Identification of melanoma‐specific serological markers using proteomic analyses

The discovery of novel melanoma markers for not only early detection but also monitoring disease status is promising to improve the clinical outcome of patients. In the present study, we performed proteomic comparative analysis of plasma proteins between healthy volunteers and melanoma patients using NanoLC and MALDI‐TOF‐MS. As a result, we were successful in identifying nine proteins that were specifically expressed in melanoma plasma compared with healthy plasma, most of which had not previously been identified as plasma markers of melanoma. The mRNA expression levels of four proteins [pro‐platelet basic protein precursor (PPBP), serum amyloid A2 (SAA2), complement factor H‐related protein 1 precursor (FHR1), inter‐alpha‐trypsin inhibitor heavy chain H4 precursor (IAIH4)] were prominently up‐regulated in several melanoma cell lines compared with melanocytes. Moreover, two proteins (PPBP, SAA) were shown to be expressed in tumor specimens from melanoma patients. In the survival time analysis regarding melanoma patients, the semi‐quantified plasma PPBP levels were statistically negatively correlated with the survival time. Most interestingly, the significant survival benefit was seen in low PBPP level group (< index 20) versus high level (≥ index 20) group. The results suggest that PPBP might be a novel promising serological marker and a prognostic factor specific to melanomas.     

Postmortem proteome degradation profiles of longissimus muscle in Yorkshire and Duroc pigs and their relationship with pork quality traits

Conversion of muscle to meat is regulated by complex interactions of biochemical processes that take place during postmortem storage of the carcass. Enzymatic proteolysis, among other postmortem biochemical phenomena; e.g. glycolysis; changes tough intact muscle tissue into more tender meat. Knowledge on proteome-wide proteolysis of muscle tissue in relation to meat quality is limited and potential breed-specific differences have received little attention. Therefore, we investigated meat quality traits and proteolysis profiles of the longissimus proteome of five Yorkshire and five Duroc pigs at slaughter and after 1, 2, 3, 7, and 10 days of ageing. Drip loss increased with ageing while cooking loss was unchanged in both breeds. Shear force varied between animals and decreased with ageing. Analysis of the proteomes showed four types of temporal expression profiles. Association analysis suggested several potential protein biomarkers for drip loss and shear force in both breeds, but none for cooking loss.     

Application to proteomics to understand and modify meat quality

The use of proteomics in the field of meat science has gained in robustness and accuracy. This is consistent with the genomic and bioinformatic tools. Its application to sensorial and technological meat quality traits is discussed as well as the emergence of sanitary and nutritional issue which will grow in a next future.     

Comparative Proteomics Analysis Reveals Trans Fatty Acid Isomers Activates Different Pathways in Human Umbilical Vein Endothelial Cell

Trans fatty acid (TFA), a group of unsaturated fats with at least one double bond in the trans configuration, plays a role in lipid metabolism, the structure of the cell membrane phospholipids, and apoptosis. Previous studies demonstrated that TFA was associated with coronary heart disease, obesity, and insulin resistance. Herein, a quantitative proteomics approach estimated the relative abundance of proteins in human umbilical vein endothelial cells treated with TFA (two different TFA structural isomers: 9t‐18:1 and 9t,12t‐18:2). The results revealed that 174 identified proteins were significantly altered with respect to expression. Furthermore, based on the cutoff values, 35 proteins were differentially expressed in the 9t‐18:1 group as compared to the control group, 69 proteins were differentially expressed in 9t,12t‐18:2 group as compared to the control group, and 120 proteins were differentially expressed in the 9t,12t‐18:2 group as compared to the 9t‐18:1 group. Based on the bioinformatics analysis, we found that TFA could alter the structural constitution of the cytoskeleton through protein interactions, localization into the cell membrane, and incorporation into the phospholipid of the cell. In addition, 17 differential apoptosis‐related proteins, including cell division cycle 42, superoxide dismutase 1, glyoxalase I, and macrophage migration inhibitory factor were also identified. Together, these results might emphasize the need for studying TFA‐induced biological processes.     

Mass spectrometry based proteomics as foodomics tool in research and assurance of food quality and safety

BackgroundAs a comprehensive discipline that studies food and nutrition, foodomics requires reliable qualitative and quantitative information about the food proteome component in order to extract new integrative information from the complex multivariable space of omics. This new information is necessary to achieve a higher level of understanding of processes in food science and technology, consequently new functions of food and improved markers of food quality and safety and completely transform concept of food safety.Scope and approachWe are making an effort to present mass spectrometry (MS) based proteomic approaches that are being utilized in different proteomic studies, not necessarily in the field of foodomics, which are important and have the potential to advance this field. Current analytical capabilities of MS-based proteomics together with sample preparation procedures and quantification strategies, and recent technical developments were presented.Key findings and conclusionsMS-based proteomics enables the analysis of different aspects of proteins and provides a variety of approaches for reliable quantification of individual proteins and/or food proteome. This is a complex field and its successful implementation requires a dedicated analyst, a thorough design of sample preparation procedure, the selection of an MS technique and approach, an adequate type of mass spectrometer, a thorough data analysis and validation. Improvements in the technology of mass spectrometers are continuously expanding capabilities of MS-based proteomics.     

Challenges and advances in systems biology analysis of Bacillus spore physiology; molecular differences between an extreme heat resistant spore forming Bacillus subtilis food isolate and a laboratory strain

Bacterial spore formers are prime organisms of concern in the food industry. Spores from the genus Bacillus are extremely stress resistant, most notably exemplified by high thermotolerance. This sometimes allows surviving spores to germinate and grow out to vegetative cells causing food spoilage and possible intoxication. Similar issues though more pending toward spore toxigenicity are observed for the anaerobic Clostridia.The paper indicates the nature of stress resistance and highlights contemporary molecular approaches to analyze the mechanistic basis of it in Bacilli. A molecular comparison between a laboratory strain and a food borne isolate, very similar at the genomic level to the laboratory strain but generating extremely heat resistant spores, is discussed. The approaches cover genome-wide genotyping, proteomics and genome-wide expression analyses studies. The analyses aim at gathering sufficient molecular information to be able to put together an initial framework for dynamic modelling of spore germination and outgrowth behaviour. Such emerging models should be developed both at the population and at the single spore level. Tools and challenges in achieving the latter are succinctly discussed.