Proteomics in nutrition research: principles, technologies and applications

2005 ◽  
Vol 94 (3) ◽  
pp. 302-314 ◽  
Author(s):  
Dagmar Fuchs ◽  
Isabel Winkelmann ◽  
Ian T. Johnson ◽  
Edwin Mariman ◽  
Uwe Wenzel ◽  
...  
Keyword(s):  
Protein Separation ◽  
Large Scale ◽  
Protein Identification ◽  
Proteome Analysis ◽  
Transcriptome Profiling ◽  
Computer Assisted ◽  
Ph Gradients ◽  
2D Page ◽  
Nutrition Research ◽  
Nutritional Studies

The global profiling of the whole protein complement of the genome expressed in a particular cell or organ, or in plasma or serum, makes it possible to identify biomarkers that respond to alterations in diet or to treatment, and that may have predictive value for the modelling of biological processes. Proteomics has not yet been applied on a large scale in nutritional studies, yet it has advantages over transcriptome profiling techniques in that it directly assesses the entities that carry out the biological functions. The present review summarizes the different approaches in proteomics research, with special emphasis on the current technical ‘workhorses’: two-dimensional (2D)-PAGE with immobilized pH gradients and protein identification by MS. Using a work-flow approach, we provide information and advice on sample handling and preparation, protein solubilization and pre-fractionation, protein separation by 2D-PAGE, detection and quantification via computer-assisted analysis of gels, and protein identification and characterization techniques by means of MS. Examples from nutritional studies employing proteomics are provided to demonstrate not only the advantages but also the limitations of current proteome analysis platforms.

scholarly journals Differential Proteome Analysis of the Preeclamptic Placenta Using Optimized Protein Extraction

2010 ◽  
Vol 2010 ◽  
pp. 1-9 ◽  
Author(s):  
Magnus Centlow ◽  
Stefan R. Hansson ◽  
Charlotte Welinder
Keyword(s):  
Signal Transduction ◽  
Gel Electrophoresis ◽  
Protein Separation ◽  
Protein Extraction ◽  
Polyacrylamide Gel Electrophoresis ◽  
Proteome Analysis ◽  
Apolipoprotein A1 ◽  
Two Dimensional ◽  
2D Page ◽  
Nutritional Effect

The human placenta is a difficult tissue to work with using proteomic technology since it contains large amounts of lipids and glycogen. Both lipids and glycogen are known to interfere with the first step in the two-dimensional polyacrylamide gel electrophoresis (2D-PAGE), the isoelectric focusing. In order to gain the best possible protein separation on 2D-PAGE, an optimized sample preparation protocol for placental proteins was developed. Two different buffers, urea/CHAPS and Hepes, were used for solubilization in combination with six different precipitation methods. The removal of glycogen from the samples by centrifugation was crucial for the final proteome maps. Solubilization with urea/CHAPS in combination with dichloromethane/methanol or acidified acetone proved to be the best precipitation procedures. When applied to clinical placenta samples apolipoprotein A1 was found to be accumulated in the preeclamptic placenta, where it may either have a nutritional effect or act as a modifier of signal transduction.

Secretagogue regulation of pancreatic acinar cell protein phosphorylation shown by large-scale 2D-PAGE

1994 ◽  
Vol 267 (4) ◽  
pp. G676-G686 ◽  
Author(s):  
M. J. Wishart ◽  
G. Groblewski ◽  
B. J. Goke ◽  
A. C. Wagner ◽  
J. A. Williams
Keyword(s):  
Large Scale ◽  
Time Course ◽  
Partial Agonist ◽  
Polyacrylamide Gel Electrophoresis ◽  
Calcium Ionophore ◽  
Pancreatic Acinar Cell ◽  
Pancreatic Acinar Cells ◽  
Cell Protein ◽  
Computer Assisted ◽  
2D Page

High-resolution large-scale two-dimensional polyacrylamide gel electrophoresis (2D-PAGE) combined with computer-assisted image analysis was used to construct a database of secretagogue/second messenger-induced phosphoprotein modifications in intact rat pancreatic acinar cells. Isolated acini were labeled with 32Pi, exposed to hormones and other test agents, and subjected to large-scale 2D-PAGE and autoradiography. This procedure resolved 500 phosphoproteins in pancreatic acinar whole cell lysates, approximately 90% of which were localized in the soluble fraction of centrifuged samples. Soluble proteins were further characterized as to heat and acid stability. Cholecystokinin (CCK), carbachol, and bombesin altered the phosphorylation state of about 27 proteins with both increases and decreases observed. Subsets of proteins were phosphorylated in response to phorbol ester 12-O-tetradecanoylphorbol 13-acetate (TPA), calcium ionophore A-23187, and adenosine 3',5'-cyclic monophosphate (cAMP) analogue 8-bromo-cAMP. One of these proteins was identified as the myristoylated, alanine-rich, C-kinase substrate (MARCKS) protein by immunoprecipitation. The time course and dose response of phosphorylation changes due to CCK showed considerable variation between proteins, although a temporal hierarchy of phosphorylation events was clearly exhibited. Particularly striking was the rapid dephosphorylation within 30 s of a 19-kDa soluble protein to a minimum of 20 +/- 1% of control. Increased phosphorylation of the MARCKS and other TPA-regulated proteins suggests that CCK, carbachol, bombesin, and the CCK partial agonist, JMV-180, all activate protein kinase C in intact acini.

scholarly journals Analysis of the Spore Membrane Proteome in Clostridium perfringens Implicates Cyanophycin in Spore Assembly

2016 ◽  
Vol 198 (12) ◽  
pp. 1773-1782 ◽  
Author(s):  
Hualan Liu ◽  
W. Keith Ray ◽  
Richard F. Helm ◽  
David L. Popham ◽  
Stephen B. Melville
Keyword(s):  
Heat Resistance ◽  
Clostridium Perfringens ◽  
Protein Separation ◽  
Large Scale ◽  
Food Poisoning ◽  
Proteome Analysis ◽  
Membrane Proteome ◽  
Gene Encoding ◽  
Content Type ◽  
Cyanophycin Synthetase

ABSTRACTHeat-resistant endospore formation plays an important role inClostridium perfringens-associated foodborne illnesses. The spores allow the bacterium to survive heating during normal cooking processes, followed by germination and outgrowth of the bacterium in contaminated foods. To identify proteins associated with germination and other spore functions, a comparative spore membrane proteome analysis of dormant and germinated spores ofC. perfringensstrain SM101 was performed by using gel-based protein separation and liquid chromatography coupled with matrix-assisted laser desorption ionization–tandem time of flight (MALDI-TOF/TOF) mass spectrometry. A total of 494 proteins were identified, and 117 of them were predicted to be integral membrane or membrane-associated proteins. Among these membrane proteins, 16 and 26 were detected only in dormant and germinated spores, respectively. One protein that was detected only in germinated spore membranes was the enzyme cyanophycinase, a protease that cleaves the polymer cyanophycin, which is composed ofl-arginine-poly(l-aspartic acid), to β-Asp-Arg. Genes encoding cyanophycinase and cyanophycin synthetase have been observed in many species ofClostridium, but their role has not been defined. To determine the function of cyanophycin inC. perfringens, a mutation was introduced into thecphAgene, encoding cyanophycin synthetase. In comparison to parent strain SM101, the spores of the mutant strain retained wild-type levels of heat resistance, but fewer spores were made, and they were smaller, suggesting that cyanophycin synthesis plays a role in spore assembly. Although cyanophycin could not be extracted from sporulatingC. perfringenscells, anEscherichia colistrain expressing thecphAgene made copious amounts of cyanophycin, confirming thatcphAencodes a cyanophycin synthetase.IMPORTANCEClostridium perfringensis a common cause of food poisoning, and germination of spores after cooking is thought to play a significant role in the disease. HowC. perfringenscontrols the germination process is still not completely understood. We characterized the proteome of the membranes from dormant and germinated spores and discovered that large-scale changes occur after germination is initiated. One of the proteins that was detected after germination was the enzyme cyanophycinase, which degrades the storage compound cyanophycin, which is found in cyanobacteria and other prokaryotes. A cyanophycin synthetase mutant was constructed and found to make spores with altered morphology but normal heat resistance, suggesting that cyanophycin plays a different role inC. perfringensthan it does in cyanobacteria.

Comparison of MS/MS Methods for Protein Identification from 2D-PAGE

2006 ◽  
Vol 5 (9) ◽  
pp. 2294-2300 ◽  
Author(s):  
Giorgio Arrigoni ◽  
Celine Fernandez ◽  
Cecilia Holm ◽  
Michaela Scigelova ◽  
Peter James
Keyword(s):  
Protein Identification ◽  
2D Page

Contributions of Proteome Profiling to the Molecular Analysis of Cancer

2002 ◽  
Vol 1 (4) ◽  
pp. 237-245 ◽  
Author(s):  
Hong Wang ◽  
S. M. Hanash
Keyword(s):  
Mass Spectrometry ◽  
Tumor Cell ◽  
Cell Lines ◽  
Molecular Analysis ◽  
Protein Separation ◽  
Protein Identification ◽  
Tumor Cell Lines ◽  
Transcriptomic Profiling ◽  
Proteome Profiling

The proteome is the most functional compartment encoded for in the genome. Technologies for protein separation and quantitation, coupled with mass spectrometry for protein identification, have provided the means for proteome profiling of tumor cell lines and tissues that complement genomic and transcriptomic profiling. The application of established and novel proteomic technologies to the molecular analysis of cancer is reviewed.

scholarly journals KK-DBP: A Multi-Feature Fusion Method for DNA-Binding Protein Identification Based on Random Forest

2021 ◽  
Vol 12 ◽  
Author(s):  
Yuran Jia ◽  
Shan Huang ◽  
Tianjiao Zhang
Keyword(s):  
Dna Binding ◽  
Prediction Accuracy ◽  
Large Scale ◽  
Protein Identification ◽  
Feature Fusion ◽  
Binding Protein ◽  
Rapid Development ◽  
Dna Binding Protein ◽  
Feature Extraction Method ◽  
Independent Test Dataset

DNA-binding protein (DBP) is a protein with a special DNA binding domain that is associated with many important molecular biological mechanisms. Rapid development of computational methods has made it possible to predict DBP on a large scale; however, existing methods do not fully integrate DBP-related features, resulting in rough prediction results. In this article, we develop a DNA-binding protein identification method called KK-DBP. To improve prediction accuracy, we propose a feature extraction method that fuses multiple PSSM features. The experimental results show a prediction accuracy on the independent test dataset PDB186 of 81.22%, which is the highest of all existing methods.

scholarly journals Citizen workshops in public libraries to disseminate and discuss primary care research results: a scaling-up study

2020 ◽  
Author(s):  
José Massougbodji ◽  
Hervé Tchala Vignon Zomahoun ◽  
Evehouenou Lionel Adisso ◽  
Jasmine Sawadogo ◽  
Valérie Borde ◽  
...  
Keyword(s):  
Knowledge Translation ◽  
Financial Incentives ◽  
General Public ◽  
Large Scale ◽  
Public Libraries ◽  
Scale Up ◽  
Scaling Up ◽  
Computer Assisted ◽  
Knowledge Gain ◽  
Research Results

Abstract Background Little is known about engaging patients and stakeholders in the process of scaling up effective knowledge translation interventions targeting the general public. Using an integrated knowledge translation approach, we aimed to scale up and evaluate an effective pilot program of disseminating research results in public libraries. Methods We conducted a scaling-up study targeting the general public. Based on our successful pilot project, we co-developed and implemented a larger-scale program of free citizen workshops in public libraries, this time in close research partnership with stakeholders and patient representatives. Citizen workshops, each facilitated by one participating physician and one science communicator, consisted of a 45-min computer-assisted presentation and a 45-min open exchange. Additional scale-up costs included offering financial incentives to stakeholders involved and the purchase of audio-visual equipment. The intervention outcome was knowledge gained. Scale-up outcomes were satisfaction, appropriateness, coverage, time and costs. An evaluation questionnaire was used to collect data of interest. Both quantitative and qualitative analyses were performed. Results The workshop theme chosen by patient and stakeholder representatives was the high prevalence of medication overuse among people over 65 years of age. From April to May 2019, 26 workshops were given in 25 public libraries reaching 362 people. Eighteen participating physicians and six science communicators facilitated the workshops. Participants reported significant knowledge gain (mean difference 2.1, 95% CI 2.0–2.2, P < .001). Median score for overall public satisfaction was 9/10 (IQR 8–10). A high level of appropriateness of the workshops was globally rated by the public participants Coverage was 92.6% of the total number of public libraries targeted. Costs were $6,051.84 CAD for workshop design and $22,935.41 CAD for scaling them up. Conclusion This project successfully established a large-scale and successful KT bridge between researchers, clinicians, and citizens via public libraries. This study provides a model for a dissemination practice that benefits the general public by both engaging them in the dissemination process and by targeting them directly.

scholarly journals Recent developments and prospects in the composition, extraction, stability, delivery system, digestion and food applications of plant oil bodies

2021 ◽  
Author(s):  
Jia Hao ◽  
Duoxia Xu ◽  
Yangping Cao
Keyword(s):  
Delivery System ◽  
Large Scale ◽  
Protein Identification ◽  
Meat Products ◽  
Calorie Intake ◽  
Oil Bodies ◽  
Plant Oil ◽  
Electrostatic Deposition ◽  
Food Applications ◽  
The Stability

Oil bodies (OBs) are micron- or submicron-sized sub-organelles widely found in plants seeds and nuts. The structure OBs is composed of a core of triglycerides covered by a phospholipid-protein layer, which ensures the stability of the OBs under extreme environmental conditions and further protects core lipids as energy reserves. As naturally pre-emulsified oil-in-water emulsions, OBs have been gradually applied to replace synthetically engineered oil droplets. In this paper, the recent research on the composition, extraction, stability, delivery system, digestion, food applications and future perspectives of plant OBs are reviewed. Recent studies have focused on the OBs surface protein identification and function, large-scale extraction techniques such as enzyme assisted, high pressure, ultrasound, and extrusion and the reconstituted OBs. Electrostatic deposition of polysaccharides significantly improves the stability of OBs emulsions. OBs emulsions have promising applications to encapsulate bioactive compounds, deliver targeted drugs, and prepare gels and edible functional films. The digestive behavior of OBs emulsions is similar to that of protein-stabilized emulsions, which can increase the satiety, effectively help reduce calorie intake and improve the bioavailability of functional factors. It has also promoted the development of simulated dairy, spices and meat products.

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