC-based proteomics analysis of a microglial cell model revealed several novel proteins whose expression is regulated by WA and probable pathways regulated by WA.


International Journal of Molecular Sciences | 2014

Evaluation of a Method for Nitrotyrosine Site Identification and Relative Quantitation Using a Stable Isotope-Labeled Nitrated Spike-In Standard and High Resolution Fourier Transform MS and MS/MS Analysis

Kent W. Seeley; Alison R. Fertig; Craig P. Dufresne; Joao Paulo Costa Pinho; Stanley M. Stevens

The overproduction of reactive oxygen and nitrogen species (ROS and RNS) can have deleterious effects in the cell, including structural and possible activity-altering modifications to proteins. Peroxynitrite is one such RNS that can result in a specific protein modification, nitration of tyrosine residues to form nitrotyrosine, and to date, the identification of nitrotyrosine sites in proteins continues to be a major analytical challenge. We have developed a method by which 15N-labeled nitrotyrosine groups are generated on peptide or protein standards using stable isotope-labeled peroxynitrite (O15NOO−), and the resulting standard is mixed with representative samples in which nitrotyrosine formation is to be measured by mass spectrometry (MS). Nitropeptide MS/MS spectra are filtered using high mass accuracy Fourier transform MS (FTMS) detection of the nitrotyrosine immonium ion. Given that the nitropeptide pair is co-isolated for MS/MS fragmentation, the nitrotyrosine immonium ions (at m/z = 181 or 182) can be used for relative quantitation with negligible isotopic interference at a mass resolution of greater than 50,000 (FWHM, full width at half-maximum). Furthermore, the standard potentially allows for the increased signal of nitrotyrosine-containing peptides, thus facilitating selection for MS/MS in a data-dependent mode of acquisition. We have evaluated the methodology in terms of nitrotyrosine site identification and relative quantitation using nitrated peptide and protein standards.


Fems Microbiology Letters | 2017

Peculiar citric acid cycle of hydrothermal vent chemolithoautotroph Hydrogenovibrio crunogenus, and insights into carbon metabolism by obligate autotrophs

Ishtiaque Quasem; Alexandra Achille; Brittany A. Caddick; Travis A. Carter; Camille A. Daniels; Jennifer Delaney; Vedad Delic; Kimberly A. Denton; Martina C. Duran; Marianne K. Fatica; Christopher M. Ference; Julie P. Galkiewicz; Ana M. Garcia; Jacqueline D. Hendrick; Steven A. Horton; Mey S. Kun; Phoebe West Koch; Tien Min Lee; C. McCabe; Sean McHale; Lauren D. McDaniel; Damian M. Menning; Kristy Jae Menning; Hamed Mirzaei-Souderjani; Salina Mostajabian; David Nicholson; Courtney K. Nugent; Nicholas P. Osman; Desiree I. Pappas; Andrea M. Rocha

The genome sequence of the obligate chemolithoautotroph Hydrogenovibrio crunogenus paradoxically predicts a complete oxidative citric acid cycle (CAC). This prediction was tested by multiple approaches including whole cell carbon assimilation to verify obligate autotrophy, phylogenetic analysis of CAC enzyme sequences and enzyme assays. Hydrogenovibrio crunogenus did not assimilate any of the organic compounds provided (acetate, succinate, glucose, yeast extract, tryptone). Enzyme activities confirmed that its CAC is mostly uncoupled from the NADH pool. 2-Oxoglutarate:ferredoxin oxidoreductase activity is absent, though pyruvate:ferredoxin oxidoreductase is present, indicating that sequence-based predictions of substrate for this oxidoreductase were incorrect, and that H. crunogenus may have an incomplete CAC. Though the H. crunogenus CAC genes encode uncommon enzymes, the taxonomic distribution of their top matches suggests that they were not horizontally acquired. Comparison of H. crunogenus CAC genes to those present in other Proteobacteria reveals that H. crunogenus and other obligate autotrophs lack the functional redundancy for the steps of the CAC typical for facultative autotrophs and heterotrophs, providing another possible mechanism for obligate autotrophy.


Biomarkers in Medicine | 2016

Identification of Apo B48 and other novel biomarkers in amyotrophic lateral sclerosis patient fibroblasts

Malathi Narayan; Kent W. Seeley; Umesh K. Jinwal

AIMnAmyotrophic lateral sclerosis (ALS) is a debilitating fatal neurodegenerative disorder. 90-95% of ALS cases are sporadic with no clear risk factors associated with the disease. Identification of biomarkers associated with ALS may lead to early detection and make it more amenable to therapeutic intervention.nnnMATERIALS & METHODSnSILAC was used to quantitatively analyze the proteomes of ALS and control human fibroblasts.nnnRESULTSnOut of total of 861 proteins identified, 33 were found to be differentially regulated. ApoB48 and Hsp20 were downregulated, while Fibulin-1 was upregulated.nnnCONCLUSIONnWe report the differential regulation of these proteins in ALS fibroblasts, and their potential as novel biomarkers and possible drug targets for ALS.


ACS Chemical Biology | 2015

Synthesis, Stereochemical Analysis, and Derivatization of Myricanol Provide New Probes That Promote Autophagic Tau Clearance

Mackenzie D. Martin; Laurent Calcul; Courtney A. Smith; Umesh K. Jinwal; Sarah N. Fontaine; April L. Darling; Kent W. Seeley; Lukasz Wojtas; Malathi Narayan; Jason E. Gestwicki; Garry R. Smith; Allen B. Reitz; Bill J. Baker; Chad A. Dickey

We previously discovered that one specific scalemic preparation of myricanol (1), a constituent of Myrica cerifera (bayberry/southern wax myrtle) root bark, could lower the levels of the microtubule-associated protein tau (MAPT). The significance is that tau accumulates in a number of neurodegenerative diseases, the most common being Alzheimers disease (AD). Herein, a new synthetic route to prepare myricanol using a suitable boronic acid pinacol ester intermediate is reported. An X-ray crystal structure of the isolated myricanol (1) was obtained and showed a co-crystal consisting of (+)-aR,11S-myricanol (2) and (-)-aS,11R-myricanol (3) coformers. Surprisingly, 3, obtained from chiral separation from 1, reduced tau levels in both cultured cells and ex vivo brain slices from a mouse model of tauopathy at reasonable mid-to-low micromolar potency, whereas 2 did not. SILAC proteomics and cell assays revealed that 3 promoted tau degradation through an autophagic mechanism, which was in contrast to that of other tau-lowering compounds previously identified by our group. During the course of structure-activity relationship (SAR) development, we prepared compound 13 by acid-catalyzed dehydration of 1. 13 had undergone an unexpected structural rearrangement through the isomyricanol substitution pattern (e.g., 16), as verified by X-ray structural analysis. Compound 13 displayed robust tau-lowering activity, and, importantly, its enantiomers reduced tau levels similarly. Therefore, the semisynthetic analogue 13 provides a foundation for further development as a tau-lowering agent without its SAR being based on chirality.


Data in Brief | 2016

Data from SILAC-based quantitative analysis of lysates from mouse microglial cells treated with Withaferin A (WA).

Malathi Narayan; Kent W. Seeley; Umesh K. Jinwal

Mass spectrometry data collected in a study analyzing the effect of withaferin A (WA) on a mouse microglial (N9) cell line is presented in this article. Data was collected from SILAC-based quantitative analysis of lysates from mouse microglial cells treated with either WA or DMSO vehicle control. This article reports all the proteins that were identified in this analysis. The data presented here is related to the published research article on the effect of WA on the differential regulation of proteins in mouse microglial cells [1]. Mass spectrometry data has also been deposited in the ProteomeXchange with the identifier PXD003032.


Journal of Archaeological Method and Theory | 2012

An Optimized Approach for Protein Residue Extraction and Identification from Ceramics After Cooking

Andrew Barker; Barney J. Venables; Stanley M. Stevens; Kent W. Seeley; Peggy Wang; Steve Wolverton

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Stanley M. Stevens

University of South Florida

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Malathi Narayan

University of South Florida

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Umesh K. Jinwal

University of South Florida

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Andrew Barker

University of North Texas

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Steve Wolverton

University of North Texas

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Alexandra Achille

University of South Florida

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Ana M. Garcia

University of South Florida

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Andrea M. Rocha

University of South Florida

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