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Università Cattolica del Sacro Cuore (Catholic University of the Sacred Heart)

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Papers by Angela Walker

Research paper thumbnail of Temporal Quantitative Proteomics by iTRAQ 2D-LC-MS/MS and Corresponding mRNA Expression Analysis Identify Post-Transcriptional Modulation of Actin-Cytoskeleton Regulators During TGF-β-Induced Epithelial-Mesenchymal Transition

Journal of Proteome Research, 2009

To gain insights into how TGF-beta regulates epithelial-mesenchymal transition (EMT), we assessed... more To gain insights into how TGF-beta regulates epithelial-mesenchymal transition (EMT), we assessed the time course of proteins and mRNAs during EMT by multiplex iTRAQ labeling and 2D-LC-MS/MS, and by hybridization, respectively. Temporal iTRAQ analysis identified 66 proteins as differentially expressed during EMT, including newly associated proteins calpain, fascin and macrophage-migration inhibitory factor (MIF). Comparing protein and mRNA expression overtime showed that all the 14 up-regulated proteins involved in the actin-cytoskeleton remodeling were accompanied by increases in corresponding mRNA expression. Interestingly, siRNA mediated knockdown of cofilin1 potentiated TGF-beta-induced EMT. Further analysis of cofilin1 and beta-actin revealed an increase in their mRNA stability in response to TGF-beta, contributing to the observed increase in mRNA and protein expression. These results are the first demonstration of post-transcriptional regulation of cytoskeletal remodelling and a key role for cofilin1 during TGF-beta-induced EMT.

Research paper thumbnail of Quantitative Organellar Proteomics Analysis of Rough Endoplasmic Reticulum from Normal and Acute Pancreatitis Rat Pancreas

Journal of Proteome Research, 2010

The rough endoplasmic reticulum (RER) is a central organelle for synthesizing and processing dige... more The rough endoplasmic reticulum (RER) is a central organelle for synthesizing and processing digestive enzymes and alteration of ER functions may participate in the pathogenesis of acute pancreatitis (AP). To comprehensively characterize the normal and diseased RER subproteome, this study quantitatively compared the protein compositions of pancreatic RER between normal and AP animals using isobaric tags (iTRAQ) and 2D LC-MALDI-MS/MS. A total of 469 unique proteins were revealed from four independent experiments using two different AP models. These proteins belong to a large number of functional categories including ribosomal proteins, translocon subunits, chaperones, secretory proteins, and glyco-and lipid-processing enzymes. 37 RER proteins (25 unique in arginine-induced, 6 unique in caerulein-induced and 6 common in both models of AP) showed significant changes during AP including translational regulators and digestive enzymes whereas only mild changes were found in some ER chaperones. The six proteins common to both AP models including a decrease in pancreatic triacylglycerol lipase precursor, Erp27, and prolyl 4-hydroxylase beta polypeptide as well as a dramatic increase in fibrinogen alpha, beta and gamma chains. These results suggest that the early stages of AP involve changes of multiple RER proteins that may affect the synthesis and processing of digestive enzymes.

Research paper thumbnail of The development of MALDI mass spectrometry for the investigation of surface-protein interactions

Research paper thumbnail of Corrigendum: A HUPO test sample study reveals common problems in mass spectrometry–based proteomics

Nature Methods, 2009

In the version of this article initially published, the author name Steven A. Carr was spelled in... more In the version of this article initially published, the author name Steven A. Carr was spelled incorrectly, and the name of an organization described in the text, the HUPO Proteomics Standards Initiative (PSI), was given incorrectly. These errors have been corrected in the PDF and HTML versions of this article.

Research paper thumbnail of Response to comment on" protein sequences from mastodon and tyrannosaurus rex revealed by mass spectrometry

Science, 2007

Endogenous peptide sequences extracted from a 68-million-year-old Tyrannosaurus rex fossil bone a... more Endogenous peptide sequences extracted from a 68-million-year-old Tyrannosaurus rex fossil bone and obtained by mass spectrometry have been shown to be statistically significant based on protein database searches using two different search engines and similarity comparisons to authentic tandem mass spectrometry spectra. Specifically, we have validated the sequence GVVGLP (OH) GQR.

Research paper thumbnail of Reactive Oxygen Species Special Feature: Quantifying changes in the thiol redox proteome upon oxidative stress in vivo

Research paper thumbnail of Reactive Oxygen Species Special Feature: Quantifying changes in the thiol redox proteome upon oxidative stress in vivo

Research paper thumbnail of Comment on "Protein Sequences from Mastodon and Tyrannosaurus rex Revealed by Mass Spectrometry

Science, 2008

We use authentication tests developed for ancient DNA to evaluate claims by Asara et al. of colla... more We use authentication tests developed for ancient DNA to evaluate claims by Asara et al. of collagen peptide sequences recovered from mastodon and Tyrannosaurus rex fossils. Although the mastodon passes, absence of amino acid composition data, lack of evidence for peptide deamidation, and association of the α1(I) peptide sequences with amphibians not birds, suggests that T. rex does not.

Research paper thumbnail of MALDI MS of Proteins Adsorbed to Modified and Unmodified Polymer Substrates

Research paper thumbnail of MALDI Mass Spectrometric Probes of Biomolecule Adsorption to Pulsed RF Plasma Modified Surfaces

Research paper thumbnail of Influence of Sample Preparation and Surface-Protein Interactions on Analyte Ionization by MALDI

Research paper thumbnail of MALDI MS as a Method for Studying Surface-Protein Interactions

Research paper thumbnail of Matrix-assisted laser desorption/ionization mass spectrometry for the quantification of protein adsorption to polymeric surfaces

Research paper thumbnail of DEFINING THE LIMITS OF MOLECULAR PHYLOGENY: THE FIRST COMPLETE PROTEIN SEQUENCE OF A 42 KA EQUUS FROM WYOMING

Research paper thumbnail of MS-Expedite: Graphical Tool For Annotation Of Spectra And Centroided Peaklists

Research paper thumbnail of Proactive care planning in diabetes: The benefit of enhanced primary and secondary care interaction

Research paper thumbnail of of Journal: Science

Research paper thumbnail of Proteomic analysis of the effects of BMP4 exposure on human embryonic stem cells. HUPO 7 th Annual World Congress, Amsterdam, The Netherlands, 16-20 August 2008

Research paper thumbnail of J. 16 R. Maddock. 2006. The Escherichia coli GTPase CgtAE is involved in late steps of 17 large ribosome assembly

Research paper thumbnail of Virtual 2-D Gel Electrophoresis by MALDI Mass Spectrometry

The Proteomics Protocols Handbook, 2005

ABSTRACT Two-dimensional (2-D) gel electrophoresis (2-DE) is capable of separating several hundre... more ABSTRACT Two-dimensional (2-D) gel electrophoresis (2-DE) is capable of separating several hundred to thousands of proteins on a single gel, depending on the format (1,2). The most commonly used methods for visualization of proteins in gels include Coomassie Brilliant Blue (CBB), silver stains, or fluorescent stains (1–3). Each staining method exhibits different levels of overall sensitivity, and they vary widely in their relative sensitivities for specific proteins. Two-dimensional gels also allow only the approximate sizes of proteins to be determined. It is desirable to develop methods that combine the high resolution of electrophoretic separations with the accurate mass measurements that can be provided by mass spectrometry (MS).

Research paper thumbnail of Temporal Quantitative Proteomics by iTRAQ 2D-LC-MS/MS and Corresponding mRNA Expression Analysis Identify Post-Transcriptional Modulation of Actin-Cytoskeleton Regulators During TGF-β-Induced Epithelial-Mesenchymal Transition

Journal of Proteome Research, 2009

To gain insights into how TGF-beta regulates epithelial-mesenchymal transition (EMT), we assessed... more To gain insights into how TGF-beta regulates epithelial-mesenchymal transition (EMT), we assessed the time course of proteins and mRNAs during EMT by multiplex iTRAQ labeling and 2D-LC-MS/MS, and by hybridization, respectively. Temporal iTRAQ analysis identified 66 proteins as differentially expressed during EMT, including newly associated proteins calpain, fascin and macrophage-migration inhibitory factor (MIF). Comparing protein and mRNA expression overtime showed that all the 14 up-regulated proteins involved in the actin-cytoskeleton remodeling were accompanied by increases in corresponding mRNA expression. Interestingly, siRNA mediated knockdown of cofilin1 potentiated TGF-beta-induced EMT. Further analysis of cofilin1 and beta-actin revealed an increase in their mRNA stability in response to TGF-beta, contributing to the observed increase in mRNA and protein expression. These results are the first demonstration of post-transcriptional regulation of cytoskeletal remodelling and a key role for cofilin1 during TGF-beta-induced EMT.

Research paper thumbnail of Quantitative Organellar Proteomics Analysis of Rough Endoplasmic Reticulum from Normal and Acute Pancreatitis Rat Pancreas

Journal of Proteome Research, 2010

The rough endoplasmic reticulum (RER) is a central organelle for synthesizing and processing dige... more The rough endoplasmic reticulum (RER) is a central organelle for synthesizing and processing digestive enzymes and alteration of ER functions may participate in the pathogenesis of acute pancreatitis (AP). To comprehensively characterize the normal and diseased RER subproteome, this study quantitatively compared the protein compositions of pancreatic RER between normal and AP animals using isobaric tags (iTRAQ) and 2D LC-MALDI-MS/MS. A total of 469 unique proteins were revealed from four independent experiments using two different AP models. These proteins belong to a large number of functional categories including ribosomal proteins, translocon subunits, chaperones, secretory proteins, and glyco-and lipid-processing enzymes. 37 RER proteins (25 unique in arginine-induced, 6 unique in caerulein-induced and 6 common in both models of AP) showed significant changes during AP including translational regulators and digestive enzymes whereas only mild changes were found in some ER chaperones. The six proteins common to both AP models including a decrease in pancreatic triacylglycerol lipase precursor, Erp27, and prolyl 4-hydroxylase beta polypeptide as well as a dramatic increase in fibrinogen alpha, beta and gamma chains. These results suggest that the early stages of AP involve changes of multiple RER proteins that may affect the synthesis and processing of digestive enzymes.

Research paper thumbnail of The development of MALDI mass spectrometry for the investigation of surface-protein interactions

Research paper thumbnail of Corrigendum: A HUPO test sample study reveals common problems in mass spectrometry–based proteomics

Nature Methods, 2009

In the version of this article initially published, the author name Steven A. Carr was spelled in... more In the version of this article initially published, the author name Steven A. Carr was spelled incorrectly, and the name of an organization described in the text, the HUPO Proteomics Standards Initiative (PSI), was given incorrectly. These errors have been corrected in the PDF and HTML versions of this article.

Research paper thumbnail of Response to comment on" protein sequences from mastodon and tyrannosaurus rex revealed by mass spectrometry

Science, 2007

Endogenous peptide sequences extracted from a 68-million-year-old Tyrannosaurus rex fossil bone a... more Endogenous peptide sequences extracted from a 68-million-year-old Tyrannosaurus rex fossil bone and obtained by mass spectrometry have been shown to be statistically significant based on protein database searches using two different search engines and similarity comparisons to authentic tandem mass spectrometry spectra. Specifically, we have validated the sequence GVVGLP (OH) GQR.

Research paper thumbnail of Reactive Oxygen Species Special Feature: Quantifying changes in the thiol redox proteome upon oxidative stress in vivo

Research paper thumbnail of Reactive Oxygen Species Special Feature: Quantifying changes in the thiol redox proteome upon oxidative stress in vivo

Research paper thumbnail of Comment on "Protein Sequences from Mastodon and Tyrannosaurus rex Revealed by Mass Spectrometry

Science, 2008

We use authentication tests developed for ancient DNA to evaluate claims by Asara et al. of colla... more We use authentication tests developed for ancient DNA to evaluate claims by Asara et al. of collagen peptide sequences recovered from mastodon and Tyrannosaurus rex fossils. Although the mastodon passes, absence of amino acid composition data, lack of evidence for peptide deamidation, and association of the α1(I) peptide sequences with amphibians not birds, suggests that T. rex does not.

Research paper thumbnail of MALDI MS of Proteins Adsorbed to Modified and Unmodified Polymer Substrates

Research paper thumbnail of MALDI Mass Spectrometric Probes of Biomolecule Adsorption to Pulsed RF Plasma Modified Surfaces

Research paper thumbnail of Influence of Sample Preparation and Surface-Protein Interactions on Analyte Ionization by MALDI

Research paper thumbnail of MALDI MS as a Method for Studying Surface-Protein Interactions

Research paper thumbnail of Matrix-assisted laser desorption/ionization mass spectrometry for the quantification of protein adsorption to polymeric surfaces

Research paper thumbnail of DEFINING THE LIMITS OF MOLECULAR PHYLOGENY: THE FIRST COMPLETE PROTEIN SEQUENCE OF A 42 KA EQUUS FROM WYOMING

Research paper thumbnail of MS-Expedite: Graphical Tool For Annotation Of Spectra And Centroided Peaklists

Research paper thumbnail of Proactive care planning in diabetes: The benefit of enhanced primary and secondary care interaction

Research paper thumbnail of of Journal: Science

Research paper thumbnail of Proteomic analysis of the effects of BMP4 exposure on human embryonic stem cells. HUPO 7 th Annual World Congress, Amsterdam, The Netherlands, 16-20 August 2008

Research paper thumbnail of J. 16 R. Maddock. 2006. The Escherichia coli GTPase CgtAE is involved in late steps of 17 large ribosome assembly

Research paper thumbnail of Virtual 2-D Gel Electrophoresis by MALDI Mass Spectrometry

The Proteomics Protocols Handbook, 2005

ABSTRACT Two-dimensional (2-D) gel electrophoresis (2-DE) is capable of separating several hundre... more ABSTRACT Two-dimensional (2-D) gel electrophoresis (2-DE) is capable of separating several hundred to thousands of proteins on a single gel, depending on the format (1,2). The most commonly used methods for visualization of proteins in gels include Coomassie Brilliant Blue (CBB), silver stains, or fluorescent stains (1–3). Each staining method exhibits different levels of overall sensitivity, and they vary widely in their relative sensitivities for specific proteins. Two-dimensional gels also allow only the approximate sizes of proteins to be determined. It is desirable to develop methods that combine the high resolution of electrophoretic separations with the accurate mass measurements that can be provided by mass spectrometry (MS).

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