Protein databases constructed by quantitative 2D gel analysis and protein identification from 2D gels

1992 ◽  
Vol 11 (4) ◽  
pp. 394-395
Author(s):  
James I. Garrels ◽  
B. Robert Franza ◽  
Scott D. Patterson ◽  
Keith Latham ◽  
Davor Solter ◽  
...  
Keyword(s):  
Protein Identification ◽  
Protein Databases ◽  
2D Gel ◽  
2D Gel Analysis

A Proteomic Approach to Discovery of Candidate Proteins Involved in the Transformation of Follicular Lymphoma.

Blood ◽  
2005 ◽  
Vol 106 (11) ◽  
pp. 984-984
Author(s):  
Guang Fan ◽  
Yanping Zhong ◽  
Cristina Smith ◽  
James Huang ◽  
Rita Braziel
Keyword(s):  
Western Blot ◽  
Blot Analysis ◽  
Gel Electrophoresis ◽  
Western Blot Analysis ◽  
Protein Identification ◽  
Differentially Expressed ◽  
Signal Transduction Pathways ◽  
Differentially Expressed Proteins ◽  
2D Gel ◽  
2D Gel Analysis

Abstract Background: Follicular lymphoma (FL) undergoes transformation to a high grade diffuse large B-cell lymphoma (tr-DLBCL) in about 50% of patients. During transformation, a more virulent subclone of tumor cells emerges, leading to a rapidly progressive clinical course and resistance to therapy. The identification of proteins involved in transformation is critical for understanding the mechanism of transformation and developing molecularly targeted therapy. In this study, we compared protein expression between grade 1- FL (G1-FL) and tr-DLBCL using 2D-gel electrophoresis and Western blot analysis. Design: Frozen tissue and frozen cells were obtained from the Department of Pathology, Oregon Health and Science University tumor bank. The protein expression profiles of 3 G1-FL and 3 tr-DLBCL were compared using 2D-gel electrophoresis. Protein identification was done using a MALDI mass spectrometer. Frozen cells of an additional 11 non-paired GI-FL and 11 non-paired tr-DLBCL, and 2 pairs of G1-FL and tr-DLBCL specimens were used for Western blot confirmation of the initial 2D-gel findings. Results: 2D-gel analysis and MALDI protein identification revealed 14 differentially expressed proteins between G1-FL and tr-DLBCL (figure 1), all of which are known to play important roles in cellular energy/metabolic pathways, signal transduction pathways, and protein and nuclear synthesis. The two most differentially expressed proteins on 2D-gel analysis were superoxide dismutase (MnSOD2) and growth factor receptor bound protein 2 (Grb2). Western blot analysis of MnSOD2 and Grb2 confirmed their relative over- or under-expression in frozen cells from multiple additional clinical lymphoma samples, including 2 paired- and 22 non-paired G1-FL and tr-DLBCL. Both 2D-gel analysis and Western Blot showed a significantly higher level of expression of MnSOD2 and a lower expression of Grb2 expression in tr-DLBCL (figure 2). Summary: Using proteomic profiling, confirmed by Western blot analysis of clinical G1-FL and tr-DLBCL samples, we have confirmed 2 proteins (MnSOD2 and Grb2) that are expressed at significantly different levels in G1-FL and DLBCL. MnSOD2 is capable of protecting cells from reactive oxygen species and regulating signal transduction pathways to influence cell growth and apoptosis. Inhibition of MnSOD2 has been shown in studies of several cancer cell lines to render cancer cells more susceptible to apoptosis. Grb2 is a member of a critical signaling pathway leading to Ras activation in hematopoietic cells. Both proteins may play a critical role in FL transformation. These proteins have the potential to be therapeutic drug targets, diagnostic and/or prognostic markers, or biomarkers for monitoring therapeutic response. Summary of Differentially Expressed Spots Summary of Differentially Expressed Spots Figure Figure

2D-gel analysis of proteins in chronic lymphocytic leukemia cells and normal B-lymphocytes

1993 ◽  
Vol 17 (3) ◽  
pp. 223-230 ◽  
Author(s):  
F.K. Saunders ◽  
R.M. Sharrard ◽  
D.A. Winfield ◽  
J. Lawry ◽  
J.R. Goepel ◽  
...  
Keyword(s):  
Chronic Lymphocytic Leukemia ◽  
B Lymphocytes ◽  
Lymphocytic Leukemia ◽  
Leukemia Cells ◽  
2D Gel ◽  
2D Gel Analysis

scholarly journals Rapid DNA preparation for 2D gel analysis of replication intermediates

1995 ◽  
Vol 23 (19) ◽  
pp. 3997-3998 ◽  
Author(s):  
Jia-Rui Wu ◽  
David M. Gilbert
Keyword(s):  
Dna Preparation ◽  
2D Gel ◽  
Replication Intermediates ◽  
2D Gel Analysis

2D-Gel Analysis of Protein Synthesis Profiles of Different Stages of Chronic Lymphocytic Leukaemia

1994 ◽  
Vol 14 (3-4) ◽  
pp. 319-322 ◽  
Author(s):  
F. Katharine Saunders ◽  
David A. Winfield ◽  
John R. Goepel ◽  
Barry W. Hancock ◽  
R. Michael Sharrard ◽  
...  
Keyword(s):  
Protein Synthesis ◽  
Chronic Lymphocytic Leukaemia ◽  
Lymphocytic Leukaemia ◽  
2D Gel ◽  
2D Gel Analysis

Abstract 1096: Predictors Of Carotid Intimal-medial Thickness In Subjects With Hyperalphalipoproteinemia

Circulation ◽  
2007 ◽  
Vol 116 (suppl_16) ◽  
Author(s):  
Michael West ◽  
Bela Asztalos ◽  
Toni Pollin ◽  
Wendy Post ◽  
Annabelle Rodriguez
Keyword(s):  
Lipid Level ◽  
Subclinical Atherosclerosis ◽  
Hdl Cholesterol ◽  
Multiple Regression Model ◽  
Community Dwelling ◽  
Cvd Risk ◽  
Carotid Imt ◽  
Intimal Medial Thickness ◽  
2D Gel ◽  
2D Gel Analysis

HDL cholesterol (HDL-C) is inversely associated with risk for CVD in the general population. However, the metabolic pathways leading to high HDL (hyperalphalipoproteinemia) are complex, and some patients with high HDL-C are not protected against atherosclerotic disease. The purpose of this study was to determine the associations between CVD risk factors, especially HDL subpopulations, and subclinical vascular disease in patients with high HDL-C. Community-dwelling adult subjects with and without CAD between the ages of 18 – 80 years with HDL-C levels above 60 mg/dl were recruited for this study (n=46, 34 women and 12 men, mean age 58.7 ± 9.7 years). After an overnight fast, blood was obtained for measurement of lipids, inflammatory markers and lipoproteins by NMR spectroscopy (Liposcience, NC) and 2D-gel analysis. Far wall common carotid artery intimal-medial thickness (IMT) was measured using carotid ultrasonography. None of the subjects were taking statins. The lipid levels (mean ± SD) were total cholesterol 225.6 ± 37.9 mg/dl, triglycerides 77.9 ± 29.4 mg/dl, HDL 90.4 ± 22.5 mg/dl and LDL 119.6 ± 33.4 mg/dl. Carotid IMT values were normally distributed, with a range of 0.46 –1.1 mm. Unadjusted pairwise-correlations showed that carotid IMT was significantly associated with LDL particle number ( p< 0.03), HDL subpopulations by 2D-gel analysis [α-3: p< 0.005; α-4: p< 0.04; and preα-1: p< 0.03], C-reactive protein ( p< 0.03), sVCAM-1 ( p< 0.02), age ( p< 0.0008), systolic blood pressure ( p< 0.02), heart rate ( p< 0.02) and corneal arcus ( p< 0.04). Carotid IMT was not associated with any traditional lipid level, gender or history of CAD. In a multiple regression model, age ( p =0.0007), α-3 ( p< 0.008) and CRP ( p< 0.03) were significant independent predictors of carotid IMT in this population. Thus, in subjects with hyperalphalipoproteinemia, increased small, dense HDL (α-3) and CRP levels were associated with increasing carotid IMT, suggesting heterogeneity in the role of HDL particles on subclinical atherosclerosis.

What's news: Comprehensive computerized 2d gel protein databases offer a global approach to the study of the mammalian cell

BioEssays ◽  
1990 ◽  
Vol 12 (2) ◽  
pp. 93-97 ◽  
Author(s):  
Julio E. Celis ◽  
Bent Honoré ◽  
Guy Bauw ◽  
Joel Vandekerckhove
Keyword(s):  
Mammalian Cell ◽  
Global Approach ◽  
Protein Databases ◽  
2D Gel

scholarly journals Metaproteomics approaches and techniques: A review

2017 ◽  
Vol 3 (5) ◽  
pp. 49
Author(s):  
Ayesha Ameen ◽  
Shahid Raza
Keyword(s):  
Mass Spectrometry ◽  
Microbial Community ◽  
Gel Electrophoresis ◽  
Protein Identification ◽  
2D Gel Electrophoresis ◽  
Computational Tools ◽  
2D Gel ◽  
Identification Function ◽  
Related Proteins ◽  
Proteins And Peptides

Extensive studies have been done on metagenomics for various microbial communities. The advancements in metagenomics level led to the need of metaproteomics approaches. Metaproteomics involve the identification, function and expression of various proteins present in microbial community, it also involves the identification and expression analysis of stress related proteins. The concepts of metaproteomics come with advancement in proteomics techniques which includes 2D gel electrophoresis for the identification of proteins and peptides in a particular microbial community. Mass spectrometry which is used to separate the proteins by desorption and ionization using a gas on a liquid medium. MALDI use for protein identification and separation, connected with TOF to give better results. The metaproteomics approaches become more advanced when HPLC and LC were used for peptides and protein with computational tools to sequence the peptide and protein. It is concluded that there is a requirement of research in metaproteomics. Many scientists have done research on these approaches but there is lack of better quality and desirable results.

scholarly journals Method for Rapid Protein Identification in a Large Database

2013 ◽  
Vol 2013 ◽  
pp. 1-7 ◽  
Author(s):  
Wenli Zhang ◽  
Xiaofang Zhao
Keyword(s):  
Mass Spectrometry ◽  
Protein Identification ◽  
Mass Spectrometry Data ◽  
Large Database ◽  
Protein Database ◽  
Complex Samples ◽  
Protein Databases ◽  
Linear Speedup ◽  
Proteomics Research ◽  
Computer Resources

Protein identification is an integral part of proteomics research. The available tools to identify proteins in tandem mass spectrometry experiments are not optimized to face current challenges in terms of identification scale and speed owing to the exponential growth of the protein database and the accelerated generation of mass spectrometry data, as well as the demand for nonspecific digestion and post-modifications in complex-sample identification. As a result, a rapid method is required to mitigate such complexity and computation challenges. This paper thus aims to present an open method to prevent enzyme and modification specificity on a large database. This paper designed and developed a distributed program to facilitate application to computer resources. With this optimization, nearly linear speedup and real-time support are achieved on a large database with nonspecific digestion, thus enabling testing with two classical large protein databases in a 20-blade cluster. This work aids in the discovery of more significant biological results, such as modification sites, and enables the identification of more complex samples, such as metaproteomics samples.

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