Laura Righetti

Characterization of Resistance Gene Analogues ( RGAs ) in Apple ( Malus × domestica Borkh.) and Their Evolutionary History of the Rosaceae Family

The family of resistance gene analogues (RGAs) with a nucleotide-binding site (NBS) domain accounts for the largest number of disease resistance genes and is one of the largest gene families in plants. We have identified 868 RGAs in the genome of the apple (Malus × domestica Borkh.) cultivar ‘Golden Delicious’. This represents 1.51% of the total number of predicted genes for this cultivar. Several evolutionary features are pronounced in M. domestica, including a high fraction (80%) of RGAs occurring in clusters. This suggests frequent tandem duplication and ectopic translocation events. Of the identified RGAs, 56% are located preferentially on six chromosomes (Chr 2, 7, 8, 10, 11, and 15), and 25% are located on Chr 2. TIR-NBS and non-TIR-NBS classes of RGAs are primarily exclusive of different chromosomes, and 99% of non-TIR-NBS RGAs are located on Chr 11. A phylogenetic reconstruction was conducted to study the evolution of RGAs in the Rosaceae family. More than 1400 RGAs were identified in six species based on their NBS domain, and a neighbor-joining analysis was used to reconstruct the phylogenetic relationships among the protein sequences. Specific phylogenetic clades were found for RGAs of Malus, Fragaria, and Rosa, indicating genus-specific evolution of resistance genes. However, strikingly similar RGAs were shared in Malus, Pyrus, and Prunus, indicating high conservation of specific RGAs and suggesting a monophyletic origin of these three genera.

Recent Advances and Future Challenges in Modified Mycotoxin Analysis: Why HRMS Has Become a Key Instrument in Food Contaminant Research

Mycotoxins are secondary metabolites produced by pathogenic fungi in crops worldwide. These compounds can undergo modification in plants, leading to the formation of a large number of possible modified forms, whose toxicological relevance and occurrence in food and feed is still largely unexplored. The analysis of modified mycotoxins by liquid chromatography–mass spectrometry remains a challenge because of their chemical diversity, the large number of isomeric forms, and the lack of analytical standards. Here, the potential benefits of high-resolution and ion mobility mass spectrometry as a tool for separation and structure confirmation of modified mycotoxins have been investigated/reviewed.

Characterization and Discrimination of Ancient Grains: A Metabolomics Approach

Hulled, or ancient, wheats were the earliest domesticated wheats by mankind and the ancestors of current wheats. Their cultivation drastically decreased during the 1960s; however, the increasing demand for a healthy and equilibrated diet led to rediscovering these grains. Our aim was to use a non-targeted metabolomic approach to discriminate and characterize similarities and differences between ancient Triticum varieties. For this purpose, 77 hulled wheat samples from three different varieties were collected: Garfagnana T. turgidum var. dicoccum L. (emmer), ID331 T. monococcum L. (einkorn) and Rouquin T. spelta L. (spelt). The ultra high performance liquid chromatography coupled to high resolution tandem mass spectrometry (UHPLC-QTOF) metabolomics approach highlighted a pronounced sample clustering according to the wheat variety, with an excellent predictability (Q2), for all the models built. Fifteen metabolites were tentatively identified based on accurate masses, isotopic pattern, and product ion spectra. Among these, alkylresorcinols (ARs) were found to be significantly higher in spelt and emmer, showing different homologue composition. Furthermore, phosphatidylcholines (PC) and lysophosphatidylcholines (lysoPC) levels were higher in einkorn variety. The results obtained in this study confirmed the importance of ARs as markers to distinguish between Triticum species and revealed their values as cultivar markers, being not affected by the environmental influences.

Untargeted metabolomics based on ultra-high-performance liquid chromatography–high-resolution mass spectrometry merged with chemometrics: A new predictable tool for an early detection of mycotoxins

In order to explore the early detection of mycotoxins in wheat three standardized approaches (Fusarium disease severity, PCR assays for Fusarium spp. identification and mycotoxin quantification) and a novel untargeted metabolomics strategy were jointly assessed. In the first phase of this research, standardized approaches were able to quantify mycotoxins and identify Fusarium spp. Then, an UHPLC-QTOF metabolic fingerprinting method was developed to investigate plant-pathogen cross-talk. At the same time, chemometrics analysis demonstrated to be a powerful tool in order to distinguish low and strong infection levels. Combining these results, the cross-talk plant pathogen related to the early detection of mycotoxins was discovered. As a rapid response to fungal infection an overexpression of phosphatidic acids was discovered. By contrast, when the infection became stronger an increase of oxylipins and diacylglycerols was revealed.

A novel approach based on untargeted lipidomics reveals differences in the lipid pattern among durum and common wheat

In the present work the possibility of using an untargeted metabolomic strategy to discriminate between common and durum wheat lipidome for an authenticity purpose was explored. A first study was conducted by analyzing 52 samples from two durum and common wheat varieties. Afterwards, an extended and independent sample set (173 samples and five varieties) was used as a confirmatory study to verify the stability and consistency of the models obtained. Putatively identified markers were evaluated applying ROC curves resulting in individual marker AUC >90% both in preliminary and confirmatory study. In addition, digalactosyl diglyceride (DGDG) 36:4 was shown to be an effective marker differentiating between authentic durum wheat and its adulterated admixture down to 3% adulteration level, which is the maximum contamination level allowed by Italian legislation. The results demonstrated that untargeted lipidomics, in conjunction with chemometric tools has a significant potential for screening and detection of wheat fraud.

Group detection of DON and its modified forms by an ELISA kit

ABSTRACT Deoxynivalenol (DON) and its modified forms (3-, and 15-acetyl-DON, DON-3-glucoside) are commonly analysed by chromatographic methods. Indeed, coupled with proper extraction and clean-up, LC-MS represents the best approach for multi-mycotoxin measurements. On the other hand, immunochemistry-based methods are possibly able to detect a family of structurally related compounds, although the determination of single contributions is not possible so far. However, ELISA methods often lead to an apparent overestimation of the mycotoxins content because modified forms and matrix components can potentially cross-react with the antibodies (designed for the parent toxin). Several data about the possible cross-reactivity of commercial DON-detecting ELISA kit are reported in the literature so far. Data are commonly obtained in buffer solutions or in matrix-matched solutions, but comparison of a set of naturally incurred samples has never been reported. In the present work the accuracy of a commercial DON-detecting ELISA kit was evaluated on naturally incurred soft wheat (n = 15) and maize (n = 15), taking into account the matrix effect. Recovery was calculated considering the DON concentration found by LC-MS/MS and the total DON concentration, expressed as the sum of DON and its modified forms found by LC-MS/MS. The obtained data clearly show that, when 3-modified forms of DON occur in the sample, the ELISA kit does actually detect them, thus returning an apparent overestimation if only DON content is considered. When the ELISA recovery is calculated on the total DON content, the accuracy of the analysis increases and the variability decreases. According to our data, the ELISA kit seems to be a promising group detection tool for the accurate evaluation of DON and its modified forms, expressed as sum of DON, DON-3Glc and 3Ac-DON, for soft wheat and maize samples. GRAPHICAL ABSTRACT

Plant organ cultures as masked mycotoxin biofactories: Deciphering the fate of zearalenone in micropropagated durum wheat roots and leaves

“Masked mycotoxins” senso strictu are conjugates of mycotoxins resulting from metabolic pathways activated by the interplay between pathogenic fungi and infected plants. Zearalenone, an estrogenic mycotoxin produced by Fusarium spp, was the first masked mycotoxin ever described in the literature, but its biotransformation has been studied to a lesser extent if compared to other compounds such as deoxynivalenol. We presented herein the first application of organ and tissue culture techniques to study the metabolic fate of zearalenone in durum wheat, using an untargeted HR-LCMS approach. A complete, quick absorption of zearalenone by uninfected plant organs was noticed, and its biotransformation into a large spectrum of phase I and phase II metabolites has been depicted. Therefore, wheat organ tissue cultures can be effectively used as a biocatalytic tool for the production of masked mycotoxins, as well as a replicable model for the investigation of the interplay between mycotoxins and wheat physiology.

High resolution-ion mobility mass spectrometry as an additional powerful tool for structural characterization of mycotoxin metabolites.

This work was designed as a proof of concept, to demonstrate the successful use of the comparison between theoretical and experimental collision cross section (CCS) values to support the identification of isomeric forms. To this purpose, thirteen mycotoxins were considered and analyzed using drift time ion mobility mass spectrometry. A good linear correlation (r2 = 0.962) between theoretical and experimental CCS was found. The average ΔCCS was 3.2%, fully consistent with the acceptability threshold value commonly set at 5%. The agreement between theoretical and experimental CCS obtained for mycotoxin glucuronides suggested the potential of the CCS matching in supporting the annotation procedure.

Ion mobility-derived collision cross section database: Application to mycotoxin analysis

The recent hyphenation of ion mobility spectrometry (IMS) with high resolution mass spectrometry (HRMS) has risen as a powerful technique for both targeted and non-targeted screening, reducing background noise and allowing separation of isomeric and isobaric compounds. Nevertheless, such an approach remains largely unexplored in food safety applications, such as mycotoxin analysis. To implement ion mobility in routinely MS-based mycotoxin workflows, searchable databases with collusion cross section (CCS) values and accurate mass-values are required. This paper provides for the first time a traveling-wave IMS (TWIMS)-derived CCS database for mycotoxins, including more than 100 CCS values. The measurements showed high reproducibility (RSD < 2%) across different instrumental conditions as well as several complex cereal matrices, showing a mean inter-matrix precision of RSD <0.9%. As a proof of concept, the database was applied to the analysis of several spiked as well as naturally incurred cereal-based samples. In addition, the effect of adducts on the drift time was studied in a series of mycotoxins in order to understand potential deviations from expected drift time behaviors. Overall, our study confirmed that CCS values represent a physicochemical property that can be used alongside the traditional molecular identifiers of precursor ion accurate mass, fragment ions, isotopic pattern, and retention time.

Zearalenone uptake and biotransformation in micropropagated Triticum durum Desf. plants: a xenobolomic approach.

A model was set up to elucidate the uptake, translocation, and metabolic fate of zearalenone (ZEN) in durum wheat. After treatment with ZEN, roots and shoots were profiled with LC-HRMS. A comprehensive description of in planta ZEN biotransformation and a biotechnological evaluation of the model were obtained. Up to 200 μg ZEN were removed by each plantlet after 14 days. Most ZEN and its masked forms were retained in roots, while minimal amounts were detected in leaves. Sixty-two chromatographic peaks were obtained, resulting in 7 putative phase I and 18 putative phase II metabolites. ZEN16Glc and ZEN14Glc were most abundant in roots, sulfo-conjugates and zearalenol derivatives were unable to gain systemic distribution, while distinct isomers of malonyl conjugates were found in leaves and roots. This study underlines the potential ZEN occurrence in plants without an ongoing Fusarium infection. Micropropagation may represent a tool to investigate the interplay between mycotoxins and wheat.