Approaches for the study of cancer: towards the integration of genomics, proteomics and metabolomics

Recent technological advances, combined with the development of bioinformatic tools, allow us to better address biological questions combining -omic approaches (i.e., genomics, metabolomics and proteomics). This novel comprehensive perspective addresses the identification, characterisation and quantitation of the whole repertoire of genes, proteins and metabolites occurring in living organisms. Here we provide an overview of recent significant advances and technologies used in genomics, metabolomics and proteomics. We also underline the importance and limits of mass accuracy in mass spectrometry-based -omics and briefly describe emerging types of fragmentation used in mass spectrometry. The range of instruments and techniques used to address the study of each -omic approach, which provide vast amounts of information (usually termed "high-throughput" technologies in the literature) is briefly discussed, including names, links and descriptions of the main databases, data repositories and resources used. Integration of multiple -omic results and procedures seems necessary. Therefore, an emerging challenge is the integration of the huge amount of data generated and the standardisation of the procedures and methods used. Functional data integration will lead to answers to unsolved questions, hopefully, applicable to clinical practice and management of patients (AU)

Changes to the proteome and targeted metabolites of xylem sap in Brassica oleracea in response to salt stress.

Root-to-shoot signalling via xylem sap is an important mechanism by which plants respond to stress. This signalling could be mediated by alteration in the concentrations of inorganic and/or organic molecules. The effect of salt stress on the contents of xylem sap in Brassica olarecea has been analysed by mass spectrometry in order to quantify these changes. Subcellular location of arabinogalactan proteins (AGPs) by immunogold labelling and peroxidase isozymes was also analysed by isoelectrofocusing. The xylem sap metabolome analysis demonstrated the presence of many organic compounds such as sugars, organic acids and amino acids. Of these, amino acid concentrations, particularly that of glutamine, the major amino acid in the sap, were substantially reduced by salt stress. The xylem sap proteome analysis demonstrated the accumulation of enzymes involved in xylem differentiation and lignification, such as cystein proteinases, acid peroxidases, and a putative hydroxycinnamoyl-CoA:shikimate hydroxycinnamoyl transferase under salt stress. The peroxidase isozyme pattern showed that salt stress induced a high accumulation of an acid isoform. These results suggest that xylem differentiation and lignification is induced by salt stress. The combination of different methods to analyse the xylem sap composition provides new insights into mechanisms in plant development and signalling under salt stress.

Analysis of root plasma membrane aquaporins from Brassica oleracea: post-translational modifications, de novo sequencing and detection of isoforms by high resolution mass spectrometry.

Plasma membrane Intrinsic Proteins (PIPs), a subfamily of aquaporins, are ubiquitous membrane channel proteins that play a crucial role in water uptake in plants. The use of high-performance liquid chromatography coupled to tandem mass spectrometry (HPLC-MS/MS) analysis of peptides has previously shown to be a valuable tool to differentiate among PIP homologues sharing a high sequence homology and also to characterize their post-translational modifications (PTMs). The recent introduction of mass spectrometers able to measure peptide mass with high mass accuracy, together with new alternative ways of peptide fragmentation allows the identification and characterization of proteins from nonsequenced organisms, such as broccoli. In this study, we combined three endoproteases (trypsin, Glu-C and Lys-C) with HPLC-MS/MS analysis and two types of peptide fragmentations, CID (collision induced dissociation) and HCD (higher-energy C-trap dissociation), to identify PIP isoforms and PTMs from broccoli roots. After de novo sequencing analysis, eight peptides showing homology to Arabidopsis thaliana PIPs were identified. Although Arabidopsis nomenclature of PIP isoforms has not been defined for broccoli, our results agree with the occurrence of seven AtPIP isoforms (PIP 1;1, PIP 1;2, PIP 1;3 and PIP2;2, PIP 2;3, PIP2;1 and PIP2;7) in broccoli roots, as compared to the plant model A. thaliana. To our knowledge, these results represent the deepest characterization of the PIPs isolated from the roots of broccoli, a crop with increasing agronomical interest.

Effect of composted sewage sludge application to soil on sweet pepper crop (Capsicum annuum var. annuum) grown under two exploitation regimes.

The aim of this study is to monitor the effect of the application of three increasing amounts of composted sewage sludge (3, 6 and 9 kg compost m(-2)) on the physico-chemical properties of a horticultural calcareous soil where sweet pepper plants (Capsicum annuum var. annuum) cv. California were grown. A comparative study of two different exploitation regimes was carried out; the first was an open-air field-grown plot and the second plot was kept under controlled conditions in a greenhouse. Changes in physical and chemical properties measured in soil and sweet pepper crop were recorded during crop growth in order to measure the evolution of these properties as a consequence of increasing compost applications. Organic matter, total nitrogen Kjeldahl and available phosphorus contents increased in soil after composted sewage sludge applications. The 9 kg compost m(-2) application promoted the appearance of deleterious effects on the properties of soil, such as salt accumulation, a significant increase in the electrical conductivity and an input of heavy metals (Pb>Cr>Cd). The 6 kg compost m(-2) application provided a supply of nutrients necessary to grow peppers plants under both exploitation regimes. Pepper fruit biomass production under greenhouse was almost 60% higher compared to that of the open-air plot. Lower contents of Ca and increased levels of Cu in fruit under greenhouse growing conditions compared to those of open-air grown peppers seemed to promote the occurrence of blossom-end rot, affecting more than 10% of the harvested fruits.

Evaluation of composted sewage sludge as nutritional source for horticultural soils.

Water deficit and soil degradation have become some of the major problems for crop production in semi-arid regions, as it is the South East of Spain. As a matter of fact, considerable productivity loss and risk of erosion have to be taken into account in these areas, especially those with an horticultural use (Davis, 1989). Utilization of sewage sludge in agriculture. Agricultural Progress 64, 72-80]. Horticultural soils are highly vulnerable and prone to erosion, as vegetables are generally fast-growing species under intensive exploitation regimes. High-rate chemical inputs contribute to horticultural soil degradation and have a dramatic effect on soil microbial population and nutrient balance whilst, at the same time, have a counter-effect on price competitiveness of the vegetables to be commercialized. In this paper we monitored variations in physical, chemical and biological properties of a cauliflower plot where four increasing quantities of compost were applied. We carried out a three-stage sampling schedule in order to check the effect of compost applications doses. We conclude that a 2 kg compost/m2 application had a positive effect on physical and biological properties of the soil and provides a supply of nutrients to grow cauliflowers on its surface under intensive exploitation regimes without loss in biomass yield.