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

Narayan, Malathi / Seeley, Kent W / Jinwal, Umesh K

2016 Volume 7, Page(s) 747–750

Abstract: 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 ... ...

Abstract	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.
Language	English
Publishing date	2016-03-14
Publishing country	Netherlands
Document type	Journal Article
ZDB-ID	2786545-9
ISSN	2352-3409
ISSN	2352-3409
DOI	10.1016/j.dib.2016.03.026
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Article ; Online: Identification of Apo B48 and other novel biomarkers in amyotrophic lateral sclerosis patient fibroblasts.

Narayan, Malathi / Seeley, Kent W / Jinwal, Umesh K

Biomarkers in medicine

2016 Volume 10, Issue 5, Page(s) 453–462

Abstract: Aim: Amyotrophic 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 ... ...

Abstract	Aim: Amyotrophic 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. Materials & methods: SILAC was used to quantitatively analyze the proteomes of ALS and control human fibroblasts. Results: Out of total of 861 proteins identified, 33 were found to be differentially regulated. ApoB48 and Hsp20 were downregulated, while Fibulin-1 was upregulated. Conclusion: We report the differential regulation of these proteins in ALS fibroblasts, and their potential as novel biomarkers and possible drug targets for ALS.
MeSH term(s)	Aged ; Amyotrophic Lateral Sclerosis/diagnosis ; Amyotrophic Lateral Sclerosis/metabolism ; Biomarkers/metabolism ; Calcium-Binding Proteins/metabolism ; Cells, Cultured ; Chromatography, High Pressure Liquid ; Down-Regulation ; Female ; Fibroblasts/cytology ; Fibroblasts/metabolism ; HSP20 Heat-Shock Proteins/metabolism ; Humans ; Male ; Metabolic Networks and Pathways ; Middle Aged ; Proteomics ; Receptors, Lipoprotein/metabolism ; Tandem Mass Spectrometry ; Up-Regulation
Chemical Substances	Biomarkers ; Calcium-Binding Proteins ; HSP20 Heat-Shock Proteins ; Receptors, Lipoprotein ; apo B48 receptor ; fibulin
Language	English
Publishing date	2016-05
Publishing country	England
Document type	Journal Article
ZDB-ID	2481014-9
ISSN	1752-0371 ; 1752-0363
ISSN (online)	1752-0371
ISSN	1752-0363
DOI	10.2217/bmm-2016-0025
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Article: Data from SILAC-based quantitative analysis of lysates from mouse microglial cells treated with Withaferin A (WA)

Narayan, Malathi / Seeley, Kent W. / Jinwal, Umesh K.

Data in Brief. 2016 June, v. 7

2016

Abstract	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 http://www.ebi.ac.uk/pride/archive/projects/PXD003032.
Keywords	cell lines ; mass spectrometry ; mice ; quantitative analysis
Language	English
Dates of publication	2016-06
Size	p. 747-750.
Publishing place	Elsevier Inc.
Document type	Article
ZDB-ID	2786545-9
ISSN	2352-3409
ISSN	2352-3409
DOI	10.1016/j.dib.2016.03.026
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Article ; Online: Investigation of local primary structure effects on peroxynitrite-mediated tyrosine nitration using targeted mass spectrometry.

Seeley, Kent W / Stevens, Stanley M

Journal of proteomics

2012 Volume 75, Issue 6, Page(s) 1691–1700

Abstract: 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 ... ...

Abstract	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.
MeSH term(s)	Amino Acid Sequence ; Molecular Sequence Data ; Oligopeptides/chemistry ; Peroxynitrous Acid/chemistry ; Protein Processing, Post-Translational ; Proteins/chemistry ; Serum Albumin, Bovine/chemistry ; Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization/methods ; Tyrosine/analogs & derivatives ; Tyrosine/chemical synthesis ; Tyrosine/chemistry
Chemical Substances	Oligopeptides ; Proteins ; Peroxynitrous Acid (14691-52-2) ; Serum Albumin, Bovine (27432CM55Q) ; 3-nitrotyrosine (3604-79-3) ; Tyrosine (42HK56048U)
Language	English
Publishing date	2012-03-16
Publishing country	Netherlands
Document type	Journal Article
ZDB-ID	2400835-7
ISSN	1876-7737 ; 1874-3919
ISSN (online)	1876-7737
ISSN	1874-3919
DOI	10.1016/j.jprot.2011.11.025
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Article ; Online: Identification and quantitative analysis of cellular proteins affected by treatment with withaferin a using a SILAC-based proteomics approach.

Narayan, Malathi / Seeley, Kent W / Jinwal, Umesh K

Journal of ethnopharmacology

2015 Volume 175, Page(s) 86–92

Abstract: Ethnopharmacological relevance: Withaferin 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 ... ...

Abstract	Ethnopharmacological relevance: Withaferin 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. Materials and methods: In 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. Results: Using 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. Conclusions: SILAC-based proteomics analysis of a microglial cell model revealed several novel proteins whose expression is regulated by WA and probable pathways regulated by WA.
MeSH term(s)	Animals ; Annexin A1/metabolism ; Carbohydrate Metabolism ; Cell Death ; Cell Line ; Cell Survival ; Heat-Shock Proteins/metabolism ; Isotope Labeling/methods ; Mass Spectrometry ; Mice ; Microglia/drug effects ; Microglia/metabolism ; Proteomics ; Withanolides/pharmacology
Chemical Substances	Annexin A1 ; Heat-Shock Proteins ; Withanolides ; withaferin A (L6DO3QW4K5)
Language	English
Publishing date	2015-12-04
Publishing country	Ireland
Document type	Journal Article
ZDB-ID	134511-4
ISSN	1872-7573 ; 0378-8741
ISSN (online)	1872-7573
ISSN	0378-8741
DOI	10.1016/j.jep.2015.09.024
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Article ; Online: Klebsiella pneumoniae O antigen loss alters the outer membrane protein composition and the selective packaging of proteins into secreted outer membrane vesicles.

Cahill, Bethaney K / Seeley, Kent W / Gutel, Dedra / Ellis, Terri N

Microbiological research

2015 Volume 180, Page(s) 1–10

Abstract: 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 ... ...

Abstract	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.
MeSH term(s)	Bacterial Outer Membrane Proteins/isolation & purification ; Bacterial Outer Membrane Proteins/metabolism ; Cell Membrane/metabolism ; Klebsiella pneumoniae/cytology ; Klebsiella pneumoniae/genetics ; Klebsiella pneumoniae/immunology ; Klebsiella pneumoniae/metabolism ; Molecular Chaperones/metabolism ; Mutation ; O Antigens/genetics ; O Antigens/metabolism ; Protein Processing, Post-Translational ; Protein Transport ; Proteome/genetics ; Proteome/secretion ; Tandem Mass Spectrometry ; Virulence Factors/metabolism
Chemical Substances	Bacterial Outer Membrane Proteins ; Molecular Chaperones ; O Antigens ; Proteome ; Virulence Factors
Language	English
Publishing date	2015-11
Publishing country	Germany
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	1189614-0
ISSN	1618-0623 ; 0944-5013
ISSN (online)	1618-0623
ISSN	0944-5013
DOI	10.1016/j.micres.2015.06.012
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Article: Investigation of local primary structure effects on peroxynitrite-mediated tyrosine nitration using targeted mass spectrometry

Seeley, Kent W / Stevens, Stanley M., Jr

Journal of proteomics. 2012 Mar. 16, v. 75, no. 6

2012

Abstract	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.
Keywords	hydrophobicity ; mass spectrometry ; post-translational modification ; prediction ; tyrosine
Language	English
Dates of publication	2012-0316
Size	p. 1691-1700.
Publishing place	Elsevier B.V.
Document type	Article
ZDB-ID	2400835-7
ISSN	1876-7737 ; 1874-3919
ISSN (online)	1876-7737
ISSN	1874-3919
DOI	10.1016/j.jprot.2011.11.025
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Article ; Online: 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.

Seeley, Kent W / Fertig, Alison R / Dufresne, Craig P / Pinho, Joao P C / Stevens, Stanley M

International journal of molecular sciences

2014 Volume 15, Issue 4, Page(s) 6265–6285

Abstract: 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 ... ...

Abstract	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.
MeSH term(s)	Angiotensin I/chemistry ; Angiotensin I/metabolism ; Animals ; Cattle ; Cell Line ; Chromatography, High Pressure Liquid ; Fourier Analysis ; Isotope Labeling ; Mass Spectrometry ; Nitrogen Isotopes/chemistry ; Peroxynitrous Acid/chemistry ; Rats ; Serum Albumin, Bovine/chemistry ; Serum Albumin, Bovine/metabolism ; Tandem Mass Spectrometry ; Tyrosine/analogs & derivatives ; Tyrosine/analysis
Chemical Substances	Nitrogen Isotopes ; Peroxynitrous Acid (14691-52-2) ; Serum Albumin, Bovine (27432CM55Q) ; 3-nitrotyrosine (3604-79-3) ; Tyrosine (42HK56048U) ; Angiotensin I (9041-90-1)
Language	English
Publishing date	2014-04-14
Publishing country	Switzerland
Document type	Journal Article ; Research Support, N.I.H., Extramural
ZDB-ID	2019364-6
ISSN	1422-0067 ; 1422-0067 ; 1661-6596
ISSN (online)	1422-0067
ISSN	1422-0067 ; 1661-6596
DOI	10.3390/ijms15046265
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Article ; Online: 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.

Stevens, Stanley M / Wolverton, Steve / Venables, Barney / Barker, Andrew / Seeley, Kent W / Adhikari, Prem

Analytical and bioanalytical chemistry

2010 Volume 396, Issue 4, Page(s) 1491–1499

Abstract: 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 ... ...

Abstract	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.
MeSH term(s)	Amino Acid Sequence ; Animals ; Archaeology/methods ; Cattle ; Chromatography, High Pressure Liquid ; Inorganic Chemicals/chemistry ; Microwaves ; Molecular Sequence Data ; Peptides/analysis ; Peptides/chemistry ; Proteins/analysis ; Proteins/chemistry ; Serum Albumin, Bovine ; Tandem Mass Spectrometry ; Trypsin/chemistry
Chemical Substances	Inorganic Chemicals ; Peptides ; Proteins ; Serum Albumin, Bovine (27432CM55Q) ; Trypsin (EC 3.4.21.4)
Language	English
Publishing date	2010-02
Publishing country	Germany
Document type	Evaluation Studies ; Journal Article ; Research Support, Non-U.S. Gov't ; Research Support, U.S. Gov't, Non-P.H.S.
ZDB-ID	201093-8
ISSN	1618-2650 ; 0016-1152 ; 0372-7920
ISSN (online)	1618-2650
ISSN	0016-1152 ; 0372-7920
DOI	10.1007/s00216-009-3341-4
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Article: 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

Stevens, Stanley M. Jr / Wolverton, Steve / Venables, Barney / Barker, Andrew / Seeley, Kent W / Adhikari, Prem

Analytical and bioanalytical chemistry. 2010 Feb., v. 396, no. 4

2010

Abstract	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.
Language	English
Dates of publication	2010-02
Size	p. 1491-1499.
Publisher	Springer-Verlag
Publishing place	Berlin/Heidelberg
Document type	Article
ISSN	1618-2642
DOI	10.1007/s00216-009-3341-4
Database	NAL-Catalogue (AGRICOLA)

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