Unsupervised principal component analysis of NMR metabolic profiles for the assessment of substantial equivalence of transgenic grapes (Vitis vinifera)

Application of HR-NMR for the Metabolic Kinetic Assessment of Red Mullet (Mullus barbatus) and Bogue (Boops boops) Samples during Different Temperature Storage

Fish freshness and quality can be measured through several indices that can be both chemical and physical. The storage temperature and the time that elapses following the catching of the fish are fundamental parameters that define and influence both the degree of freshness and nutritional quality. Moreover, they particularly effect the kind of fish we considered. In this research, it was observed how different temperatures of storage and shelf-life (+4 °C and 0 °C) may affect the metabolic profile of red mullet (Mullus barbatus) and bogue (Boops boops) fish samples over time, specifically observing the alteration of freshness and quality. In particular, a High-Resolution Nuclear Magnetic Resonance (HR-NMR)-based metabolomics approach was applied to study the metabolic profile changes that occur in fish spoilage. The HR-NMR spectroscopy data were useful for calculating a kinetic model that was able to predict the evolution of different compounds related to fish freshness, such as trimethylamine (TMA-N) and adenosine-5′-triphosphate (ATP) catabolites for the K-index. Furthermore, NMR in combination with chemometrics allowed us to estimate a further kinetic model able to represent the spoilage evolution by considering the entire metabolome. In this way, it was also possible to detect further biomarkers characterizing the freshness and quality status of both red mullets and bogues.

Combined metabolic analyses for the biosynthesis pathway of l-threonine in Escherichia coli

Currently, industrial production of l-threonine (Thr) is based on direct fermentation with microorganisms such as Escherichia coli, which has the characteristics of low cost and high productivity. In order to elucidate the key metabolic features of the synthesis pathway of Thr in E. coli to provide clues for metabolic regulation or engineering of the strain, this study was carried out on an l-threonine over-producing strain, in terms of analyses of metabolic flux, enzyme control and metabonomics. Since environmental disturbance and genetic modification are considered to be two important methods of metabolic analysis, addition of phosphate in the media and comparison of strains with different genotypes were selected as the two candidates due to their significant influence in the biosynthesis of Thr. Some important targets including key nodes, enzymes and biomarkers were identified, which may provide target sites for rational design through engineering the Thrproducing strain. Finally, metabolic regulation aimed at one biomarker identified in this study was set as an example, which confirms that combined metabolic analyses may guide to improve the production of threonine in E. coli.

Aronia melanocarpa Fruits as a Rich Dietary Source of Chlorogenic Acids and Anthocyanins: 1H-NMR, HPLC-DAD, and Chemometric Studies

Aronia melanocarpa (Michx.) Elliott's (chokeberry) besides anthocyanins contains significant amounts of hydroxycinnamic acids: Chlorogenic and its isomer neochlorogenic acid. They exhibit antioxidant, anti-inflammatory, antidiabetic, and antibacterial activities, thus they can have a significant impact on the health-promoting properties of Aronia. The aim of our research was to determine the changes in the content of chlorogenic acids (CGAs) and anthocyanins during fruit development and ripening, with a particular emphasis on acids. Aronia fruit samples were collected from July to October on two organic farms in Poland. The chemical composition of the extracts was determined by NMR spectroscopy and HPLC-DAD. ¹H-NMR and HPLC data were analyzed using chemometric analysis and multivariate statistics (PCA). The results showed that the content of chlorogenic acids and anthocyanins changes during ripening and depends on the time of harvest and the region of cultivation. A correlation between the time of CGAs reduction and the appearance of anthocyanins was also noticed. The result of our research was also a database in the form of NMR parameters, which allows analysis of the metabolite profile and tracking of its changes. The ¹H-NMR spectrum showing anthocyanin and CGA resonance can be considered the Aronia berry fingerprint.

Substantial Equivalence of a Transgenic Lemon Fruit Showing Postharvest Fungal Pathogens Resistance

The development of genetically modified (GM) crops speeds up the obtainment of novel varieties with improved agronomic characteristics. However, the risk evaluation of the use of GMs is mandatory before their release in the market. In this paper, an untargeted and comprehensive nuclear magnetic resonance-based metabolomic study was carried out on the peel and flesh of a transgenic lemon clone (E23) expressing the chit42 gene and exhibiting an increased tolerance to some pathogenic fungi and on its wild type. Results highlighted a substantial equivalence of the metabolomics profile of the transgenic clone compared to the wild type. In addition, an enhanced response of the E23 clone toward fungal pathogens affecting the postharvest management in lemon was evidenced. These results confirm the potential of genetic engineering for the punctual modification of specific agronomic traits without altering the whole pattern of metabolites and open new perspectives for a more sustainable and effective management of specific postharvest diseases in citrus.

Contribution of Untargeted Metabolomics for Future Assessment of Biotech Crops

The nutritional value and safety of food crops are ultimately determined by their chemical composition. Recent developments in the field of metabolomics have made it possible to characterize the metabolic profile of crops in a comprehensive and high-throughput manner. Here, we propose that state-of-the-art untargeted metabolomics technology should be leveraged for safety assessment of new crop products. We suggest generally applicable experimental design principles that facilitate the efficient and rigorous identification of both intended and unintended metabolic alterations associated with a newly engineered trait. Our proposition could contribute to increased transparency of the safety assessment process for new biotech crops.

Nuclear Magnetic Resonance (NMR) Spectroscopy in Food Science: A Comprehensive Review

Nuclear magnetic resonance (NMR) spectroscopy is a robust method, which can rapidly analyze mixtures at the molecular level without requiring separation and/or purification steps, making it ideal for applications in food science. Despite its increasing popularity among food scientists, NMR is still an underutilized methodology in this area, mainly due to its high cost, relatively low sensitivity, and the lack of NMR expertise by many food scientists. The aim of this review is to help bridge the knowledge gap that may exist when attempting to apply NMR methodologies to the field of food science. We begin by covering the basic principles required to apply NMR to the study of foods and nutrients. A description of the discipline of chemometrics is provided, as the combination of NMR with multivariate statistical analysis is a powerful approach for addressing modern challenges in food science. Furthermore, a comprehensive overview of recent and key applications in the areas of compositional analysis, food authentication, quality control, and human nutrition is provided. In addition to standard NMR techniques, more sophisticated NMR applications are also presented, although limitations, gaps, and potentials are discussed. We hope this review will help scientists gain some of the knowledge required to apply the powerful methodology of NMR to the rich and diverse field of food science.

Foodomics and Food Safety: Where We Are

The power of foodomics as a discipline that is now broadly used for quality assurance of food products and adulteration identification, as well as for determining the safety of food, is presented. Concerning sample preparation and application, maintenance of highly sophisticated instruments for both high-performance and high-throughput techniques, and analysis and data interpretation, special attention has to be paid to the development of skilled analysts. The obtained data shall be integrated under a strong bioinformatics environment. Modern mass spectrometry is an extremely powerful analytical tool since it can provide direct qualitative and quantitative information about a molecule of interest from only a minute amount of sample. Quality of this information is influenced by the sample preparation procedure, the type of mass spectrometer used and the analyst's skills. Technical advances are bringing new instruments of increased sensitivity, resolution and speed to the market. Other methods presented here give additional information and can be used as complementary tools to mass spectrometry or for validation of obtained results. Genomics and transcriptomics, as well as affinity-based methods, still have a broad use in food analysis. Serious drawbacks of some of them, especially the affinity-based methods, are the cross-reactivity between similar molecules and the influence of complex food matrices. However, these techniques can be used for pre-screening in order to reduce the large number of samples. Great progress has been made in the application of bioinformatics in foodomics. These developments enabled processing of large amounts of generated data for both identification and quantification, and for corresponding modeling.

Multivariate classification of the geographic origin of Chinese cabbage using an electronic nose-mass spectrometry

An electronic nose-mass spectrometry (EN-MS) that profiles volatile compounds is a candidate device for identifying the geographic origin of cultivation of agricultural products when an adequate algorithm is derived. The objectives of this study were to apply two types of multivariate analysis, discriminant function analysis (DFA) and principal component analysis (PCA), to the volatile compounds detected by an EN-MS for the geographic classification of Chinese cabbage cultivated in Korea (42 samples) or in China (29 samples). DFA showed that Chinese cabbage from Korea were completely separable from those originating in China with 12 volatile compounds among the 151 detected. PCA revealed that Chinese cabbage data fell into two completely separable origins of Korea and China. This is the first study involving EN-MS data of volatile compounds with multivariate statistics to discriminate the geographical origin of Chinese cabbage, with further applications for other agricultural products.

A 90-day subchronic feeding study of genetically modified rice expressing Cry1Ab protein in Sprague-Dawley rats

Bacillus thuringiensis (Bt) transgenic rice line (mfb-MH86) expressing a synthetic cry1Ab gene can be protected against feeding damage from Lepidopteran insects, including Sesamia inferens, Chilo suppressalis, Tryporyza incertulas and Cnaphalocrocis medinalis. Rice flour from mfb-MH86 and its near-isogenic control MH86 was separately formulated into rodent diets at concentrations of 17.5, 35 and 70 % (w/w) for a 90-day feeding test with rats, and all of the diets were nutritionally balanced. In this study, the responses of rats fed diets containing mfb-MH86 were compared to those of rats fed flour from MH86. Overall health, body weight and food consumption were comparable between groups fed diets containing mfb-MH86 and MH86. Blood samples were collected prior to sacrifice and a few significant differences (p < 0.05) were observed in haematological and biochemical parameters between rats fed genetically modified (GM) and non-GM diets. However, the values of these parameters were within the normal ranges of values for rats of this age and sex, thus not considered treatment related. In addition, upon sacrifice a large number of organs were weighed, macroscopic and histopathological examinations were performed with only minor changes to report. In conclusion, these results demonstrated that no toxic effect was observed in the conditions of the experiment, based on the different parameters assessed. GM rice mfb-MH86 is as safe and nutritious as non-GM rice.

Changes in the metabolome of lettuce leaves due to exposure to mancozeb pesticide

This paper describes a proton high resolution magic angle spinning (HRMAS) nuclear magnetic resonance (NMR) metabolomic study of lettuce (Lactuca sativa L.) leaves to characterise metabolic adaptations during leaf growth and exposure to mancozeb. Metabolite variations were identified through multivariate analysis and checked through spectral integration. Lettuce growth was accompanied by activation of energetic metabolism, preferential glucose use and changes in amino acids, phospholipids, ascorbate, nucleotides and nicotinate/nicotinamide. Phenylalanine and polyphenolic variations suggested higher oxidative stress at later growth stages. Exposure to mancozeb induced changes in amino acids, fumarate and malate, suggesting Krebs cycle up-regulation. In tandem disturbances in sugar, phospholipid, nucleotide and nicotinate/nicotinamide metabolism were noted. Additional changes in phenylalanine, dehydroascorbate, tartrate and formate were consistent with a higher demand for anti-oxidant defence mechanisms. Overall, lettuce exposure to mancozeb was shown to have a significant impact on plant metabolism, with mature leaves tending to be more extensively affected than younger leaves.

Rifaximin modulates the vaginal microbiome and metabolome in women affected by bacterial vaginosis

Bacterial vaginosis (BV) is a common vaginal disorder characterized by the decrease of lactobacilli and overgrowth of Gardnerella vaginalis and resident anaerobic vaginal bacteria. In the present work, the effects of rifaximin vaginal tablets on vaginal microbiota and metabolome of women affected by BV were investigated by combining quantitative PCR and a metabolomic approach based on (1)H nuclear magnetic resonance. To highlight the general trends of the bacterial communities and metabolomic profiles in response to the antibiotic/placebo therapy, a multivariate statistical strategy was set up based on the trajectories traced by vaginal samples in a principal component analysis space. Our data demonstrated the efficacy of rifaximin in restoring a health-like condition in terms of both bacterial communities and metabolomic features. In particular, rifaximin treatment was significantly associated with an increase in the lactobacillus/BV-related bacteria ratio, as well as with an increase in lactic acid concentration and a decrease of a pool of metabolites typically produced by BV-related bacteria (acetic acid, succinate, short-chain fatty acids, and biogenic amines). Among the tested dosages of rifaximin (100 and 25 mg for 5 days and 100 mg for 2 days), 25 mg for 5 days was found to be the most effective.

Biosafety considerations of RNAi-mediated virus resistance in fruit-tree cultivars and in rootstock

A major application of RNA interference (RNAi) is envisaged for the production of virus-resistant transgenic plants. For fruit trees, this remains the most, if not the only, viable option for the control of plant viral disease outbreaks in cultivated orchards, due to the difficulties associated with the use of traditional and conventional disease-control measures. The use of RNAi might provide an additional benefit for woody crops if silenced rootstock can efficiently transmit the silencing signal to non-transformed scions, as has already been demonstrated in herbaceous plants. This would provide a great opportunity to produce non-transgenic fruit from transgenic rootstock. In this review, we scrutinise some of the concerns that might arise with the use of RNAi for engineering virus-resistant plants, and we speculate that this virus resistance has fewer biosafety concerns. This is mainly because RNAi-eliciting constructs only express small RNA molecules rather than proteins, and because this technology can be applied using plant rootstock that can confer virus resistance to the scion, leaving the scion untransformed. We discuss the main biosafety concerns related to the release of new types of virus-resistant plants and the risk assessment approaches in the application of existing regulatory systems (in particular, those of the European Union, the USA, and Canada) for the evaluation and approval of RNAi-mediated virus-resistant plants, either as transgenic varieties or as plant virus resistance induced by transgenic rootstock.

A combined approach for characterisation of fresh and brined vine leaves by X-ray powder diffraction, NMR spectroscopy and direct infusion high resolution mass spectrometry

X-ray powder diffraction was combined, for the first time, with Nuclear Magnetic Resonance spectroscopy and direct infusion mass spectrometry to characterise fresh and brined grape leaves. Covariance analysis of data generated by the three techniques was performed with the aim to correlate information deriving from the solid part with those obtained for soluble metabolites. The results obtained indicate that crystalline components can be correlated to the metabolites contained in the grape leaves, paving the way to the use of X-ray diffraction analysis for food fingerprinting purposes. Moreover it was ascertained that, differently from most of the metabolites present in the fresh vine leaves, linolenic acid (an omega-3-fatty acid) and quercetin-3-O-glucuronide (a polyphenol metabolite) do not undergo sensible degradation during the brining process, which is used as preservative method for the grape leaves.

Foodomics: a new comprehensive approach to food and nutrition

In the past 20 years, the scientific community has faced a great development in different fields due to the development of high-throughput, omics technologies. Starting from the four major types of omics measurements (genomics, transcriptomics, proteomics, and metabolomics), a variety of omics subdisciplines (epigenomics, lipidomics, interactomics, metallomics, diseasomics, etc.) has emerged. Thanks to the omics approach, researchers are now facing the possibility of connecting food components, foods, the diet, the individual, the health, and the diseases, but this broad vision needs not only the application of advanced technologies, but mainly the ability of looking at the problem with a different approach, a "foodomics approach". Foodomics is the comprehensive, high-throughput approach for the exploitation of food science in the light of an improvement of human nutrition. Foodomics is a new approach to food and nutrition that studies the food domain as a whole with the nutrition domain to reach the main objective, the optimization of human health and well-being.