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.

Distinct Signatures of Tumor-Associated Microbiota and Metabolome in Low-Grade vs. High-Grade Dysplastic Colon Polyps: Inference of Their Role in Tumor Initiation and Progression.

According to the driver-passenger model for colorectal cancer (CRC), the tumor-associated microbiota is a dynamic ecosystem of bacterial species where bacteria with carcinogenic features linked to CRC initiation are defined as "drivers", while opportunistic bacteria colonizing more advanced tumor stages are known as "passengers". We reasoned that also gut microbiota-associated metabolites may be differentially enriched according to tumor stage, and be potential determinants of CRC development. Thus, we characterized the mucosa- and lumen-associated microbiota (MAM and LAM, respectively) and mucosa-associated metabolites in low- vs. high-grade dysplastic colon polyps from 78 patients. We show that MAM, obtained with a new biopsy-preserving approach, and LAM differ in composition and α/ß-diversity. By stratifying patients for polyp histology, we found that bacteria proposed as passengers by previous studies colonized high-grade dysplastic adenomas, whereas driver taxa were enriched in low-grade polyps. Furthermore, we report altered "mucosa-associated metabolite" levels in low- vs. high-grade groups. Integrated microbiota-metabolome analysis suggests the involvement of the gut microbiota in the production and consumption of these metabolites. Altogether, our findings support the involvement of bacterial species and associated metabolites in CRC mucosal homeostasis in a tumor-stage-specific manner. These distinct signatures may be used to distinguish low-grade from high-grade dysplastic polyps.

Identification of Illicit Conservation Treatments in Fresh Fish by Micro-Raman Spectroscopy and Chemometric Methods.

In the field of food control for fresh products, the identification of foods subjected to illicit conservation treatments to extend their shelf life is fundamental. Fresh fish products are particularly subjected to this type of fraud due to their high commercial value and the fact that they often have to be transported over a long distance, keeping their organoleptic characteristics unaltered. Treatments of this type involve, e.g., the bleaching of the meat and/or the momentary abatement of the microbial load, while the degradation process continues. It is therefore important to find rapid methods that allow the identification of illicit treatments. The study presented here was performed on 24 sea bass samples divided into four groups: 12 controls (stored on ice in the fridge for 3 or 24 h), and 12 treated with a Cafodos-like solution for 3 or 24 h. Muscle and skin samples were then characterized using micro-Raman spectroscopy. The data were pre-processed by smoothing and taking the first derivative and then PLS-DA models were built to identify short- and long- term effects on the fish's muscle and skin. All the models provided the perfect classification of the samples both in fitting and cross-validation and an analysis of the bands responsible for the effects was also reported. To the best of the authors' knowledge, this is the first time Raman spectroscopy has been applied for the identification of a Cafodos-like illicit treatment, focusing on both fish muscle and skin evaluation. The procedure could pave the way for a future application directly on the market through the use of a portable device.

Solar photodegradation of irinotecan in water: optimization and robustness studies by experimental design.

Irinotecan, a widely prescribed anticancer drug, is an emerging contaminant of concern that has been detected in various aquatic environments due to ineffective removal by traditional wastewater treatment systems. Solar photodegradation is a viable approach that can effectively eradicate the drug from aqueous systems. In this study, we used the design of experiment (DOE) approach to explore the robustness of irinotecan photodegradation under simulated solar irradiation. A full factorial design, including a star design, was applied to study the effects of three parameters: initial concentration of irinotecan (1.0-9.0 mg/L), pH (5.0-9.0), and irradiance (450-750 W/m2). A high-performance liquid chromatography coupled with a high-resolution mass spectrometry (HPLC-HRMS) system was used to determine irinotecan and identify transformation products. The photodegradation of irinotecan followed a pseudo-first order kinetics. In the best-fitted linear model determined by the stepwise model fitting approach, pH was found to have about 100-fold greater effect than either irinotecan concentration or solar irradiance. Under optimal conditions (irradiance of 750 W/m2, 1.0 mg/L irinotecan concentration, and pH 9.0), more than 98% of irinotecan was degraded in 60 min. With respect to irradiance and irinotecan concentration, the degradation process was robust in the studied range, implying that it may be effectively applied in locations and/or seasons with solar irradiance as low as 450 W/m2. However, pH needs to be strictly controlled and kept between 7.0 and 9.0 to maintain the degradation process robust. Considerations about the behavior of degradation products were also drawn.

On the Traceability of the Hazelnut Production Chain by Means of Trace Elements.

The production chain of hazelnuts has been studied by analyzing three sets of samples produced in purity from three different pools of hazelnuts of cultivar "Tonda Gentile Trilobata", "Tonda Gentile Romana" and "Mortarella", all cultivated in Italy. From each pool, five processed products were obtained: roasted hazelnuts, hazelnut paste, hazelnut cream, Gianduja paste and Gianduiotto paste. After pre-treatment by means of dry ashing, all samples from each cultivar, including raw hazelnuts, were then analyzed by means of Inductively Coupled Plasma-Optical Emission Spectroscopy (ICP-OES) and Inductively Coupled Plasma-Mass Spectrometry (ICP-MS). A good discrimination was obtained among the different chain stages according to the distribution of the trace elements, as expected. More interesting was the discrimination among the different cultivars: it was possible to distinguish the samples produced from the respective cultivar by means of specific chemical markers, particularly Mo and Ni.

Transcriptional Biomarkers and Immunohistochemistry for Detection of Illicit Dexamethasone Administration in Veal Calves.

Corticosteroids such as Dexamethasone (DEX) are commonly licensed for therapy in meat animals due to their known pharmacological properties. However, their misuse aimed to achieve anabolic effects is often found by National Residues Control Plans. The setup of a complementary "biomarker based" methods to unveil such illicit practices is encouraged by current European legislation. In this study, the combined use of molecular and histological quantitative techniques was applied on formalin fixed paraffin embedded (FFPE) muscle samples to assess the effects of illicit DEX treatment on veal calves. A PCR array, including 28 transcriptional biomarkers related to DEX exposure, was combined with a histochemical analysis of muscle fiber. An analysis based on unsupervised (PCA) and supervised (PLS-DA and Kohonen's SOM) methods, was applied in order to define multivariate models able to classify animals suspected of illicit treatment by DEX. According to the conventional univariate approach, a not-significant reduction in type I fibres was recorded in the DEX-treated group, and only 12 out of 28 targeted genes maintained their expected differential expression, confirming the technical limitations of a quantitative analysis on FFPE samples. However, the multivariate models developed highlighted the possibility to establish complementary screening strategies, particularly when based on transcriptional biomarkers characterised by low expression profiles.

Prolonged exposure to simulated microgravity promotes stemness impairing morphological, metabolic and migratory profile of pancreatic cancer cells: a comprehensive proteomic, lipidomic and transcriptomic analysis.

BACKGROUND: The impact of the absence of gravity on cancer cells is of great interest, especially today that space is more accessible than ever. Despite advances, few and contradictory data are available mainly due to different setup, experimental design and time point analyzed. METHODS: Exploiting a Random Positioning Machine, we dissected the effects of long-term exposure to simulated microgravity (SMG) on pancreatic cancer cells performing proteomic, lipidomic and transcriptomic analysis at 1, 7 and 9 days. RESULTS: Our results indicated that SMG affects cellular morphology through a time-dependent activation of Actin-based motility via Rho and Cdc42 pathways leading to actin rearrangement, formation of 3D spheroids and enhancement of epithelial-to-mesenchymal transition. Bioinformatic analysis reveals that SMG may activates ERK5/NF-κB/IL-8 axis that triggers the expansion of cancer stem cells with an increased migratory capability. These cells, to remediate energy stress and apoptosis activation, undergo a metabolic reprogramming orchestrated by HIF-1α and PI3K/Akt pathways that upregulate glycolysis and impair ß-oxidation, suggesting a de novo synthesis of triglycerides for the membrane lipid bilayer formation. CONCLUSIONS: SMG revolutionizes tumor cell behavior and metabolism leading to the acquisition of an aggressive and metastatic stem cell-like phenotype. These results dissect the time-dependent cellular alterations induced by SMG and pave the base for altered gravity conditions as new anti-cancer technology.

A Fully Automated Online SPE-LC-MS/MS Method for the Determination of 10 Pharmaceuticals in Wastewater Samples.

The increasing use of pharmaceuticals, their presence in the aquatic environment, and the associated toxic effects, have raised concerns in recent years. In this work, a new multi-residue analytical method was developed and validated for the determination of 10 pharmaceuticals in wastewaters using online solid-phase extraction (online SPE) and liquid chromatography-tandem mass spectrometry (LC-MS/MS). The compounds included in the method were antineoplastics (cabazitaxel, docetaxel, doxorubicin, etoposide, irinotecan, methotrexate, paclitaxel, and topotecan), renin inhibitors (aliskiren), and antidepressants (maprotiline). The method was developed through several experiments on four online SPE cartridges, three reversed phase chromatography columns, and four combinations of mobile phase components. Under optimal conditions, very low limits of detection (LODs) of 1.30 to 10.6 ng L-1 were obtained. The method was repeatable, with relative standard deviations (RSD, %) for intraday and interday precisions ranged from 1.6 to 7.8 and from 3.3 to 13.2, respectively. Recovery values ranged from 78.4 to 111.4%, indicating the reproducibility of the method. Matrix effects were mainly presented as signal suppression, with topotecan and doxorubicin being the two most affected compounds (31.0% signal suppression). The proposed method was successfully applied to hospital effluents, detecting methotrexate (4.7-9.3 ng L-1) and maprotiline (11.2-23.1 ng L-1). Due to the shorter overall run time of 15 min, including sample preparation, and reduced sample volume (0.9 mL), this on-line SPE-LC-MS/MS method was extremely convenient and efficient in comparison to the classical off-line SPE method. The proposed method was also highly sensitive and can be used for ultratrace quantification of the studied pharmaceuticals in wastewaters, providing useful data for effective environmental monitoring.

A Systematic Study of the Antibacterial Activity of Basidiomycota Crude Extracts.

The excessive consumption of antibiotics in clinical, veterinary and agricultural fields has resulted in tremendous flow of antibiotics into the environment. This has led to enormous selective pressures driving the evolution of antimicrobial resistance genes in pathogenic and commensal bacteria. In this context, the World Health Organization (WHO) has promoted research aiming to develop medical features using natural products that are often competitive with synthetic drugs in clinical performance. Fungi are considered an important source of bioactive molecules, often effective against other fungi and/or bacteria, and thus are potential candidates in the search of new antibiotics. Fruiting bodies of sixteen different fungal species of Basidiomycota were collected in the Italian Alps. The identification of fungal species was performed through Internal Transcribed Spacer (ITS) sequencing. Most species belong to genera Cortinarius, Mycena and Ramaria, whose metabolite contents has been scarcely investigated so far. The crude extracts obtained from the above mushrooms were tested for their inhibition activity against five human pathogens: Candida albicans ATCC 14053, C. glabrata ATCC 15126, Staphylococcus aureus NCTC 6571, Pseudomonas aeruginosa ATCC 27853 and Klebsiella pneumoniae ATCC 13883. Twelve crude extracts showed activity against P. aeruginosa ATCC 27853. Highest activity was shown by some Cortinarius species, as C. nanceiensis.

Kohonen Artificial Neural Network and Multivariate Analysis in the Identification of Proteome Changes during Early and Long Aging of Bovine Longissimus dorsi Muscle Using SWATH Mass Spectrometry.

To study proteomic changes involved in tenderization of Longissimus dorsi, Charolais heifers and bulls muscles were sampled after early and long aging (12 or 26 days). Sensory evaluation and instrumental tenderness measurement were performed. Proteins were analyzed by gel-free proteomics. By pattern recognition (principal component analysis and Kohonen's self-organizing maps) and classification (partial least squares-discriminant analysis) tools, 58 and 86 dysregulated proteins were detected after 12 and 26 days of aging, respectively. Tenderness was positively correlated mainly with metabolic enzymes (PYGM, PGAM2, TPI1, PGK1, and PFKM) and negatively with keratins. Downregulation in hemoglobin subunits and carbonic anhydrase 3 levels was relevant after 12 days of aging, while mimecan and collagen chains levels were reduced after 26 days of aging. Bioinformatics indicated that aging involves a prevalence of metabolic pathways after late and long periods. These findings provide a deeper understanding of changes involved in aging of beef and indicate a powerful method for future proteomics studies.

A new method for investigating microbiota-produced small molecules in adenomatous polyps.

The intestinal microbiota is composed of a large number of different bacteria that produce a variety of metabolites. Colorectal cancer, which typically develops from adenomatous polyps, is highly influenced by microbiota. Since a variety of molecular changes may occur as these polyps transform from benign tumor to malignant carcinoma, the ability to study the microbiota-produced metabolites can lead to new discoveries about the development and progression of this cancer. However, to address the complexity of the microbiota-produced molecules, novel methods are needed. To this aim, in the present work, we developed a high-throughput metabolomics method to capture the metabolic complexity of the microbiota metabolome adherent to adenomatous polyps and adenocarcinoma. For the first time, the method enables the simultaneous quantification of almost 300 metabolites, while preserving the integrity of the original sample. The metabolomics approach was analytically validated and had excellent performances in terms of recovery, linearity, specificity, intra- and inter-day precision, limits of detection, and quantification. Furthermore, the clinical potential of the method was demonstrated in adenoma collected for a colorectal adenoma study.

Two-Dimensional Gel Electrophoresis Image Analysis.

Gel-based proteomics is still quite widespread due to its high-resolution power; the experimental approach is based on differential analysis, where groups of samples (e.g., control vs diseased) are compared to identify panels of potential biomarkers. However, the reliability of the result of the differential analysis is deeply influenced by 2D-PAGE maps image analysis procedures. The analysis of 2D-PAGE images consists of several steps, such as image preprocessing, spot detection and quantitation, image warping and alignment, spot matching. Several approaches are present in literature, and classical or last-generation commercial software packages exploit different algorithms for each step of the analysis. Here, the most widespread approaches and a comparison of the different strategies are presented.

Chemometric Tools for 2D-PAGE Data Analysis.

Two-Dimensional Polyacrylamide Gel Electrophoresis (2D-PAGE) provides two-dimensional maps where proteins appear separated according to their isoelectric point (pI) and molecular weight (MW). Usually these maps are very complex (i.e., hundreds or thousands of spots can be present in each map), and characterized by a low reproducibility, which hinders the possibility to identify reliable biomarkers unless robust methods are applied. The analysis of different sets of 2D-PAGE maps (e.g., control vs. pathological or control vs. drug-treated samples) to identify candidate biomarkers (proteins under- or over-expressed in different conditions) is usually carried out through image analysis systems providing a so-called spot volume dataset where each sample corresponds to a map described by the optical densities of all the detected spots. The identification of candidate biomarkers can be therefore accomplished by comparing different maps by classical monovariate statistical tests applied spotwise, or by multivariate chemometric tools applied to the entire set of spots present on each map. Here, the most exploited multivariate techniques will be considered, ranging from pattern recognition to classification methods.

Determination by ICP-MS and multivariate data analysis of elemental urine excretion profile during the EDTA chelation therapy: A case study.

BACKGROUND: Based on the medical history and laboratory analytical tests, a patient presenting symptoms compatible with Chronic Fatigue Syndrome was suspected of metal intoxication; therefore, a chelating therapy was attempted. In parallel, the profile of elemental excretion in urine was determined. METHODS: Chelation therapy by CaNa2EDTA was administered every two weeks and urine samples were routinely collected for 17 months. The samples were mineralized with HNO3 69 % and analyzed by Inductively-Coupled Plasma - Mass Spectrometry. Data were processed by multivariate statistical methods. RESULTS: Most of the toxic elements showed a peak of excretion in 12-24 h after EDTA administration, which returned to basal level by 24-36 h after the treatment. Yet, the excretion of some trace elements persisted in the urine collected 26 h after the treatment. CONCLUSIONS: The analysis of excreted metals following the CaNa2EDTA infusion allowed to monitor dynamically the chelation therapy. The chelation therapy was effective in mobilizing and eliminating the principal heavy metals present from the body. However, since such clearance almost vanished 24 h after the treatment, a protocol with more frequent and low-dose administrations is advisable to improve the metal excretion.

Development and validation of a UHPLC-MS/MS method for the identification of irinotecan photodegradation products in water samples.

Irinotecan (CPT-11) is a water-soluble anticancer drug widely used to treat several types of cancer. Even if the metabolites of CPT-11 are well-known and investigated, only limited information is available in the literature about the formation of photo-degradation products that can naturally originate from sunlight irradiation when the drug is released in aqueous systems. CTP-11 solutions at 10.0 mg L-1 were irradiated by simulated sunlight. The intensity of the drug decreased by 90% after 7.5 days of irradiation and no significant reduction of absorbance values was observed after 13 days. A sensitive UHPLC-MS/MS method was developed employing a hybrid triple quadrupole/linear ion trap mass spectrometer, that is able to work in data-dependent acquisition mode and to obtain information about the compounds formed during the photoirradiation. Moreover, a selected reaction monitoring method was built using the MS/MS fragmentation pattern of the compounds previously investigated. The method was validated considering LOD, LOQ, linearity, precision, selectivity, recovery and matrix effect. LOD and LOQ values were 0.02 and 0.05 ng mL-1, respectively, whereas MDL and MQL values in real water samples (river water, groundwater, well water, and wastewater) were lower than 0.05 and 0.2 ng mL-1, respectively. Eight photodegradation products were identified, among which five for the first time. Based on the MS and MS/MS fragmentation, the chemical structures of the degradation products were proposed. Hydrolysis experiments were carried out on the same solutions preserved in the dark, but no formation of other species was highlighted. The method was applied to several real samples: CPT-11 was detected and quantified only in a hospital effluent sample at the concentration of 0.41 ±â€¯0.2 ng mL-1 together with the occurrence of PDP3. The outcomes of this study may be useful for updating the pollutant screening in water samples.

Monitoring of water quality inflow and outflow of a farm in Italian Padana plain for rice cultivation: a case study of two years.

Rice cultivation requires a large use of pesticides and nutrients to control weed proliferation and improve production. The water quality of four neighboring rice fields located in the Lomellina area (Italian Padana plain) was monitored in this study along with the cultivation period (before, during, and after the period of planting), for two successive agricultural seasons (2015 and 2016). Two paddy fields were traditionally cultivated with wet-seeding and the other fields with dry-seeding. Eighteen sampling points were considered: eight points for surface water, two points for underground water, and eight points for porous cups with two different depths. In order to evaluate the goodness of the paddy field system to maintain unchanged the quality of the inflow with respect to the outflow water, three of the most used herbicides in Italian rice cultivation (imazamox, oxadiazon, and profoxydim) and other physical-chemical parameters were determined, namely biological oxygen demand after 5 days; chemical oxygen demand; total suspended solids; anionic surfactants; total hardness; total amount of phosphorus, nitrogen, and potassium; and heavy metal concentrations. In general, all the collected data confirmed that paddy fields did not contribute to worsen the environmental pollution. The different flooding techniques adopted in the fields did not highlight significant differences in concentrations of pesticides or metals. The pesticides reached their maximum concentration (of the magnitude order of few ng mL-1) on the day after the administration and on the day after the application in the adjacent field. A slight reduction of total As in grain was obtained adopting a dry period from steam elongation up to booting. From the collected data, it was possible to identify a general water flow direction in the paddy fields from north-west to south-east: this prevailing flow direction was useful to understand not only the diffusion of the pesticides and their degradation products in the fields but also that of the nutrients. Concerning nutrients, it was important not to activate a recirculation of the water in the field during the first 10 days from the administration, in order to avoid loss of nitrogen in the water vents or for percolation. Moreover, the monitoring of potassium concentration allowed to avoid the use of unnecessary potassic fertilization when there was already a high amount of this element in the paddy field derived from irrigation. However, all the investigated water quality parameters were under the limits fixed by the European regulation. In addition, the presence of seven unexpected compounds was identified by the nontarget approach in both campaigns in samples collected in the early summer period. Four of these emerging contaminants were identified as N,N-diethyl-meta-toluamide, tricyclazole, amidosulfuron, and one of the imazamox photodegradation products. Although the obtained low concentrations of oxadiazion, tricyclazole, and arsenic, in particular, justified a preexisting contamination of the water inflow or of the investigated paddy area, the obtained results supported the good quality of the paddy water outflow, confirming the rational use of the water resource and the correct use of agronomic practices.

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.

Plasma Proteome Profiles of Stable CAD Patients Stratified According to Total Apo C-III Levels.

PURPOSE: The present research reports the study the of plasma proteome profile of stable coronary artery disease (CAD) patients characterized by different levels of total Apolipoprotein-CIII (Apo C-III), a prognostic marker for cardiovascular risk. EXPERIMENTAL DESIGN: Two subgroups of CAD patients (n = 52) with divergent concentrations of total circulating Apo C-III (≤ and ≥10 mg dL-1 ) are examined using a shotgun proteomic approach. Validation experiments are also performed with immunochemistry methods including both the patients affected by CAD (n = 119) and the subjects without CAD (CAD-free; n = 58). Results are analyzed by bioinformatics tools and multivariate statistics. RESULTS: A total of 188 proteins are quantified among the patients. The fold change analysis and the partial least square discriminant analysis show a clear separation of the two groups. Lipoproteins (Apo C-II and Apo E), retinol-binding protein 4, and vitronectin are upregulated in patients with high Apo C-III, while alpha-1 antitrypsin is downregulated. CONCLUSIONS AND CLINICAL RELEVANCE: In this pilot study, the differential expression of plasma proteins related to different concentrations of Apo C-III is defined, suggesting possible new players involved in the Apo C-III-associated process of arterial damage. Data are available via ProteomeXchange with identifier PXD005973.

Integrated serum proteins and fatty acids analysis for putative biomarker discovery in inflammatory bowel disease.

The diagnosis and management of Inflammatory bowel disease (IBD), including Crohn's disease (CD) and ulcerative colitis (UC), is still challenging. There is no definitive gold standard diagnostic test, which is made on patient history and with endoscopic and histological findings. This study analyzed serum proteins and fatty acids using mass spectrometry-based techniques. Quantitation of serum proteins was performed by depleting 14 high-abundance proteins, followed by tryptic digestion and LC-MS analysis, while fatty acids were analyzed using GC-MS. Bioinformatic tools were used to identify several new potential biomarkers for an early and non-invasive diagnosis of IBD, and to differentiate CD from UC. Moreover, the diagnostic power of the MS-identified biomarkers was also corroborated by Western Blot and ELISA assays. Hence, we identified the biological functions and pathways involved in the various subsets of IBD. Coagulation, fibrinolysis and acute phase response processes were found to be strongly involved in the condition. The involvement of several fatty acids, such as anti-inflammatory mediators, was also identified. Finally, proteomic and lipidomic data were integrated by using combinatorial and multivariate analyses to discover new combined biomarkers and to study the molecular pathways involved in IBD.

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.