Changes in protein abundance between tender and tough meat from bovine Longissimus thoracis muscle assessed by isobaric Tag for Relative and Absolute Quantitation (iTRAQ) and 2-dimensional gel electrophoresis analysis1

2012 ◽  
Vol 90 (6) ◽  
pp. 2035-2043 ◽  
Author(s):  
S. G. Bjarnadóttir ◽  
K. Hollung ◽  
M. Høy ◽  
E. Bendixen ◽  
M. C. Codrea ◽  
...  
Keyword(s):  
Gel Electrophoresis ◽  
Protein Abundance ◽  
Absolute Quantitation ◽  
Isobaric Tag

scholarly journals A Sampling of the Yeast Proteome

1999 ◽  
Vol 19 (11) ◽  
pp. 7357-7368 ◽  
Author(s):  
B. Futcher ◽  
G. I. Latter ◽  
P. Monardo ◽  
C. S. McLaughlin ◽  
J. I. Garrels
Keyword(s):  
Gel Electrophoresis ◽  
Protein Turnover ◽  
Codon Bias ◽  
Quantitative Information ◽  
Protein Abundance ◽  
2D Gel Electrophoresis ◽  
Two Dimensional ◽  
Yeast Proteome ◽  
Global View ◽  
2D Gel

ABSTRACT In this study, we examined yeast proteins by two-dimensional (2D) gel electrophoresis and gathered quantitative information from about 1,400 spots. We found that there is an enormous range of protein abundance and, for identified spots, a good correlation between protein abundance, mRNA abundance, and codon bias. For each molecule of well-translated mRNA, there were about 4,000 molecules of protein. The relative abundance of proteins was measured in glucose and ethanol media. Protein turnover was examined and found to be insignificant for abundant proteins. Some phosphoproteins were identified. The behavior of proteins in differential centrifugation experiments was examined. Such experiments with 2D gels can give a global view of the yeast proteome.

83 STAGE-SPECIFIC PROTEOME SIGNATURES IN EARLY BOVINE EMBRYO DEVELOPMENT

2015 ◽  
Vol 27 (1) ◽  
pp. 134
Author(s):  
D. R. Deutsch ◽  
T. Fröhlich ◽  
K. A. Otte ◽  
A. Beck ◽  
F. A. Habermann ◽  
...  
Keyword(s):  
Liquid Chromatography ◽  
Principal Component ◽  
Proteome Analysis ◽  
Early Embryogenesis ◽  
Bovine Embryo ◽  
Protein Abundance ◽  
Absolute Quantitation ◽  
Cell Stage ◽  
Proteolytic Activation

Development of early embryonic stages before activation of the embryonic genome depends on sufficiently stored products of the maternal genome and adequate activation, deactivation, and relocation of proteins. To establish protein function, several posttranslational events (e.g. proteolytic activation, phosphorylation, or secretion) are frequently essential and thereby prevent prediction of protein abundance from transcript abundance. Consequently, proteomic studies are indispensable to characterise the molecular processes governing early embryonic development and to establish corresponding regulatory networks. Here, we present a quantitative proteome analysis of bovine zygotes and embryos at the 2-cell and 4-cell stage. Cumulus-oocyte complexes (COC) were prepared from bovine ovaries obtained from a local abattoir and selected for a compact layer of cumulus cells. In vitro maturation, fertilization, and embryo production were performed according to standard procedures. For quantitative isobaric tags for relative and absolute quantitation (iTRAQ)-liquid chromatography-tandem mass spectrometry (LC-MS/MS) analysis, protein from batches of 50 MII oocytes (serving as a reference), zygotes, 2-cell and 4-cell stage embryos, respectively, was extracted. Quantitative proteome analysis of iTRAQ-labelled tryptic peptides was performed on an Orbitrap XL instrument (Thermo Fisher, Waltham, MA, USA) coupled to an Eksigent nano-liquid chromatography system (AB Sciex, Framingham, MA, USA). The tandem MS data were analysed by MASCOT and filtered for a false discovery rate (FDR) of <1%. Quantification of iTRAQ signals was accomplished with the Q+ module of the Scaffold software (Proteome Software Inc., Portland, OR, USA). t-Tests, ANOVA and principal component analysis (PCA) analysis were performed using R (R Core Development Team, Vienna, Austria). From 4 biological replicates, 1072 proteins were identified and quantified. Eighty-seven differed significantly in abundance between the 4 stages (log2 fold change ≥ |0.6|, P ≤ 0.05). The proteomes of 2-cell and 4-cell embryos differed most from the reference MII oocyte, and a considerable fraction of proteins continuously increases in abundance during the stages analysed. Bioinformatic analysis of abundance altered proteins provided evidence that the proteins RPS14 and HNRNPK involved in the p53 pathway play a major role during early development, as well as proteins of the lipid metabolism, in particular APOA1. Furthermore, a group of proteins (e.g. SPTBN1, PPP1CC, RABGAP1, STMN1, and WEE2) is engaged in mitosis. In addition, we detected relevant differences between transcript and protein abundance levels; for example, for WEE2. In conclusion, this study identified and quantified numerous proteins important for early embryogenesis so far not described in the mammalian system, and contributed protein profiles for key players previously described. Our results highlight the importance of innovative proteomic tools and workflows to complement transcriptome data of early embryogenesis.

scholarly journals Proteomic Analysis of Beef Tenderloin and Flank Assessed Using an Isobaric Tag for Relative and Absolute Quantitation (iTRAQ)

Animals ◽  
2020 ◽  
Vol 10 (1) ◽  
pp. 150
Author(s):  
Zhaomin Lei ◽  
Jianping Wu ◽  
Deyin Zhang ◽  
Ting Liu ◽  
Shengguo Zhao ◽  
...  
Keyword(s):  
Proteomic Analysis ◽  
Expression Patterns ◽  
Tca Cycle ◽  
Absolute Quantification ◽  
Absolute Quantitation ◽  
Oxidation Reduction ◽  
The Tca Cycle ◽  
Isobaric Tag ◽  
Isobaric Tags

Herein, we performed a proteomic analysis of tenderloin and flank steaks from Simmental cattle using the isobaric tags for a relative and absolute quantification (iTRAQ) approach. We identified 17 amino acids in both steaks, and Gly, Cys, Ile, Lys, and Pro differed most in abundance between the steak types (p < 0.05). A comparison of the expression patterns in steaks revealed 128 differentially expressed proteins (DEPs), of which 44 were up-regulated and 84 were down-regulated. Furthermore, 27 DEPs (p < 0.05) were subjected to gene ontology (GO) analysis, and many were found to be related to oxidation-reduction, metabolism, hydrogen ion transmembrane transport, transport, the tricarboxylic acid (TCA) cycle, mitochondrial electron transport, and the conversion of nicotinamide adenine dinucleotide (NADH) to ubiquinone. Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis also implicated these DEPs in various signalling pathways, including oxidative phosphorylation, cardiac muscle contraction, the TCA cycle, biosynthesis, and the metabolism. These findings provide a new insight into key proteins involved in the determination of amino acid composition in beef.

scholarly journals Identification of novel pathways in pathogenesis of ketosis in dairy cows via iTRAQ/MS

2016 ◽  
Vol 60 (3) ◽  
pp. 309-314 ◽  
Author(s):  
Shi Shu ◽  
Chuchu Xu ◽  
Cheng Xia ◽  
Xinhuan Xiao ◽  
Gang Wang ◽  
...  
Keyword(s):  
Protein Expression ◽  
Dairy Cows ◽  
Expression Profiles ◽  
The Novel ◽  
Absolute Quantitation ◽  
Subclinical Ketosis ◽  
Isobaric Tag ◽  
Production Increase ◽  
Protein Expression Profiles ◽  
New Evidence

AbstractIntroduction: To identify novel pathways involved in the pathogenesis of ketosis, an isobaric tag for relative and absolute quantitation/mass spectrometry was used to define differences in protein expression profiles between healthy dairy cows and those with clinical or subclinical ketosis.Material and Methods: To define the novel pathways of ketosis in cattle, the differences in protein expression were analysed by bioinformatics. Go Ontology and Pathway analysis were carried out for enrich the role and pathway of the different expression proteins between healthy dairy cows and those with clinical or subclinical ketosis.Results: Differences were identified in 19 proteins, 16 of which were relatively up-regulated while the remaining 3 were relatively down-regulated. Sorbitol dehydrogenase (SORD) and glyceraldehyde-3-phosphate dehydrogenase (G3PD) were up-regulated in cattle with ketosis. SORD and G3PD promoted glycolysis. These mechanisms lead to pyruvic acid production increase and ketone body accumulation.Conclusion: The novel pathways of glycolysis provided new evidence for the research of ketosis.

scholarly journals Investigation of the Protective Effects of Phlorizin on Diabetic Cardiomyopathy indb/dbMice by Quantitative Proteomics

2013 ◽  
Vol 2013 ◽  
pp. 1-9 ◽  
Author(s):  
Qian Cai ◽  
Baoying Li ◽  
Fei Yu ◽  
Weida Lu ◽  
Zhen Zhang ◽  
...  
Keyword(s):  
Diabetic Cardiomyopathy ◽  
Body Weight Gain ◽  
Fasting Blood Glucose ◽  
Interaction Network ◽  
Diabetic Patients ◽  
Protective Effects ◽  
Absolute Quantitation ◽  
Patients With Diabetes ◽  
Itraq Proteomics ◽  
Isobaric Tag

Patients with diabetes often develop hypertension and atherosclerosis leading to cardiovascular disease. However, some diabetic patients develop heart failure without hypertension and coronary artery disease, a process termed diabetic cardiomyopathy. Phlorizin has been reported to be effective as an antioxidant in treating diabetes mellitus, but little is known about its cardioprotective effects on diabetic cardiomyopathy. In this study, we investigated the role of phlorizin in preventing diabetic cardiomyopathy indb/dbmice. We found that phlorizin significantly decreased body weight gain and the levels of serum fasting blood glucose (FBG), triglycerides (TG), total cholesterol (TC), and advanced glycation end products (AGEs). Morphologic observations showed that normal myocardial structure was better preserved after phlorizin treatment. Using isobaric tag for relative and absolute quantitation (iTRAQ) proteomics, we identified differentially expressed proteins involved in cardiac lipid metabolism, mitochondrial function, and cardiomyopathy, suggesting that phlorizin may prevent the development of diabetic cardiomyopathy by regulating the expression of key proteins in these processes. We used ingenuity pathway analysis (IPA) to generate an interaction network to map the pathways containing these proteins. Our findings provide important information about the mechanism of diabetic cardiomyopathy and also suggest that phlorizin may be a novel therapeutic approach for the treatment of diabetic cardiomyopathy.

scholarly journals Identification of Novel Biomarker Candidates for Hypertrophic Cardiomyopathy and Other Cardiovascular Diseases Leading to Heart Failure

2016 ◽  
pp. 751-762 ◽  
Author(s):  
H. REHULKOVA ◽  
P. REHULKA ◽  
A. MYSLIVCOVA FUCIKOVA ◽  
J. STULIK ◽  
R. PUDIL
Keyword(s):  
Hypertrophic Cardiomyopathy ◽  
Cardiovascular Diseases ◽  
Stable Coronary Artery Disease ◽  
Specific Protein ◽  
Protein Markers ◽  
Protein Biomarkers ◽  
Absolute Quantitation ◽  
Obstructive Hypertrophic Cardiomyopathy ◽  
Isobaric Tag ◽  
Cardiovascular Pathologies

In-depth proteome discovery analysis represents new strategy in an effort to identify novel reliable specific protein markers for hypertrophic cardiomyopathy and other life threatening cardiovascular diseases. To systematically identify novel protein biomarkers of cardiovascular diseases with high mortality we employed an isobaric tag for relative and absolute quantitation (iTRAQ) proteome technology to make comparative analysis of plasma samples obtained from patients suffering from non-obstructive hypertrophic cardiomyopathy, stable dilated cardiomyopathy, aortic valve stenosis, chronic stable coronary artery disease and stable arterial hypertension. We found 128 plasma proteins whose abundances were uniquely regulated among the analyzed cardiovascular pathologies. 49 of them have not been described yet. Additionally, application of statistical exploratory analyses of the measured protein profiles indicated the relationship in pathophysiology of the examined cardiovascular pathologies.

scholarly journals Insights on bio-degumming of kenaf bast based on metagenomic and proteomics

2020 ◽  
Author(s):  
Shengwen Duan ◽  
Lifeng Cheng ◽  
Xiangyuan Feng ◽  
Qi Yang ◽  
Zhiyuan Liu ◽  
...  
Keyword(s):  
18S Rrna ◽  
Hibiscus Cannabinus ◽  
Sequencing Analysis ◽  
Absolute Quantitation ◽  
Itraq Analysis ◽  
Fermentation Liquid ◽  
Rrna Sequencing ◽  
Isobaric Tag ◽  
Ferredoxin I ◽  
Kenaf Bast

Abstract Background: Microbes play important roles in kanef-degumming. This study aims at identifying the key candidate microbes and proteins responsible for the degumming of kenaf bast (Hibiscus cannabinus). Kenaf bast was cut into pieces and immersed into microbia fermentation liquid collected from different sites. Fermentation liquid samples were collected at 0, 40, 110 and 150 h and then subjected to the 16S/18S rRNA sequencing analysis and isobaric tag for relative and absolute quantitation (iTRAQ) analysis. The microbial (bacterial and fungal) diversity and the differentially expressed proteins/peptides (DEPs) were identified.Results: With the prolonged degumming time, the weight loss rate increased, the bacterial diversity was decreased. [Weeksellaceae], Enterobacteriaceae and Moraxellaceae were rapidly increased at 0~40 h, and then decreased and were gradually replaced by Bacteroidaceae from 40 h to 150 h. Similarly, Chryseobacterium and Dysgonomonas were gradually increased at 0~110 h and then decreased; Acinetobacter and Lactococcus were increased at 0~40 h, followed by decrease. Bacteroides was the dominant genus at 150 h. Sequencing 18S rRNA-seq showed the gradually decreased Wallemia hederae and increased Codosiga hollandica during degumming. iTRAQ data analysis showed Rds1, and pyruvate kinase I was decreased and increased in the kanef-degumming, respectively. Other DEPs of ferredoxin I, superoxide dismutase and aconitatehydratase were identified to be related to the Glyoxylate and dicarboxylate metabolism (ko00630).Conclusions: Bacteria including Chryseobacterium, Dysgonomonas, Acinetobacter, Lactococcus and Bacteroidesand fungi like Wallemia hederae and Codosiga hollandica are key candidate microbes for kanef degumming.

Isobaric Tag for Relative and Absolute Quantitation (iTRAQ)-Based Protein Profiling in Plants

2016 ◽  
pp. 213-221 ◽  
Author(s):  
Isabel Cristina Vélez-Bermúdez ◽  
Tuan-Nan Wen ◽  
Ping Lan ◽  
Wolfgang Schmidt
Keyword(s):  
Protein Profiling ◽  
Absolute Quantitation ◽  
Isobaric Tag

scholarly journals Electroacupuncture Improves Antidepressant Effects in CUMS Rats by Protecting Hippocampal Synapse and Mitochondrion: An Ultrastructural and iTRAQ Proteomic Study

2019 ◽  
Vol 2019 ◽  
pp. 1-11
Author(s):  
Jialing Zhang ◽  
Zhinan Zhang ◽  
Jiping Zhang ◽  
Zheng Zhong ◽  
Zengyu Yao ◽  
...  
Keyword(s):  
Molecular Mechanism ◽  
Complementary Therapy ◽  
Therapeutic Effects ◽  
Absolute Quantitation ◽  
Ultrastructure Study ◽  
Mitochondrial Functions ◽  
Study Results ◽  
Proteomics Approach ◽  
Proteomic Study ◽  
Isobaric Tag

Electroacupuncture (EA) is considered a complementary therapy for depression. Trials also found that EA has additive benefits when combined with medication compared with medication alone. It is revealed that EA restores altered hippocampal synaptic plasticity in depressed brain. But precise molecular mechanism is poorly understood. Here, we evaluated the therapeutic effects of EA and EA combined with selective serotonin reuptake inhibitor (SSRI) on depressed (CUMS) rats. Then a new proteomics approach, isobaric tag for relative and absolute quantitation (iTRAQ), was used to explore the differential expressed synaptic protein in hippocampus between CUMS and EA-treated rats to identify the possible target molecular mechanism of its effects. We found that EA had additive benefit against depressive behaviors when combined with SSRI. Ultrastructure study on neuron showed significant change in postsynapse density (PSD) and mitochondrion. Through iTRAQ, it is found that synaptic and mitochondrial proteins were significantly changed after EA, consisting with ultrastructure study results. These findings suggest that EA improves antidepressant performance in depressed rats through protecting synaptic and mitochondrial functions in hippocampus.

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