Changes in cod muscle proteins during frozen storage revealed by proteome analysis and multivariate data analysis

TMT-based proteomics analysis of sea urchin (Strongylocentrotus intermedius) under high temperature stress

In the context of global warming and continuous high temperatures in the northern part of China in summer, the mortality rate of Strongylocentrotus intermedius through the summer reaches 70-80 %. The protein regulatory mechanism of S. intermedius in response to high temperature stress is still unclear. In order to investigate the protein expression of S. intermedius under high temperature stress, the study was conducted with the high-temperature resistant strain of S. intermedius and the control group of S. intermedius. Tandem Mass Tag (TMT) tagging technique was applied to resolve the protein expression profile of S. intermedius in response to high temperature stress. The results showed that, compared to 15 °C，136 DEPs were screened in high-temperature resistant strain groups of S. intermedius under high temperature stress and 87 DEPs were screened in the control group of S. intermedius. There were 33 common differential proteins in the two groups, such as APOLP, HSP 70, CDC37 and CALM. Further Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways analyses revealed that the up-regulated proteins CALM and HSP70 are significantly enriched in the "Phosphatidylinositol signaling system" and "Protein processing in endoplasmic reticulum" in heat-tolerant S. intermedius strains under high temperature stress. The control group of S. intermedius DEPs were significantly enriched in protein processing in the endoplasmic reticulum. These results provide a theoretical basis for the molecular mechanism of sea urchin heat tolerance and fundamental data for sea urchin selection and breeding for high temperature tolerance.

Multi-Omics Approaches for Freshness Estimation and Detection of Illicit Conservation Treatments in Sea Bass (Dicentrarchus Labrax): Data Fusion Applications

Fish freshness consists of complex endogenous and exogenous processes; therefore, the use of a few parameters to unravel illicit practices could be insufficient. Moreover, the development of strategies for the identification of such practices based on additives known to prevent and/or delay fish spoilage is still limited. The paper deals with the identification of the effect played by a Cafodos solution on the conservation state of sea bass at both short-term (3 h) and long-term (24 h). Controls and treated samples were characterized by a multi-omic approach involving proteomics, lipidomics, metabolomics, and metagenomics. Different parts of the fish samples were studied (muscle, skin, eye, and gills) and sampled through a non-invasive procedure based on EVA strips functionalized by ionic exchange resins. Data fusion methods were then applied to build models able to discriminate between controls and treated samples and identify the possible markers of the applied treatment. The approach was effective in the identification of the effect played by Cafodos that proved to be different in the short- and long-term and complex, involving proteins, lipids, and small molecules to a different extent.

Proteomic changes involved in water holding capacity of frozen bovine longissimus dorsi muscles based on DIA strategy

As freeze/thaw procedure leads to inevitable drip loss, elucidation of mechanism on dynamic changes in water holding capacity (WHC) of muscle is urgently needed. In this study, the proteomic profile by DIA-based strategy, muscle microstructure, water mobility, and WHC indices of bovine longissimus dorsi muscles were investigated under different freezing conditions as well as the correlations among them. Results indicated that slow freezing (SF) sample exhibited significantly higher water mobility, thaw loss, total loss, and shear force value than the samples subjected to fast freezing (FF) and non-frozen control (CON). According to the protein profile, we have identified 272 differential abundance proteins (DAPs), in which more significant proteome changes were found in SF/CON samples as compared with FF/CON. Among the 132 DAPs in FF/SF comparison, correlation analysis revealed that MYL3, DES, SYNE2, EXR, RPL35A, RPS6, and Hsp40 were closely correlated with T₂₃ , thaw loss, and total loss. Accordingly, we considered those seven proteins as potential biomarkers related to WHC of frozen muscle. Our study should give a further understanding on mechanisms behind the various WHC of muscle when subjected to different freezing conditions. PRACTICAL APPLICATIONS: Freezing plays a key role in the preservation method for meat and meat products. However, the drip loss during freezing and subsequent thawing procedure causes considerable economic and nutritional losses. To minimize the losses, elucidation of mechanism on the mechanism of thaw loss formation is urgently needed. DIA-based proteomics is a novel, robust method that provides further understanding on the mechanisms behind the dynamic changes in water holding capacity of muscle. The screened protein biomarkers in frozen muscle would play key roles in the development of WHC, especially for the thaw loss formation. Through this perspective, we can explain the origin of thaw loss and the variation under different freezing conditions, which should provide the meat industries with theoretical basis for reducing losses.

Quantitative proteomics insights into gel properties changes of myofibrillar protein from Procambarus clarkii under cold stress

The impacts of cold stress (4 ℃ for 0 h, 12 h, 24 h, 36 h and 48 h, respectively) on the components, structural and physical properties of myofibrillar protein (MP) gel from Procambarus clarkii were investigated. The physicochemical analysis indicated the secondary and tertiary structure of MP were unfolding to different degrees after cold stress when compared to the control. The MP gel hardness reached a maximum when the cold stress reached 24 h. Furthermore, the quantitative proteomics results indicated that 20 up-regulated differentially abundant proteins (DAPs) were detected in 24 h when compared to control, specifically include myosin light chain 1 (MLC1) and skeletal muscle actin 6. Additionally, the combined analysis confirmed that MLC1 and skeletal muscle actin 6 might play key roles in hardening shrimp meat under cold stress. The results could provide a theoretical reference for the changes in crayfish muscle quality during cold chain transportation.

Proteomics for species authentication of cod and corresponding fishery products

Seafood substitutions is a global problem and come under the spotlight in recent years. In Taiwan, Greenland halibut is usually substituted for the cod because of its lower price. Nowadays, DNA technology is widely used for fish species identifications; however, it still has concern about the DNA of processed fishery products might be destroyed. This study was designed to develop a proteomic-based method for fish and fishery product authentication by using ultra performance liquid chromatography/quadrupole time-of-flight mass spectrometry (UPLC-QTOF-MS/MS) with Sequential window acquisition of all theoretical fragment ion spectra (SWATH). The protein biomarkers from the meat of Alaska pollock, Atlantic cod, and Greenland halibut were identified and validated for species authentication of cod and corresponding fishery products, which might prevent consumer substitutions and fish product mislabeling. Besides, the E. coli proteins can be measured from existing SWATH-MS data though retrospective analysis successfully, it might present the quality of fish meat.

Effects of ultrasound on the thawing of quick-frozen small yellow croaker (Larimichthys polyactis) based on TMT-labeled quantitative proteomic

The effect of dual-frequency sequential ultrasonic thawing (DUT) on the quality of quick-frozen small yellow croaker was studied by TMT-labeled quantitative proteomic method. A total number of 75 proteins were identified as differentially abundant proteins (DAPs) in fish meat treated by DUT, while 72 DAPs were in flow water thawing (FWT). The Kyoto encyclopedia of genes and genomes (KEGG) pathway analysis indicated that the DAPs in the significant enrichment pathway of DUT group were enzymes. Compared with FWT, DUT had a significant effect on the enzyme content. The correlation analyses indicated that 40 DAPs were related with the quality traits. The 11 highly correlated DAPs are expected to be used as potential protein markers for texture profile analyses, color, thawing loss, water-holding capacity, and pH of thawed small yellow croaker quality. These results provide a further understanding of the quality stability of quick-frozen small yellow croaker treated by the DUT.

Protein Signatures to Trace Seafood Contamination and Processing

This review presents some applications of proteomics and selected spectroscopic methods to validate certain aspects of seafood traceability. After a general introduction to traceability and the initial applications of proteomics to authenticate traceability information, it addresses the application of proteomics to trace seafood exposure to some increasingly abundant emergent health hazards with the potential to indicate the geographic/environmental origin, such as microplastics, triclosan and human medicinal and recreational drugs. Thereafter, it shows the application of vibrational spectroscopy (Fourier-Transform Infrared Spectroscopy (FTIR) and Fourier-Transform Raman Spectroscopy (FT Raman)) and Low Field Nuclear Magnetic Resonance (LF-NMR) relaxometry to discriminate frozen fish from thawed fish and to estimate the time and temperature history of frozen fillets by monitoring protein modifications induced by processing and storage. The review concludes indicating near future trends in the application of these techniques to ensure seafood safety and traceability.

Two-dimensional gel and shotgun proteomics approaches to distinguish fresh and frozen-thawed curled octopus (Eledone cirrhosa)

The substitution and sale of frozen-thawed fish labeled as fresh is a widespread, difficult to unmask commercial fraud and a potential risk for consumer health. Proteomics could help to identify markers for the rapid screening of food samples and the identification of frozen-thawed seafood. Using two-dimensional electrophoresis (2-DE) and high-resolution liquid chromatography tandem mass spectrometry (LC-MS/MS), we identified biomarkers that are able to discriminate between fresh and frozen-thawed tissue samples of curled octopus (Eledone cirrhosa). The 2-DE analysis showed a significant reduction in two protein spots (molecular weight of 45-50 kDa, isoelectric point of 6.5-7) identified as transgelin. At shotgun analysis, nine proteins resulted modulated and transgelin was confirmed as down-regulated, making it a potentially useful marker for differentiating between fresh and frozen-thawed fish product samples.

BIOLOGICAL SIGNIFICANCE

This work, based on two different proteomics approaches, investigated differentially expressed proteins in the tentacles of the curled octopus (E. cirrhosa) after freezing-thawing processes. We were able to characterize the proteome of the tentacles, increasing our knowledge on this species, and a common down-regulated protein was identified by 2-DE and shotgun analysis, a calponin-like protein called transgelin, suggesting a potential use as a marker to distinguish different states of conservation in this species.

New Insights into the Changes of the Proteome and Microbiome of Shrimp ( Litopenaeus vannamei) Stored in Acidic Electrolyzed Water Ice

Acidic electrolyzed water (AEW) ice is a novel technique for prolonging the shelf life of foods, but there is limited knowledge of its preservation mechanism. A proteomics approach and 16S rRNA-based Illumina sequencing were employed to investigate the changes of key proteins and bacterial communities in shrimp stored in AEW ice and tap water ice (TW ice) for 7 days. Compared with TW ice, AEW ice markedly retards the degradation of myofibrillar proteins in shrimp, including myosin, actin, and tropomyosin. Moreover, sarcoplasmatic proteins that participate in the carbohydrate catabolic process and amino acid metabolism were also influenced. Furthermore, the growth of spoilage bacteria, which includes the genera Psychrobacter, Shewanella, and Flavobacterium, was significantly inhibited by AEW ice, and the inhibition rates at day 7 were 71.6, 47.8, and 100%, respectively ( p < 0.05). Further correlation analysis showed the links between spoilage bacteria and protein changes can be broken by AEW ice treatment. Collectively, our findings indicated AEW ice can improve the quality of shrimp via previously undescribed mechanisms, which retarded the degradation of myofibrillar proteins and inhibited the growth of spoilage bacteria.

Muscle Protein Profiles Used for Prediction of Texture of Farmed Salmon (Salmo salar L.)

A soft texture is undesired in Atlantic salmon as it leads to downgrading and reduced yield, yet it is a factor for which the cause is not fully understood. This lack of understanding highlights the need for identifying the cause of the soft texture and developing solutions by which the processing industry can improve the yield. Changes in muscle protein profiles can occur both pre- and postharvest and constitute an overall characterization of the muscle properties including texture. The aim of this study was to investigate this relationship between specific muscle proteins and the texture of the salmon fillet. Samples for 2D-gel-based proteomics were taken from the fillet above the lateral line at the same position as where the texture had been measured. The resulting protein profiles were analyzed using multivariate data analysis. Sixteen proteins were found to correlate to the measured texture, showing that it is possible to predict peak force based on a small subset of proteins. Additionally, eight of the 16 proteins were identified by tandem mass spectrometry including serum albumin, dipeptidyl peptidase 3, heat shock protein 70, annexins, and a protein presumed to be a titin fragment. It is contemplated that the identification of these proteins and their significance for the measured texture will contribute to further understanding of the Atlantic salmon muscle texture.

Differential abundance of muscle proteome in cultured channel catfish (Ictalurus punctatus) subjected to ante-mortem stressors and its impact on fillet quality

The effects of environmental and handling stress during catfish (Ictalurus punctatus) aquaculture were evaluated to identify the biochemical alterations they induce in the muscle proteome and their impacts on fillet quality. Temperature (25°C and 33°C) and oxygen (~2.5mg/L [L] and >5mg/L [H]) were manipulated followed by sequential socking (S) and transport (T) stress to evaluate changes in quality when fish were subjected to handling (25-H-ST; temperature-oxygen-handling), oxygen stress (25-L-ST), temperature stress (33-H-ST) and severe stress (33-L-ST). Instrumental color and texture of fillets were evaluated, and muscle proteome profile was analyzed. Fillet redness, yellowness and chroma decreased, and hue angle increased in all treatments except temperature stress (33-H-ST). Alterations in texture compared to controls were observed when oxygen levels were held high. In general, changes in the abundance of structural proteins and those involved in protein regulation and energy metabolism were identified. Rearing under hypoxic conditions demonstrated a shift in metabolism to ketogenic pathways and a suppression of the stress-induced changes as the severity of the stress increased. Increased proteolytic activity observed through the down-regulation of various structural proteins could be responsible for the alterations in color and texture.

Proteomics in food: Quality, safety, microbes, and allergens

Food safety and quality and their associated risks pose a major concern worldwide regarding not only the relative economical losses but also the potential danger to consumer's health. Customer's confidence in the integrity of the food supply could be hampered by inappropriate food safety measures. A lack of measures and reliable assays to evaluate and maintain a good control of food characteristics may affect the food industry economy and shatter consumer confidence. It is imperative to create and to establish fast and reliable analytical methods that allow a good and rapid analysis of food products during the whole food chain. Proteomics can represent a powerful tool to address this issue, due to its proven excellent quantitative and qualitative drawbacks in protein analysis. This review illustrates the applications of proteomics in the past few years in food science focusing on food of animal origin with some brief hints on other types. Aim of this review is to highlight the importance of this science as a valuable tool to assess food quality and safety. Emphasis is also posed in food processing, allergies, and possible contaminants like bacteria, fungi, and other pathogens.

Fourteen years of plant proteomics reflected in Proteomics: moving from model species and 2DE-based approaches to orphan species and gel-free platforms

In this article, the topic of plant proteomics is reviewed based on related papers published in the journal Proteomics since publication of the first issue in 2001. In total, around 300 original papers and 41 reviews published in Proteomics between 2000 and 2014 have been surveyed. Our main objective for this review is to help bridge the gap between plant biologists and proteomics technologists, two often very separate groups. Over the past years a number of reviews on plant proteomics have been published . To avoid repetition we have focused on more recent literature published after 2010, and have chosen to rather make continuous reference to older publications. The use of the latest proteomics techniques and their integration with other approaches in the "systems biology" direction are discussed more in detail. Finally we comment on the recent history, state of the art, and future directions of plant proteomics, using publications in Proteomics to illustrate the progress in the field. The review is organized into two major blocks, the first devoted to provide an overview of experimental systems (plants, plant organs, biological processes) and the second one to the methodology.

Animal board invited review: advances in proteomics for animal and food sciences

Animal production and health (APH) is an important sector in the world economy, representing a large proportion of the budget of all member states in the European Union and in other continents. APH is a highly competitive sector with a strong emphasis on innovation and, albeit with country to country variations, on scientific research. Proteomics (the study of all proteins present in a given tissue or fluid - i.e. the proteome) has an enormous potential when applied to APH. Nevertheless, for a variety of reasons and in contrast to disciplines such as plant sciences or human biomedicine, such potential is only now being tapped. To counter such limited usage, 6 years ago we created a consortium dedicated to the applications of Proteomics to APH, specifically in the form of a Cooperation in Science and Technology (COST) Action, termed FA1002--Proteomics in Farm Animals: www.cost-faproteomics.org. In 4 years, the consortium quickly enlarged to a total of 31 countries in Europe, as well as Israel, Argentina, Australia and New Zealand. This article has a triple purpose. First, we aim to provide clear examples on the applications and benefits of the use of proteomics in all aspects related to APH. Second, we provide insights and possibilities on the new trends and objectives for APH proteomics applications and technologies for the years to come. Finally, we provide an overview and balance of the major activities and accomplishments of the COST Action on Farm Animal Proteomics. These include activities such as the organization of seminars, workshops and major scientific conferences, organization of summer schools, financing Short-Term Scientific Missions (STSMs) and the generation of scientific literature. Overall, the Action has attained all of the proposed objectives and has made considerable difference by putting proteomics on the global map for animal and veterinary researchers in general and by contributing significantly to reduce the East-West and North-South gaps existing in the European farm animal research. Future activities of significance in the field of scientific research, involving members of the action, as well as others, will likely be established in the future.

Differentiation between fresh and frozen-thawed sea bass (Dicentrarchus labrax) fillets using two-dimensional gel electrophoresis

This study aimed to identify a protein marker that can differentiate between fresh skinless and frozen-thawed sea bass (Dicentrarchus labrax) fillets using the two-dimensional polyacrylamide gel electrophoresis (2-DE) technique. Distinct gel patterns, due to proteins with low molecular weight and low isoelectric points, distinguished fresh fillets from frozen-thawed ones. Frozen-thawed fillets showed two specific protein spots as early as the first day of the study. However, these spots were not observed in fresh fillets until at least 13days of storage between 0 and 4°C, fillets were judged, beyond this period, fish were unfit for human consumption as revealed by complementary studies on fish spoilage indicators namely total volatile basic nitrogen and biogenic amines. Mass spectrometry identified the specific proteins as parvalbumin isoforms. Parvalbumins may thus be useful markers of differentiation between fresh and frozen-thawed sea bass fillets.

PROTEOMICS in aquaculture: applications and trends

Over the last forty years global aquaculture presented a growth rate of 6.9% per annum with an amazing production of 52.5 million tonnes in 2008, and a contribution of 43% of aquatic animal food for human consumption. In order to meet the world's health requirements of fish protein, a continuous growth in production is still expected for decades to come. Aquaculture is, though, a very competitive market, and a global awareness regarding the use of scientific knowledge and emerging technologies to obtain a better farmed organism through a sustainable production has enhanced the importance of proteomics in seafood biology research. Proteomics, as a powerful comparative tool, has therefore been increasingly used over the last decade to address different questions in aquaculture, regarding welfare, nutrition, health, quality, and safety. In this paper we will give an overview of these biological questions and the role of proteomics in their investigation, outlining the advantages, disadvantages and future challenges. A brief description of the proteomics technical approaches will be presented. Special focus will be on the latest trends related to the aquaculture production of fish with defined nutritional, health or quality properties for functional foods and the integration of proteomics techniques in addressing this challenging issue.

Time-dependent changes in protein expression in rainbow trout muscle following hypoxia

Adaptation to hypoxia is a complex process, and individual proteins will be up- or down-regulated in order to address the main challenges at any given time. To investigate the dynamics of the adaptation, rainbow trout (Oncorhynchus mykiss) was exposed to 30% of normal oxygen tension for 1, 2, 5 and 24 h respectively, after which muscle samples were taken. The successful investigation of numerous proteins in a single study was achieved by selectively separating the sarcoplasmic proteins using 2-DE. In total 46 protein spots were identified as changing in abundance in response to hypoxia using one-way ANOVA and multivariate data analysis. Proteins of interest were subsequently identified by MS/MS following tryptic digestion. The observed regulation following hypoxia in skeletal muscle was determined to be time specific, as only a limited number of proteins were regulated in response to more than one time point. The cellular response to hypoxia included regulation of proteins involved in maintaining iron homeostasis, energy levels and muscle structure. In conclusion, this proteome-based study presents a comprehensive investigation of the expression profiles of numerous proteins at four different time points. This increases our understanding of timed changes in protein expression in rainbow trout muscle following hypoxia.

Antioxidants from barley husks impregnated in films of low-density polyethylene and their effect over lipid deterioration of frozen cod (Gadus morhua)

BACKGROUND

The changes in quality of cod fillets packaged in films with and without antioxidants during 12 months of frozen storage at - 20 °C were investigated in the present study. The following parameters were determined in order to study lipid hydrolysis and primary and secondary lipid oxidation in the samples during frozen storage: peroxide value, conjugated dienes, conjugated triene hydroperoxides, free fatty acids, totox value, thiobarbituric acid-reactive substances and p-anisidine value.

RESULTS

Films containing antioxidants isolated from barley husks were effective in slowing down lipid hydrolysis and primary and secondary lipid oxidation processes. Secondary lipid oxidation reached maximum values in the 12th month of storage in control samples and samples packaged with antioxidant-containing film. Maximum lipid hydrolysis and lipid oxidation values for control cod samples were significantly higher than the maximum values found in samples packaged with antioxidant-containing film.

CONCLUSION

The results confirm the efficacy of natural antioxidants derived from barley husks in slowing down lipid hydrolysis and increasing the oxidative stability of cod flesh. They also demonstrate the potential usefulness of natural antioxidants extracted from barley husks in the development of active packaging films for food preservation.

Liquid chromatography and mass spectrometry in food allergen detection

Food allergy is an important issue in the field of food safety because of the hazards for affected persons and the hygiene requirements and legal regulations imposed on the food industry. Consumer protection and law enforcement require suitable analytical techniques for the detection of allergens in foods. Immunological methods are currently preferred; however, confirmatory alternatives are needed. The determination of allergenic proteins by liquid chromatography and mass spectrometry has greatly advanced in recent years, and gel-free allergenomics is becoming a routinely used approach for the identification and quantitation of food allergens. The present review provides a brief overview of the principles of proteomic procedures, various chromatographic set ups, and mass spectrometry instrumentation used in allergenomics. A compendium of published liquid chromatography methods, proteomic analyses, typical marker peptides, and quantitative assays for 14 main allergy-causing foods is also included.

Cod (Gadus morhua) muscle proteome cataloging using 1D-PAGE protein separation, nano-liquid chromatography peptide fractionation, and linear trap quadrupole (LTQ) mass spectrometry

Because Atlantic cod (Gadus morhua) has high economic value and its protein-rich muscle tissue is a food source, an increased understanding of the effects and consequences of environmental, nutritional, biological, and industrial factors on meat quality is necessary. To gain insight into cod muscle tissue protein composition, a large-scale proteomics approach has been used. One-dimensional polyacrylamide gel electrophoresis, nanoflow liquid chromatography peptide separation, and linear trap quadrupole mass spectrometry were used to identify 4804 peptides, which retrieved 9113 cod expressed sequence tags (ESTs), which in turn were mapped to 446 unique proteins. The same data set identified 3924 proteins from the zebrafish protein database, which highlights the complementary value of the two approaches. The generated data sets will act as a foundation for studies related to physiological status assessment of cod under different environmental conditions, screening for diseases, and biomarker identification for assessment of fish quality during industrial processing and preservation.

Effects of thawing, refreezing and storage conditions of tissue samples and protein extracts on 2-DE spot intensity

We report that reliable quantitative proteome analyses can be performed with tissue samples stored at -80 degrees C for up to 10 years. However, storing protein extracts at 4 degrees C for 24 h and freezing protein extracts at -80 degrees C and thawing them significantly altered 41.6 and 17.5% of all spot intensities on 2-DE gels, respectively. Fortunately, these storing effects did not impair the reliability of quantifying 2-DE experiments. Nonetheless, the results show that freezing and storage conditions should be carefully controlled in proteomic experiments.

Evaluation of the variables characterized by significant discriminating power in the application of SIMCA classification method to proteomic studies

SIMCA classification can be applied to 2D-PAGE maps to identify changes occurring in cellular protein contents as a consequence of illnesses or therapies. These data sets are complex to treat due to the large number of proteins detected. A method for identifying relevant proteins from SIMCA discriminating powers is proposed, based on the Box-Cox transformation coupled to probability papers. The method successfully allowed the identification of the relevant spots from 2D maps.

Multivariate data analysis of two-dimensional gel electrophoresis protein patterns from few samples

One application of 2D gel electrophoresis is to reveal differences in protein pattern between two or more groups of individuals, attributable to their group membership. Multivariate data analytical methods are useful in pinpointing the spots relevant for discrimination by focusing not only on single spot differences, but on the covariance structure between proteins. However, their outcome is dependent on data scaling, and they may fail in producing valid multivariate models due to the much higher number of "irrelevant" spots present in the gels. The case where only few gels are available and where the aim is to find as many as possible of the group-dependent proteins seems particularly difficult to handle. The present paper investigates such a case regarding the effect of scaling and of prefiltering by univariate nonparametric statistics on the selection of spots. Besides, a modified 'autoscaling' of the full data set based on within-group standard deviations is introduced and shown to be advantageous in revealing potential group-dependent proteins additional to those found by prefiltering.

Application of partial least squares discriminant analysis and variable selection procedures: a 2D-PAGE proteomic study

2D gel electrophoresis is a tool for measuring protein regulation, involving image analysis by dedicated software (PDQuest, Melanie, etc.). Here, partial least squares discriminant analysis was applied to improve the results obtained by classic image analysis and to identify the significant spots responsible for the differences between two datasets. A human colon cancer HCT116 cell line was analyzed, treated and not treated with a new histone deacetylase inhibitor, RC307. The proteins regulated by RC307 were detected by analyzing the total lysates and nuclear proteome profiles. Some of the regulated spots were identified by tandem mass spectrometry. The preliminary data are encouraging and the protein modulation reported is consistent with the antitumoral effect of RC307 on the HCT116 cell line. Partial least squares discriminant analysis coupled with backward elimination variable selection allowed the identification of a larger number of spots than classic PDQuest analysis. Moreover, it allows the achievement of the best performances of the model in terms of prediction and provides therefore more robust and reliable results. From this point of view, the multivariate procedure applied can be considered a good alternative to standard differential analysis, also taking into account the interdependencies existing among the variables.

2D-PAGE maps analysis

Due to the low reproducibility affecting 2D gel-electrophoresis and the complex maps provided by this technique, the use of effective and robust methods for the comparison and classification of 2D maps is a fundamental tool for the development of automated diagnostic methods. A review of classical and recently developed methods for the comparison of 2D maps is presented here. The methods proposed regard both the analysis of spot volume datasets through multivariate statistical tools (pattern recognition methods, cluster analysis, and classification methods) and the analysis of 2D map images through fuzzy logic, three-way PCA, and the use of moment functions. The theoretical basis of each procedure is briefly introduced, together with a review of the most interesting applications present in recent literature.

Proteomic profiling of chronic low-frequency stimulated fast muscle

Skeletal muscle fibre transitions occur in many biological processes, in response to alterations in neuromuscular activity, in muscular disorders, during age-induced muscle wasting and in myogenesis. It was therefore of interest to perform a comprehensive proteomic profiling of muscle transformation. Chronic low-frequency stimulation of the rabbit tibialis anterior muscle represents an established model system for studying the response of fast fibres to enhanced neuromuscular activity under conditions of maximum activation. We have conducted a DIGE analysis of unstimulated control specimens versus 14- and 60-day conditioned muscles. A differential expression pattern was observed for 41 protein species with 29 increased and 12 decreased muscle proteins. Identified classes of proteins that are changed during the fast-to-slow transition process belong to the contractile machinery, ion homeostasis, excitation-contraction coupling, capillarization, metabolism and stress response. Results from immunoblotting agreed with the conversion of the metabolic, regulatory and contractile molecular apparatus to support muscle fibres with slower twitch characteristics. Besides confirming established muscle elements as reliable transition markers, this proteomics-based study has established the actin-binding protein cofilin-2 and the endothelial marker transgelin as novel biomarkers for evaluating muscle transformation.

Proteomic analysis of core breakdown disorder in Conference pears (Pyrus communis L.)

2-DE was applied to study core breakdown disorder in controlled atmosphere stored 'Conference' pears. This physiological disorder is characterized by internal browning of the fruit tissue and the development of cavities. Suitable protein phenol extraction/ammonium acetate-methanol precipitation and 2-DE protocols for a wide pH range were established for pear tissue. The protein expression profiles of healthy, sound (intact tissue of pears with core breakdown) and brown tissue were analyzed with the univariate non-parametric Kolmogorov-Smirnov test and multivariate statistical techniques such as principal component analysis and partial least square discriminant analysis. Both statistical approaches revealed interesting differentially expressed proteins between healthy and disordered pears. LC-ESI-MS/MS identification of differentially expressed proteins between healthy and sound tissue revealed their participation in the energy metabolism, the antioxidant system and ethylene biosynthesis. Up-regulated characteristic proteins in brown tissue were mainly involved in energy metabolism and defense mechanisms. Proteomics coupled to univariate and multivariate statistical techniques seems to be an efficient approach to get a better insight into the different mechanisms and pathways leading to the core breakdown disorder.

Proteomic Profiling of the Silkworm Skeletal Muscle Proteins during Larval−Pupal Metamorphosis

The silkworm is a typical holometabolous insect going through drastic morphological changes upon metamorphosis from larvae to pupae. Comprehensive studies focusing on the changes help elucidate understanding of a biogenic mechanism. Here, we report the initial profile of the intersegmental muscle (ISM) proteins of the silkworm during larval-pupal metamorphosis. In total, 258 protein spots were resolved by two-dimensional gel electrophoresis (2-DE). Fifty-seven larval proteins were identified, where 3 proteins were exclusively detected in larval samples. Fifty-four other proteins were common in pupal samples. Of these, 12 proteins belonging to the contractile apparatus, metabolism, regulation, and signal transduction were altered in their contents during the metamorphosis from larvae to pupae. Three pupa-defective proteins were identified as isoforms of troponin I, followed by an immunoblotting validation. This data will be helpful in understanding the biochemistry of an insect ISM.