Proteomic changes involved in tenderization of bovine Longissimus dorsi muscle during prolonged ageing

To study proteomic changes involved in tenderization of bovine Longissimus dorsi four Charolaise heifers and four Charolaise bull's muscles were sampled at slaughter after early and long ageing (2-4°C for 12 and 26days respectively). Descriptive sensory evaluation of samples were performed and their tenderness evaluated by Warner-Bratzler shear force test. Protein composition of fresh muscle and of meat aged was analysed by cartesian and polar 2-D electrophoresis. Student's t-test and Ranking-PCA analyses were performed to detect proteomic modulation, and the selected protein spots were identified by nano-HPLC-Chip MS/MS. This research has demonstrated that there are no differences between proteomic patterns of male and females Longissimus dorsi muscle, and that the extension of ageing beyond 12days, did not brings any concrete advantage in terms of sensory quality. Furthermore, the data presented here demonstrated that meat maturation caused changes of the abundance of proteins involved in metabolic, structural, and stress related processes.

Numerical approaches for quantitative analysis of two-dimensional maps: A review of commercial software and home-made systems

The present review attempts to cover a number of methods that have appeared in the last few years for performing quantitative proteome analysis. However, due to the large number of methods described for both electrophoretic and chromatographic approaches, we have limited this review to conventional two-dimensional (2-D) map analysis which couples orthogonally a charge-based step (isoelectric focusing) to a size-based separation step (sodium dodecyl sulfate-electrophoresis). The first and oldest method applied to 2-D map data reduction is based on statistical analysis performed on sets of gels via powerful software packages, such as Melanie, PDQuest, Z3 and Z4000, Phoretix and Progenesis. This method calls for separately running a number of replicas for control and treated samples. The two sets of data are then merged and compared via a number of software packages which we describe. In addition to commercially-available systems, a number of home made approaches for 2-D map comparison have been recently described and are also reviewed. They are based on fuzzyfication of the digitized 2-D gel image coupled to linear discriminant analysis, three-way principal component analysis or a combination of principal component analysis and soft-independent modeling of class analogy. These statistical tools appear to perform well in differential proteomic studies.

Determination of perfluorochemicals in biological, environmental and food samples by an automated on-line solid phase extraction ultra high performance liquid chromatography tandem mass spectrometry method

A rapid on-line solid phase extraction ultra high performance liquid chromatography tandem mass spectrometry method was developed for the identification and quantitation of nine perfluorinated compounds in matrices of environmental, biological and food interest. Pre-treatment, solid phase extraction, chromatographic and mass detection conditions were optimised, in order to apply the whole methodology to the analysis of different matrices. Particular attention was devoted to the evaluation of matrix effect and the correlated phenomena of ion enhancement or suppression in mass spectrometry detection. LOD and LOQ range from 3 to 15ngL(-1) and from 10 to 50ngL(-1), respectively. Method detection limits (MDLs) were also calculated for each kind of matrix. The recovery, evaluated for each analyte, does not depend on analyte concentration in the explored concentration range: average R¯% values are always greater than 82.9%. In the whole, the results obtained for samples of river waters, blood serum, blood plasma, and fish confirm the ubiquitous presence of perfluorinated compounds, as recently denounced by many sources.

Extracellular Vesicles Mediate Mesenchymal Stromal Cell-Dependent Regulation of B Cell PI3K-AKT Signaling Pathway and Actin Cytoskeleton

Mesenchymal stromal cells (MSCs) are adult, multipotent cells of mesodermal origin representing the progenitors of all stromal tissues. MSCs possess significant and broad immunomodulatory functions affecting both adaptive and innate immune responses once MSCs are primed by the inflammatory microenvironment. Recently, the role of extracellular vesicles (EVs) in mediating the therapeutic effects of MSCs has been recognized. Nevertheless, the molecular mechanisms responsible for the immunomodulatory properties of MSC-derived EVs (MSC-EVs) are still poorly characterized. Therefore, we carried out a molecular characterization of MSC-EV content by high-throughput approaches. We analyzed miRNA and protein expression profile in cellular and vesicular compartments both in normal and inflammatory conditions. We found several proteins and miRNAs involved in immunological processes, such as MOES, LG3BP, PTX3, and S10A6 proteins, miR-155-5p, and miR-497-5p. Different in silico approaches were also performed to correlate miRNA and protein expression profile and then to evaluate the putative molecules or pathways involved in immunoregulatory properties mediated by MSC-EVs. PI3K-AKT signaling pathway and the regulation of actin cytoskeleton were identified and functionally validated in vitro as key mediators of MSC/B cell communication mediated by MSC-EVs. In conclusion, we identified different molecules and pathways responsible for immunoregulatory properties mediated by MSC-EVs, thus identifying novel therapeutic targets as safer and more useful alternatives to cell or EV-based therapeutic approaches.

Blood transcriptomics of drug-naïve sporadic Parkinson's disease patients

BACKGROUND

Parkinson's disease (PD) is a chronic progressive neurodegenerative disorder that is clinically defined in terms of motor symptoms. These are preceded by prodromal non-motor manifestations that prove the systemic nature of the disease. Identifying genes and pathways altered in living patients provide new information on the diagnosis and pathogenesis of sporadic PD.

METHODS

Changes in gene expression in the blood of 40 sporadic PD patients and 20 healthy controls ("Discovery set") were analyzed by taking advantage of the Affymetrix platform. Patients were at the onset of motor symptoms and before initiating any pharmacological treatment. Data analysis was performed by applying Ranking-Principal Component Analysis, PUMA and Significance Analysis of Microarrays. Functional annotations were assigned using GO, DAVID, GSEA to unveil significant enriched biological processes in the differentially expressed genes. The expressions of selected genes were validated using RT-qPCR and samples from an independent cohort of 12 patients and controls ("Validation set").

RESULTS

Gene expression profiling of blood samples discriminates PD patients from healthy controls and identifies differentially expressed genes in blood. The majority of these are also present in dopaminergic neurons of the Substantia Nigra, the key site of neurodegeneration. Together with neuronal apoptosis, lymphocyte activation and mitochondrial dysfunction, already found in previous analysis of PD blood and post-mortem brains, we unveiled transcriptome changes enriched in biological terms related to epigenetic modifications including chromatin remodeling and methylation. Candidate transcripts as CBX5, TCF3, MAN1C1 and DOCK10 were validated by RT-qPCR.

CONCLUSIONS

Our data support the use of blood transcriptomics to study neurodegenerative diseases. It identifies changes in crucial components of chromatin remodeling and methylation machineries as early events in sporadic PD suggesting epigenetics as target for therapeutic intervention.

High-performance liquid chromatography-ultraviolet detection method for the simultaneous determination of typical biogenic amines and precursor amino acids. Applications in food chemistry

A reversed-phase high-performance liquid chromatography (HPLC) method was developed for the simultaneous determination in food of biogenic amines and their precursor amino acids after a precolumn derivatization with dansyl chloride. The chromatographic conditions, selected to be suitable for mass spectrometry detection, were optimized through experimental design and artificial neural networks. The HPLC-UV method was validated by comparing the separation results with those obtained through a HPLC method, working under the same chromatographic conditions but employing mass spectrometry detection. The HPLC-UV method was then applied to the analysis of different food samples, namely, cheese, clams, salami, and beer. For all of the matrices, recoveries (relative standard deviation always <5%) always >92% were obtained. The results are discussed as a function of the total biogenic amine content and of the concentration ratio between amines and precursor amino acids.

Secretome protein signature of human pancreatic cancer stem-like cells

Emerging research has demonstrated that pancreatic ductal adenocarcinoma (PDAC) contains a sub-population of cancer stem cells (CSCs) characterized by self-renewal, anchorage-independent-growth, long-term proliferation and chemoresistance. The secretome analysis of pancreatic CSCs has not yet been performed, although it may provide insight into tumour/microenvironment interactions and intracellular processes, as well as to identify potential biomarkers. To characterize the secreted proteins of pancreatic CSCs, we performed an iTRAQ-based proteomic analysis to compare the secretomes of Panc1 cancer stem-like cells (Panc1 CSCs) and parental cell line. A total of 72 proteins were found up-/down-regulated in the conditioned medium of Panc1 CSCs. The pathway analysis revealed modulation of vital physiological pathways including glycolysis, gluconeogenesis and pentose phosphate. Through ELISA immunoassays we analysed the presence of the three proteins most highly secreted by Panc1 CSCs (ceruloplasmin, galectin-3, and MARCKS) in sera of PDAC patient. ROC curve analysis suggests ceruloplasmin as promising marker for patients negative for CA19-9. Overall, our study provides a systemic secretome analysis of pancreatic CSCs revealing a number of secreted proteins which participate in pathological conditions including cancer differentiation, invasion and metastasis. They may serve as a valuable pool of proteins from which biomarkers and therapeutic targets can be identified.

BIOLOGICAL SIGNIFICANCE

The secretome of CSCs is a rich reservoir of biomarkers of cancer progression and molecular therapeutic targets, and thus is a topic of great interest for cancer research. The secretome analysis of pancreatic CSCs has not yet been performed. Recently, our group has demonstrated that Panc-1 CSCs isolated from parental cell line by using the CSC selective medium, represent a model of great importance to deepen the understanding of the biology of pancreatic adenocarcinoma. To our knowledge, this is the first proteomic study of pancreatic CSC secretome. We performed an iTRAQ-based analysis to compare the secretomes of Panc1 CSCs and Panc1 parental cell line and identified a total of 43 proteins secreted at higher level by pancreatic cancer stem cells. We found modulation of different vital physiological pathways (such as glycolysis and gluconeogenesis, pentose phosphate pathway) and the involvement of CSC secreted proteins (for example 72kDa type IV collagenase, galectin-3, alpha-actinin-4, and MARCKS) in pathological conditions including cancer differentiation, invasion and metastasis. By ELISA verification we found that MARCKS and ceruloplasmin discriminate between controls and PDAC patients; in addition ROC curve analyses indicate that MARCKS does not have diagnostic accuracy, while ceruloplasmin could be a promising marker only for patients negative for CA19-9. We think that the findings reported in our manuscript advance the understanding of the pathways implicated in tumourigenesis, metastasis and chemoresistance of pancreatic cancer, and also identify a pool of proteins from which novel candidate diagnostic and therapeutic biomarkers could be discovered.

Chemical profiling and multivariate data fusion methods for the identification of the botanical origin of honey

The characterization of 72 Italian honey samples from 8 botanical varieties was carried out by a comprehensive approach exploiting data fusion of IR, NIR and Raman spectroscopies, Proton Transfer Reaction - Time of Flight - Mass Spectrometry (PTR-MS) and electronic nose. High-, mid- and low-level data fusion approaches were tested to verify if the combination of several analytical sources can improve the classification ability of honeys from different botanical origins. Classification was performed on the fused data by Partial Least Squares - Discriminant Analysis; a strict validation protocol was used to estimate the predictive performances of the models. The best results were obtained with high-level data fusion combining Raman and NIR spectroscopy and PTR-MS, with classification performances better than those obtained on single analytical sources (accuracy of 99% and 100% on test and training samples respectively). The combination of just three analytical sources assures a limited time of analysis.

Impact of Beneficial Microorganisms on Strawberry Growth, Fruit Production, Nutritional Quality, and Volatilome

Arbuscular mycorrhizal fungi (AMF) colonize the roots of most terrestrial plant species, improving plant growth, nutrient uptake and biotic/abiotic stress resistance and tolerance. Similarly, plant growth promoting bacteria (PGPB) enhance plant fitness and production. In this study, three different AMF (Funneliformis mosseae, Septoglomus viscosum, and Rhizophagus irregularis) were used in combination with three different strains of Pseudomonas sp. (19Fv1t, 5Vm1K and Pf4) to inoculate plantlets of Fragaria × ananassa var. Eliana F1. The effects of the different fungus/bacterium combinations were assessed on plant growth parameters, fruit production and quality, including health-promoting compounds. Inoculated and uninoculated plants were maintained in a greenhouse for 4 months and irrigated with a nutrient solution at two different phosphate levels. The number of flowers and fruits were recorded weekly. At harvest, fresh and dry weights of roots and shoots, mycorrhizal colonization and concentration of leaf photosynthetic pigments were measured in each plant. The following fruit parameters were recorded: pH, titratable acids, concentration of organic acids, soluble sugars, ascorbic acids, and anthocyanidins; volatile and elemental composition were also evaluated. Data were statistically analyzed by ANOVA and PCA/PCA-DA. Mycorrhizal colonization was higher in plants inoculated with R. irregularis, followed by F. mosseae and S. viscosum. In general, AMF mostly affected the parameters associated with the vegetative portion of the plant, while PGPB were especially relevant for fruit yield and quality. The plant physiological status was differentially affected by inoculations, resulting in enhanced root and shoot biomass. Inoculation with Pf4 bacterial strain increased flower and fruit production per plant and malic acid content in fruits, while decreased the pH value, regardless of the used fungus. Inoculations affected fruit nutritional quality, increasing sugar and anthocyanin concentrations, and modulated pH, malic acid, volatile compounds and elements. In the present study, we show for the first time that strawberry fruit concentration of some elements and/or volatiles can be affected by the presence of specific beneficial soil microorganisms. In addition, our results indicated that it is possible to select the best plant-microorganism combination for field applications, and improving fruit production and quality, also in terms of health promoting properties.

The distally based superficial sural flap: our experience in reconstructing the lower leg and foot

The treatment of soft-tissue defects of the lower third of the leg and foot is often an awkward problem to tackle because of the frequent involvement of muscle, tendon, and bone, which is caused by the thinness and poor circulation of the skin covering them and by the small quantity of local tissue available for reconstruction. The authors present their experience with the use of sural flaps for the treatment of small- and medium-size defects of the distal region of the lower limb. The flap used was a distally based fasciocutaneous flap raised in the posterior region of the lower two thirds of the leg. Vascularization was ensured by the superficial sural artery, which accompanies the sural nerve together with the short saphenous vein. The authors treated 18 patients (12 men and 6 women) from May 1997 to August 1999 at the Division of Plastic Surgery, University of Turin, Italy. Superficial necrosis without involvement of the deep fascia (which was grafted 1 month later) occurred in 1 patient of the 18 treated. In another 2 patients, defects were found in the flap margins, but no additional surgical revision was necessary, and recovery occurred by secondary intention. In every patient the sural flaps provided good coverage of the defects, both from a functional and an aesthetic point of view. The major advantages of this flap are its easy and quick dissection. Because the major arterial axis is not sacrificed, this flap can be used in a traumatic leg with damaged major arteries.

Preliminary toxicological assessment of phthalate esters from drinking water consumed in Portugal

This paper reports, for the first time, the concentrations of selected phthalates in drinking water consumed in Portugal. The use of bottled water in Portugal has increased in recent years. The main material for bottles is polyethylene terephthalate (PET). Its plasticizer components can contaminate water by leaching, and several scientific studies have evidenced potential health risks of phthalates to humans of all ages. With water being one of the most essential elements to human health and because it is consumed by ingestion, the evaluation of drinking water quality, with respect to phthalate contents, is important. This study tested seven commercial brands of bottled water consumed in Portugal, six PET and one glass (the most consumed) bottled water. Furthermore, tap water from Lisbon and three small neighbor cities was analyzed. Phthalates (di-n-butyl phthalate ester (DnBP), bis(2-ethylhexyl) phthalate ester (DEHP), and di-i-butyl phthalate ester (DIBP)) in water samples were quantified (PET and glass) by means of direct immersion solid-phase microextraction and ionic liquid gas chromatography associated with flame ionization detection or mass spectrometry due to their high boiling points and water solubility. The method utilized in this study showed a linear range for target phthalates between 0.02 and 6.5 μg L(-1), good precision and low limits of detection that were between 0.01 and 0.06 μg L(-1), and quantitation between 0.04 and 0.19 μg L(-1). Only three phthalates were detected in Portuguese drinking waters: dibutyl (DnBP), diisobutyl (DIBP), and di(ethylhexyl) phthalate (DEHP). Concentrations ranged between 0.06 and 6.5 μg L(-1) for DnBP, between 0.02 and 0.16 μg L(-1) for DEHP, and between 0.1 and 1.89 μg L(-1) for DIBP. The concentration of DEHP was found to be up to five times higher in PET than in glass bottled water. Surprisingly, all the three phthalates were detected in glass bottled water with the amount of DnBP being higher (6.5 μg L(-1)) than in PET bottled water. These concentrations do not represent direct risk to human health. Regarding potable tap water, only DIBP and DEHP were detected. Two of the cities showed concentration of all three phthalates in their water below the limits of detection of the method. All the samples showed phthalate concentrations below 6 μg L(-1), the maximum admissible concentration in water established by the US Environmental Protection Agency. The concentrations measured in Portuguese bottled waters do not represent any risk for adult's health.

A new integrated statistical approach to the diagnostic use of two-dimensional maps

Two-dimensional (2-D) electrophoresis is a very useful technique for the analysis of proteins in biological tissues. The complexity of the 2-D maps obtained causes many difficulties in the comparison of different samples. A new method is proposed for comparing different 2-D maps, based on five steps: (i) the digitalisation of the image; (ii) the transformation of the digitalised map in a fuzzy entity, in order to consider the variability of the 2-D electrophoretic separation; (iii) the calculation of a similarity index for each pair of maps; (iv) the analysis by multidimensional scaling of the previously obtained similarity matrix; (v) the analysis by classification or cluster analysis techniques of the resulting map co-ordinates. The method adopted was first tested on some simulated samples in order to evaluate its sensitivity to small changes in the spots position and size. The optimal setting of the method parameters was also investigated. Finally, the method was successfully applied to a series of real samples corresponding to the electrophoretic bidimensional analysis of sera from normal and nicotine-treated rats. Multidimensional scaling allowed the separation of the two classes of samples without any misclassification.

Multivariate statistical tools applied to the characterization of the proteomic profiles of two human lymphoma cell lines by two-dimensional gel electrophoresis

Mantle cell lymphoma (MCL) cell lines have been difficult to generate, since only few have been described so far and even fewer have been thoroughly characterized. Among them, there is only one cell line, called GRANTA-519, which is well established and universally adopted for most lymphoma studies. We succeeded in establishing a new MCL cell line, called MAVER-1, from a leukemic MCL, and performed a thorough phenotypical, cytogenetical and molecular characterization of the cell line. In the present report, the phenotypic expression of GRANTA-519 and MAVER-1 cell lines has been compared and evaluated by a proteomic approach, exploiting 2-D map analysis. By univariate statistical analysis (Student's t-test, as commonly used in most commercial software packages), most of the protein spots were found to be identical between the two cell lines. Thirty spots were found to be unique for the GRANTA-519, whereas another 11 polypeptides appeared to be expressed only by the MAVER-1 cell line. A number of these spots could be identified by MS. These data were confirmed and expanded by multivariate statistical tools (principal component analysis and soft-independent model of class analogy) that allowed identification of a larger number of differently expressed spots. Multivariate statistical tools have the advantage of reducing the risk of false positives and of identifying spots that are significantly altered in terms of correlated expression rather than absolute expression values. It is thus suggested that, in future work in differential proteomic profiling, both univariate and multivariate statistical tools should be adopted.

Proteins involved in biotic and abiotic stress responses as the most significant biomarkers in the ripening of Pinot Noir skins

We propose an integrated approach, obtained by the combination of multivariate statistics and proteomics, useful to isolate candidate biomarkers for the evaluation of grape ripening. We carried out a comparative 2-DE analysis of grape skins collected in three moments of ripening and analyzed the spot volume dataset through the application of principal component analysis followed by forward stepwise-linear discriminant analysis. This technique allowed to discriminate véraison, quite mature and mature samples, and to sort the matched spots according to their significance. We identified 36 spots showing high discriminating coefficients through liquid chromatography - electrospray ionization - tandem mass spectrometry (LC-ESI-MS/MS). Most of them were involved in biotic and abiotic stress responses indicating these enzymes as good candidate markers of berry ripening. These evidences hint at a likely developmental role of these proteins, in addition to their reported activity in stress events. Restricting the same statistical analysis to the samples belonging to the two last stages, it was indicated that this approach can clearly distinguish these close and similar phases of berry development. Taken all together, these results bear out that the employment of the combination of 2-DE and multivariate statistics is a reliable tool in the identification of new protein markers for describing the ripening phases and to assess the overall quality of the fruit.

A Method for Monitoring the Surface Conservation of Wooden Objects by Raman Spectroscopy and Multivariate Control Charts

The principles of quality control and multivariate statistical analysis were applied to the monitoring of the conservation state of wooden works of art. Three degradation processes (exposure to a wet atmosphere, to an acidic attack, and to UV light) were simulated on the surface of wooden boards of the XVI century and were monitored by the use of Raman spectroscopy. The resulting spectra were treated by principal component analysis, which allowed reduction of the system dimensionality. The relevant principal components were used to build multivariate control charts, namely, the Shewhart, CUSUM, and SMART (simultaneous scores monitoring and residual tracking) control charts. The Shewhart charts allowed identification of the effects due to the degradation processes. The CUSUM charts permitted identifcation of the exact moment in which the degradation treatment was started. The SMART charts provided a synthetic description of the conservation state of the wooden surface by means of only two charts: the T2 Hotelling and the DModX charts.

Monitoring of the surface of paper samples exposed to UV light by ATR-FT-IR spectroscopy and use of multivariate control charts

The effect of exposure of paper samples to UV light was monitored by use of ATR-FT-IR spectroscopy and multivariate statistical tools. Three types of paper were tested: common laser-printer paper, news print, and thermal fax paper. The samples were first characterised by ATR-FT-IR spectroscopy to determine natural experimental variability. They were then exposed to UV light for 30 h and the effects of the exposure were monitored by use of the same spectroscopic technique. Finally, multivariate statistical tools were applied to the final dataset, coupled with construction of multivariate control charts, to identify the effects of UV light on the sample surfaces.

Application of three-way principal component analysis to the evaluation of two-dimensional maps in proteomics

Three-way PCA has been applied to proteomic pattern images to identify the classes of samples present in the dataset. The developed method has been applied to two different datasets: a rat sera dataset, constituted by five samples of healthy Wistar rat sera and five samples of nicotine-treated Wistar rat sera; a human lymph-node dataset constituted by four healthy lymph-nodes and four lymph-nodes affected by a non-Hodgkin's lymphoma. The method proved to be successful in the identification of the classes of samples present in both of the groups of 2D-PAGE images, and it allowed us to identify the regions of the two-dimensional maps responsible for the differences occurring between the classes for both rat sera and human lymph-nodes datasets.