Joel Sevinsky
University of Colorado Boulder
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Featured researches published by Joel Sevinsky.
Molecular & Cellular Proteomics | 2005
William M. Old; Karen Meyer-Arendt; Lauren D. Aveline-Wolf; Kevin G. Pierce; Alex M. Mendoza; Joel Sevinsky; Katheryn A. Resing; Natalie G. Ahn
Measurements of mass spectral peak intensities and spectral counts are promising methods for quantifying protein abundance changes in shotgun proteomic analyses. We describe Serac, software developed to evaluate the ability of each method to quantify relative changes in protein abundance. Dynamic range and linearity using a three-dimensional ion trap were tested using standard proteins spiked into a complex sample. Linearity and good agreement between observed versus expected protein ratios were obtained after normalization and background subtraction of peak area intensity measurements and correction of spectral counts to eliminate discontinuity in ratio estimates. Peak intensity values useful for protein quantitation ranged from 107 to 1011 counts with no obvious saturation effect, and proteins in replicate samples showed variations of less than 2-fold within the 95% range (±2ς) when ≥3 peptides/protein were shared between samples. Protein ratios were determined with high confidence from spectral counts when maximum spectral counts were ≥4 spectra/protein, and replicates showed equivalent measurements well within 95% confidence limits. In further tests, complex samples were separated by gel exclusion chromatography, quantifying changes in protein abundance between different fractions. Linear behavior of peak area intensity measurements was obtained for peptides from proteins in different fractions. Protein ratios determined by spectral counting agreed well with those determined from peak area intensity measurements, and both agreed with independent measurements based on gel staining intensities. Overall spectral counting proved to be a more sensitive method for detecting proteins that undergo changes in abundance, whereas peak area intensity measurements yielded more accurate estimates of protein ratios. Finally these methods were used to analyze differential changes in protein expression in human erythroleukemia K562 cells stimulated under conditions that promote cell differentiation by mitogen-activated protein kinase pathway activation. Protein changes identified with p < 0.1 showed good correlations with parallel measurements of changes in mRNA expression.
Molecular and Cellular Biology | 2004
Joel Sevinsky; Anne M. Whalen; Natalie G. Ahn
ABSTRACT Extracellular signal-regulated kinase (ERK) facilitates cell cycle progression in most mammalian cells, but in certain cell types prolonged signaling through this pathway promotes differentiation and lineage-specific gene expression through mechanisms that are poorly understood. Here, we characterize the transcriptional regulation of platelet GPIIb integrin (CD41) by ERK during megakaryocyte differentiation. ERK-dependent transactivation involves the proximal promoter of GPIIb within 114 bp upstream of the transcriptional start site. GATA, Ets, and Sp1 consensus sequences within this region are each necessary and function combinatorially in ERK-activated transcription. MafB/Kreisler is induced in response to ERK and synergizes with GATA and Ets to enhance transcription from the proximal promoter. The requirement for MafB in promoter regulation is demonstrated by inhibition of transactivation following dominant-negative or antisense suppression of MafB function. Thus, ERK promotes megakaryocyte differentiation by coordinate regulation of nuclear factors that synergize in GPIIb promoter regulation. These results establish a novel role for MafB as a regulator of ERK-induced gene expression.
Journal of Theoretical Biology | 2006
Joshua Downer; Joel Sevinsky; Natalie G. Ahn; Katheryn A. Resing; M.D. Betterton
Integrating biological information from different sources to understand cellular processes is an important problem in systems biology. We use data from mRNA expression arrays and chemical kinetics to formulate a metabolic model relevant to K562 erythroleukemia cells. MAP kinase pathway activation alters the expression of metabolic enzymes in K562 cells. Our array data show changes in expression of lactate dehydrogenase (LDH) isoforms after treatment with phorbol 12-myristate 13-acetate (PMA), which activates MAP kinase signaling. We model the change in lactate production which occurs when the MAP kinase pathway is activated, using a non-equilibrium, chemical-kinetic model of homolactic fermentation. In particular, we examine the role of LDH isoforms, which catalyse the conversion of pyruvate to lactate. Changes in the isoform ratio are not the primary determinant of the production of lactate. Rather, the total concentration of LDH controls the lactate concentration.
Journal of biomolecular techniques | 2005
Benjamin J. Cargile; Joel Sevinsky; Amal S. Essader; James L. Stephenson; Jonathan L. Bundy
Analytical Chemistry | 2007
Joel Sevinsky; Kristy J. Brown; Benjamin J. Cargile; Jonathan L. Bundy; James L. Stephenson
Journal of Proteome Research | 2007
Maureen K. Bunger; Benjamin J. Cargile; Joel Sevinsky; Ekaterina G. Deyanova; Nathan A. Yates; Ronald C. Hendrickson; James L. Stephenson
Journal of Proteome Research | 2008
Joel Sevinsky; Benjamin J. Cargile; Maureen K. Bunger; Fanyu Meng; Nathan A. Yates; Ronald C. Hendrickson; James L. Stephenson
Archive | 2008
Benjamin J. Cargile; Joel Sevinsky; Amal S. Essader; J Eu; James L. Stephenson
Journal of biomolecular techniques | 2007
Joel Sevinsky; Benjamin J. Cargile; Amal S. Essader; J. P. Eu; James L. Stephenson
Molecular & Cellular Proteomics | 2006
Maureen Bunger; Benjamin J. Cargile; Joel Sevinsky; James L. Stephenson