Comparative metabolomic study of transgenic versus conventional soybean using capillary electrophoresis-time-of-flight mass spectrometry

Emerging trends and applications of metabolomics in food science and nutrition

The study of all chemical processes involving metabolites is known as metabolomics. It has been developed into an essential tool in several disciplines, such as the study of plant physiology, drug development, human diseases, and nutrition. The field of food science, diagnostic biomarker research, etiological analysis in the field of medical therapy, and raw material quality, processing, and safety have all benefited from the use of metabolomics recently. Food metabolomics includes the use of metabolomics in food production, processing, and human diets. As a result of changing consumer habits and the rising of food industries all over the world, there is a remarkable increase in interest in food quality and safety. It requires the employment of various technologies for the food supply chain, processing of food, and even plant breeding. This can be achieved by understanding the metabolome of food, including its biochemistry and composition. Additionally, Food metabolomics can be used to determine the similarities and differences across crop kinds, as an indicator for tracking the process of ripening to increase crops' shelf life and attractiveness, and identifying metabolites linked to pathways responsible for postharvest disorders. Moreover, nutritional metabolomics is used to investigate the connection between diet and human health through detection of certain biomarkers. This review assessed and compiled literature on food metabolomics research with an emphasis on metabolite extraction, detection, and data processing as well as its applications to the study of food nutrition, food-based illness, and phytochemical analysis. Several studies have been published on the applications of metabolomics in food but further research concerning the use of standard reproducible procedures must be done. The results published showed promising uses in the food industry in many areas such as food production, processing, and human diets. Finally, metabolome-wide association studies (MWASs) could also be a useful predictor to detect the connection between certain diseases and low molecular weight biomarkers.

Integrating (Nutri-)Metabolomics into the One Health Tendency-The Key for Personalized Medicine Advancement

Metabolomics is an advanced technology, still under development, with multiple research applications, especially in the field of health. Individual metabolic profiles, the functionality of the body, as well as its interaction with the environment, can be established using this technology. The body's response to various external factors, including the food consumed and the nutrients it contains, has increased researchers' interest in nutrimetabolomics. Establishing correlations between diet and the occurrence of various diseases, or even the development of personalized nutrition plans, could contribute to advances in precision medicine. The interdependence between humans, animals, and the environment is of particular importance today, with the dramatic emergence and spread of zoonotic diseases, food, water and soil contamination, and the degradation of resources and habitats. All these events have led to an increase in risk factors for functional diseases, burdening global health. Thus, this study aimed to highlight the importance of metabolomics, and, in particular, nutrimetabolomics, as a technical solution for a holistic, collaborative, and precise approach for the advancement of the One Health strategy.

Spatial Lipidomics of EPSPS and PAT Transgenic and Non-Transgenic Soybean Seeds Using Matrix-Assisted Laser Desorption/Ionization Mass Spectrometry Imaging

Herbicide-resistant soybeans are among the most widely planted transgenic crops. The in situ evaluation of spatial lipidomics in transgenic and non-transgenic soybeans is important for directly assessing the unintended effects of exogenous gene introduction. In this study, matrix-assisted laser desorption/ionization mass spectrometry imaging (MALDI-MSI)-based non-targeted analytical strategies were used for the first time for in situ detection and imaging of endogenous lipid distributions in transgenic (EPSPS and PAT genes) herbicide-resistant soybean (Glycine max Merrill) (S4003.14) and non-transgenic soybean (JACK) seeds. Statistical analysis revealed significant differences in lipids between S4003.14 and JACK seeds. The variable importance of projection analysis further revealed that 18 identified lipids, including six phosphatidylcholines (PCs), four phosphatidylethanolamines (PEs), five triacylglycerols (TAGs), and three cytidine diphosphate-diacylglycerols (CDP-DAGs), had the strongest differential expression between S4003.14 and JACK seeds. Among those, the upregulated expressions of PC(P-36:1), PC(36:2), PC(P-36:0), PC(37:5), PE(40:2), TAG(52:1), TAG(55:5), and CDP-DAG(37:2) and the downregulated expressions of PC (36:1), TAG(43:0), and three PEs (i.e., PE(P-38:1), PE(P-38:0), and PE(P-40:3)) were successfully found in the S4003.14 seeds, compared to these lipids detected in the JACK seeds. Meanwhile, the lipids of PC (44:8), CDP-DAG(38:0), and CDP-DAG(42:0) were uniquely detected in the S4003.14 soybean seeds, and TAG(45:2) and TAG(57:10) were detected as the unique lipids in the JACK seeds. The heterogeneous distribution of these lipids in the soybean seeds was also clearly visualized using MALDI-MSI. MSI results showed that lipid expression was significantly up/downregulated in S4003.14 seeds, compared to that in JACK seeds. This study improves our understanding of the unintended effects of herbicide-resistant EPSPS and PAT gene transfers on spatial lipidomes in soybean seeds and enables the continued progression of MALDI-MSI as an emerging, reliable, and rapid molecular imaging tool for evaluating unintended effects in transgenic plants.

Nontargeted detection and recognition of adulterants in milk powder using Raman imaging and neural networks

Raman imaging technology combined with targeted chemometrics can play a vital role in the rapid detection of milk powder adulteration, which threatens the lives of infants and other people. However, these methods always suffer from a narrow detection range. Nontargeted methods show a broader detection range but cannot recognize adulterants. Here, a novel nontargeted chemometric method, named as the adversarial discrimination neural network (ADNN), is proposed to detect and recognize adulterants simultaneously. The method comprises building a tight boundary in the feature space of Raman images to discriminate milk powder samples from the majority of adulterated cases. Then a first-order partial derivative of the ADNN is calculated to recognize different adulterants through a local approximation strategy. A validation set containing samples adulterated with various adulterants at concentrations ranging from 0.3% to 1.5% w/w was provided to challenge the proposed method. The validated detection accuracy of the proposed method for authentic and adulterated samples was 99.9% and 99.7% and the adulterants were recognized correctly. The ADNN-Raman represents a novel nontargeted and end-to-end tool for detecting and recognizing adulterants in milk powder simultaneously, providing new insights into nontargeted chemometric analysis.

Metabolomics as a Prospective Tool for Soybean (Glycine max) Crop Improvement

Global demand for soybean and its products has stimulated research into the production of novel genotypes with higher yields, greater drought and disease tolerance, and shorter growth times. Genetic research may be the most effective way to continue developing high-performing cultivars with desirable agronomic features and improved nutritional content and seed performance. Metabolomics, which predicts the metabolic marker for plant performance under stressful conditions, is rapidly gaining interest in plant breeding and has emerged as a powerful tool for driving crop improvement. The development of increasingly sensitive, automated, and high-throughput analytical technologies, paired with improved bioinformatics and other omics techniques, has paved the way for wide characterization of genetic characteristics for crop improvement. The combination of chromatography (liquid and gas-based) with mass spectrometry has also proven to be an indisputable efficient platform for metabolomic studies, notably plant metabolic fingerprinting investigations. Nevertheless, there has been significant progress in the use of nuclear magnetic resonance (NMR), capillary electrophoresis, and Fourier-transform infrared spectroscopy (FTIR), each with its own set of benefits and drawbacks. Furthermore, utilizing multivariate analysis, principal components analysis (PCA), discriminant analysis, and projection to latent structures (PLS), it is possible to identify and differentiate various groups. The researched soybean varieties may be correctly classified by using the PCA and PLS multivariate analyses. As metabolomics is an effective method for evaluating and selecting wild specimens with desirable features for the breeding of improved new cultivars, plant breeders can benefit from the identification of metabolite biomarkers and key metabolic pathways to develop new genotypes with value-added features.

Evaluation and Optimization of APGC Parameters for the Analysis of Selected Hop Essential Oil Volatiles

Hop essential oil is a mixture of several hundred volatile metabolites that quantitatively and qualitatively distinguish hop varieties. Given the commercial relevance of hops in the brewing industry and the complexity of hop oil, analytical tools enabling a comprehensive characterization of oil constituents are required. At this, atmospheric pressure chemical ionization interfaced to gas chromatography and high-resolution mass spectrometry (APGC-MS) is a promising option that combines soft ionization, high sensitivity, and high resolution. While high sensitivity is required to detect minor or trace-level volatile metabolites, soft ionization and high resolution enable the reliable identification of unknowns based on exact masses of the molecular ion or the protonated molecule. Twenty-two volatile metabolites typically found in hop oil were studied in respect to their APGC ionization behavior. For 15 compounds, APGC-MS did not yield high molecular ion or protonated molecule intensities and considerable in-source fragmentation was observed. APGC-MS parameter optimization (cone gas flow and cone voltage) was able to yield the maximum absolute intensity for the base peak. However, in-source fragmentation could not be prevented, leading to spectra with either the protonated molecule or a characteristic fragment ion as the base peak. APGC-MS operated under optimized parameters was applied to a hop essential oil sample to verify the effect of optimization. By estimating the limit of quantification for the 22 compounds, it is concluded that APGC-MS is well suited to analyze major, minor, and trace-level volatiles from hops.

Food Metabolites as Tools for Authentication, Processing, and Nutritive Value Assessment

Secondary metabolites are molecules with unlimited applications that have been gaining importance in various industries and studied from many angles. They are mainly used for their bioactive capabilities, but due to the improvement of sensibility in analytical chemistry, they are also used for authentication and as a quality control parameter for foods, further allowing to help avoid food adulteration and food fraud, as well as helping understand the nutritional value of foods. This manuscript covers the examples of secondary metabolites that have been used as qualitative and authentication molecules in foods, from production, through processing and along their shelf-life. Furthermore, perspectives of analytical chemistry and their contribution to metabolite detection and general perspectives of metabolomics are also discussed.

A green and sustainable method for monitoring the chemical composition of soybean: an alternative for quality control

INTRODUCTION

Soybean is one of the most important crops in the world, an important source of isoflavones, and used to treat various chronic diseases. High-performance liquid chromatography (HPLC), associated with multivariate experiments and green solvents, is increasingly used to develop comprehensive elution methods for quality control of plants and derivatives.

OBJECTIVE

The work aims to establish a HPLC fingerprinting method for soybean seeds employing Green Chemistry Principles, a sustainable solvent with low toxicity, and a comprehensive experimental design that reduces the number of experiments.

MATERIALS AND METHODS

The fingerprinting method was optimised through Design of Experiments by evaluating seven chromatographic variables: initial percentage of ethanol (X1), final percentage of ethanol (X2), temperature (X3), percentage of acetic acid in water (X4), flow rate (X5), run time (X6), and stationary phase (X7). The dependent variable was the number of peaks (n).

RESULTS

An initial factorial design for screening purposes indicated that the most significant quantitative parameters to separate soybean metabolites were X1 and X3. The conditions were optimised by a Doehlert design, to obtain a HPLC-PAD (photodiode array detector) fingerprinting of the polar extract of soybean seeds with the markers identified by liquid chromatography electrospray ionisation tandem mass spectrometry (LC-ESI-MS/MS). The optimum fingerprinting method was determined as 5-55% of ethanol in 30 min, at 35°C, and flow rate of 1 mL/min, by employing a phenyl-hexyl column (150 mm × 4.6 mm).

CONCLUSION

The developed green method enabled markers of soybean to be separated and identified and could be an eco-friendlier alternative for soybean quality control that covered seven Green Analytical Chemistry Principles.

Metabolomics as a Tool to Study Underused Soy Parts: In Search of Bioactive Compounds

The valorization of agri-food by-products is essential from both economic and sustainability perspectives. The large quantity of such materials causes problems for the environment; however, they can also generate new valuable ingredients and products which promote beneficial effects on human health. It is estimated that soybean production, the major oilseed crop worldwide, will leave about 597 million metric tons of branches, leaves, pods, and roots on the ground post-harvesting in 2020/21. An alternative for the use of soy-related by-products arises from the several bioactive compounds found in this plant. Metabolomics studies have already identified isoflavonoids, saponins, and organic and fatty acids, among other metabolites, in all soy organs. The present review aims to show the application of metabolomics for identifying high-added-value compounds in underused parts of the soy plant, listing the main bioactive metabolites identified up to now, as well as the factors affecting their production.

Glyphosate-based herbicide formulations and reproductive toxicity in animals

The adoption of genetically engineered (GE) crops in agriculture has increased dramatically over the last few decades. Among the transgenic plants, those tolerant to the herbicide glyphosate are among the most common. Weed resistance to glyphosate-based herbicides (GBHs) has been on the rise, leading to increased herbicide applications. This, in turn, has led to increased glyphosate residues in feed. Although glyphosate has been considered to be generally safe to animal health, recent studies have shown that GBHs have potential to cause adverse effects in animal reproduction, including disruption of key regulatory enzymes in androgen synthesis, alteration of serum levels of estrogen and testosterone, damage to reproductive tissues and impairment of gametogenesis. This review emphasizes known effects of GBHs on reproductive health as well as the potential risk GBH residues pose to animal agriculture.

Recent advances in the application of metabolomics for food safety control and food quality analyses

As one of the omics fields, metabolomics has unique advantages in facilitating the understanding of physiological and pathological activities in biology, physiology, pathology, and food science. In this review, based on developments in analytical chemistry tools, cheminformatics, and bioinformatics methods, we highlight the current applications of metabolomics in food safety, food authenticity and quality, and food traceability. Additionally, the combined use of metabolomics with other omics techniques for "foodomics" is comprehensively described. Finally, the latest developments and advances, practical challenges and limitations, and requirements related to the application of metabolomics are critically discussed, providing new insight into the application of metabolomics in food analysis.

Utilization of GC-MS untargeted metabolomics to assess the delayed response of glufosinate treatment of transgenic herbicide resistant (HR) buffalo grasses (Stenotaphrum secundatum L.)

INTRODUCTION

Herbicide resistant (HR) buffalo grasses were genetically engineered to resist the non-selective herbicide, glufosinate in order to facilitate a modern, 'weeding program' which is highly effective in terms of minimizing costs and labor. The resistant trait was conferred by an insertion of the pat gene to allow for the production of the enzyme phosphinothricin acetyltransferase (PAT) to detoxify the glufosinate inhibitive effect. To date, there are only a few reports using metabolomics as well as molecular characterizations published for glufosinate-resistant crops with no reports on HR turfgrass. Therefore, for the first time, this study examines the metabolome of glufosinate-resistant buffalo grasses which not only will be useful to future growers but also the scientific community.

OBJECTIVE

A major aim of this present work is to characterize and evaluate the metabolic alterations which may arise from a genetic transformation of HR buffalo grasses by comprehensively using gas chromatography-mass spectrometry (GC-MS) based untargeted metabolomics.

METHODS

Eight-week old plants of 4 HR buffalo grasses, (93-1A, 93-2B, 93-3C and 93-5A) and 3 wild type varieties (WT 8-4A, WT 9-1B and WT 9-1B) were selected for physiological, molecular and metabolomics experiments. Plants were either sprayed with 1, 5, 10 and 15% v/v of glufosinate to evaluate the visual injuries or submerged in 5% v/v of glufosinate 3 days prior to a GC-MS based untargeted metabolomics analysis. In contrast, the control group was treated with distilled water. Leaves were extracted in 1:1 methanol:water and then analysed, using an in-house GC-MS untargeted workflow.

RESULTS

Results identified 199 metabolites with only 6 of them (cis-aconitic acid, allantoin, cellobiose, glyceric acid, maltose and octadecanoic acid) found to be statistically significant (p < 0.05) between the HR and wild type buffalo grass varieties compared to the control experiment. Among these metabolites, unusual accumulation of allantoin was prominent and was an unanticipated effect of the pat gene insertion. As expected, glufosinate treatment caused significant metabolic alterations in the sensitive wild type, with the up-regulation of several amino acids (e.g. phenylalanine and isoleucine) which was likely due to glufosinate-induced senescence. The aminoacyl-tRNA biosynthetic pathway was identified as the most significant enriched pathway as a result of glufosinate effects because a number of its intermediates were amino acids.

CONCLUSION

HR buffalo grasses were very similar to its wild type comparator based on a comprehensive GC-MS based untargeted metabolomics and therefore, should guarantee the safe use of these HR buffalo grasses. The current metabolomics analyses not only confirmed the effects of glufosinate to up-regulate free amino acid pools in the sensitive wild type but also several alterations in sugar, sugar phosphate and organic acid metabolism have been reported.

Safety Assessment of Genetically Modified Feed: Is There Any Difference From Food?

Food security is one of major concerns for the growing global population. Modern agricultural biotechnologies, such as genetic modification, are a possible solution through enabling an increase of production, more efficient use of natural resources, and reduced environmental impacts. However, new crop varieties with altered genetic materials may be subjected to safety assessments to fulfil the regulatory requirements, prior to marketing. The aim of the assessment is to evaluate the impact of products from the new crop variety on human, animal, and the environmental health. Although, many studies on the risk assessment of genetically modified (GM) food have been published, little consideration to GM feedstuff has been given, despite that between 70 to 90% of all GM crops and their biomass are used as animal feed. In addition, in some GM plants such as forages that are only used for animal feeds, the assessment of the genetic modification may be of relevance only to livestock feeding. In this article, the regulatory framework of GM crops intended for animal feed is reviewed using the available information on GM food as the baseline. Although, the majority of techniques used for the safety assessment of GM food can be used in GM feed, many plant parts used for livestock feeding are inedible to humans. Therefore, the concentration of novel proteins in different plant tissues and level of exposure to GM feedstuff in the diet of target animals should be considered. A further development of specific methodologies for the assessment of GM crops intended for animal consumption is required, in order to provide a more accurate and standardized assessment to the GM feed safety.

Assessing the fate of recombinant plant DNA in rabbit's tissues fed genetically modified cotton

Various feeding studies have been conducted with the different species of animals to evaluate the possible transfer of transgenic DNA (tDNA) from genetically modified (GM) feed into the animal tissues. However, the conclusions drawn from most of such studies are sometimes controversial. Thus, in the present study, an attempt has been made to evaluate the fate of tDNA in rabbits raised on GM cotton-based diet through PCR analysis of the DNA extracted specifically from blood, liver, kidney, heart and intestine (jejunum). A total of 48 rabbits were fed a mixed diet consisting variable proportions of transgenic cottonseeds meal (i.e. 0% w/w, 20% w/w, 30% w/w and 40% w/w) for 180 days. The presence of transgenic DNA fragments (Cry1Ac, Cry2A and CP4 EPSPS) or plant endogenous gene (Sad1) was traced in those specific tissues and organs. The presence of β-actin (ACTB) was also monitored as an internal control. Neither the transgenic fragments (459 bp of Cry1Ac gene, 167 bp of Cry2A gene and111 bp of CP4 EPSPS gene) nor cotton endogenous reference gene (155 bp of Sad1) could be detected in any of the DNA samples extracted from the rabbit's tissues in both control and transgenic groups. However, 155 bp fragment of the rabbit's reference gene (ACTB) was recovered in all the DNA samples extracted from rabbit tissues. The results obtained from this study revealed that both plant endogenous and transgenic DNA fragments have same fate in rabbit's tissues and were efficiently degraded in the gastrointestinal tract (GIT).

Insight Into the Prospects for the Improvement of Seed Starch in Legume-A Review

In addition to proteins and/or oils, mature seeds of most legume crops contain important carbohydrate components, including starches and sugars. Starch is also an essential nutritional component of human and animal diets and has various food and non-food industrial applications. Starch is a primary insoluble polymeric carbohydrate produced by higher plants and consists of amylose and amylopectin as a major fraction. Legume seeds are an affordable source of not only protein but also the starch, which has an advantage of being resistant starch compared with cereal, root, and tuber starch. For these reasons, legume seeds form a good source of resistant starch-rich healthy food with a high protein content and can be utilized in various food applications. The genetics and molecular details of starch and other carbohydrate components are well studied in cereal crops but have received little attention in legumes. In order to improve legume starch content, quality, and quantity, it is necessary to understand the genetic and molecular factors regulating carbohydrate metabolism in legume crops. In this review, we assessed the current literature reporting the genetic and molecular basis of legume carbohydrate components, primarily focused on seed starch content. We provided an overview of starch biosynthesis in the heterotrophic organs, the chemical composition of major consumable legumes, the factors influencing starch digestibility, and advances in the genetic, transcriptomic, and metabolomic studies in important legume crops. Further, we discussed breeding and biotechnological approaches for the improvement of the starch composition in major legume crops. The information reviewed in this study will be helpful in facilitating the food and non-food applications of legume starch and provide economic benefits to farmers and industries.

Opportunities and Challenges Using Non-targeted Methods for Food Fraud Detection

In recent years, non-targeted methods have been a popular "buzz" phrase in food fraud detection. Using analytical instrumentation techniques, non-targeted methods have been developed and applied in many food and agricultural situations. However, confusion and misstatements remain regarding how the methods are used. This perspective will discuss the definitions related to non-targeted testing, the procedure of developing and validating methods, the techniques and data analysis, and opportunities and challenges regarding the use of this class of analytical methods. The perspective seeks to provide readers with the latest information regarding recent advances in the use of non-targeted methods.

Nontargeted Detection Methods for Food Safety and Integrity

Nontargeted workflows for chemical hazard analyses are highly desirable in the food safety and integrity fields to ensure human health. Two different analytical strategies, nontargeted metabolomics and chemical database filtering, can be used to screen unknown contaminants in food matrices. Sufficient mass and chromatographic resolutions are necessary for the detection of compounds and subsequent componentization and interpretation of candidate ions. Analytical chemistry–based technologies, including gas chromatography–mass spectrometry (GC-MS), liquid chromatography–mass spectrometry (LC-MS), nuclear magnetic resonance (NMR), and capillary electrophoresis–mass spectrometry (CE-MS), combined with chemometrics analysis are being used to generate molecular formulas of compounds of interest. The construction of a chemical database plays a crucial role in nontargeted detection. This review provides an overview of the current sample preparation, analytical chemistry–based techniques, and data analysis as well as the limitations and challenges of nontargeted detection methods for analyzing complex food matrices. Improvements in sample preparation and analytical platforms may enhance the relevance of food authenticity, quality, and safety.

Recent developments in metabolomics-based research in understanding transgenic grass metabolism

BACKGROUND

Transgenic herbicide-resistant (HR) turfgrass together with its associated, broad spectrum herbicides promise cheap, selective and efficient weed control by excluding infested weeds resulting in turf lawn with high uniformity and aesthetic value. The concept of this "weeding program" initiated from modern biotechnology has been widely implemented in several principal crops including maize, soybean, canola and cotton as early as the 1990s. Transgenic HR turfgrass classified as a genetically modified organism (GMO) has undoubtedly caused public concern with respect to its biosafety and legalities similar to well-established HR crops. Nevertheless, applying metabolomics-based approaches which focuses on the identification of the global metabolic state of a biological system in response to either internal or external stimuli can also provide a comprehensive characterization of transgenic grass metabolism and its involvement in biosecurity and public perception.

AIM OF REVIEW

This review summaries the recent applications of metabolomics applied to HR crops to predict the molecular and physiological phenotypes of HR turfgrass species, glyphosate-resistant Kentucky bluegrass (Poa pratensis L.) and glufosinate-resistant creeping bentgrass (Agrotis stonifera L.). Additionally, this review also presents background knowledge with respect to the application of metabolomics, transformation of HR crops and its biosafety concerns, turfgrass botanical knowledge and its economic and aesthetic value.

KEY SCIENTIFIC CONCEPTS OF REVIEW

The purpose of this review is to demonstrate the molecular and physiological phenotypes of HR turfgrass based on several lines of evidence primarily derived from metabolomics data applied to HR crops to identify alterations on HR turfgrass metabolism as a result of genetic modification that confers resistant traits.

Overexpression of cytochrome p450 125 in Mycobacterium: a rational strategy in the promotion of phytosterol biotransformation

Androst-4-ene-3, 17-dione (AD) and androst-1, 4-diene-3, 17-dione (ADD) are generally produced by the biotransformation of phytosterols in Mycobacterium. The AD (D) production increases when the strain has high NAD+/NADH ratio. To enhance the AD (D) production in Mycobacterium neoaurum TCCC 11978 (MNR M3), a rational strategy was developed through overexpression of a gene involved in the phytosterol degradation pathway; NAD+ was generated as well. Proteomic analysis of MNR cultured with and without phytosterols showed that the steroid C27-monooxygenase (Cyp125-3), which performs sequential oxidations of the sterol side chain at the C27 position and has the oxidative cofactor of NAD+ generated, played an important role in the phytosterol biotransformation process of MNR M3. To improve the productivity of AD (D), the cyp125-3 gene was overexpressed in MNR M3. The specific activity of Cyp125-3 in the recombinant strain MNR M3C3 was improved by 22% than that in MNR M3. The NAD+/NADH ratio in MNR M3C3 was 131% higher than that in the parent strain. During phytosterol biotransformation, the conversion of sterols increased from 84 to 96%, and the yield of AD (D) by MNR M3C3 was increased by approximately 18% for 96 h fermentation. This rational strain modification strategy may also be applied to develop strains with important application values for efficient production of cofactor-dependent metabolites.

Recent advances in the application of capillary electromigration methods for food analysis and Foodomics

This review work presents and discusses the main applications of capillary electromigration methods in food analysis and Foodomics. Papers that were published during the period February 2015-February 2017 are included following the previous review by Acunha et al. (Electrophoresis 2016, 37, 111-141). The paper shows the large variety of food related molecules that have been analyzed by CE including amino acids, biogenic amines, carbohydrates, chiral compounds, contaminants, DNAs, food additives, heterocyclic amines, lipids, peptides, pesticides, phenols, pigments, polyphenols, proteins, residues, toxins, vitamins, small organic and inorganic compounds, as well as other minor compounds. This work describes the last results on food quality and safety, nutritional value, storage, bioactivity, as well as uses of CE for monitoring food interactions and food processing including recent microchips developments and new applications of CE in Foodomics.

A Comparative Study of Selected Physical and Biochemical Traits of Wild-Type and Transgenic Sorghum to Reveal Differences Relevant to Grain Quality

Transgenic sorghum featuring RNAi suppression of certain kafirins was developed recently, to address the problem of poor protein digestibility in the grain. However, it was not firmly established if other important quality parameters were adversely affected by this genetic intervention. In the present study several quality parameters were investigated by surveying several important physical and biochemical grain traits. Important differences in grain weight, density and endosperm texture were found that serve to differentiate the transgenic grains from their wild-type counterpart. In addition, ultrastructural analysis of the protein bodies revealed a changed morphology that is indicative of the effect of suppressed kafirins. Importantly, lysine was found to be significantly increased in one of the transgenic lines in comparison to wild-type; while no significant changes in anti-nutritional factors could be detected. The results have been insightful for demonstrating some of the corollary changes in transgenic sorghum grain, that emerge from imposed kafirin suppression.

Phosphate Fertilizer and Growing Environment Change the Phytochemicals, Oil Quality, and Nutritional Composition of Roundup Ready Genetically Modified and Conventional Soybean

Phosphorus (P) intake, genotype, and growth environment in soybean cultivation can affect the composition of the soybean. This experiment was conducted in two locations (microregions I and II) using a randomized complete block design, including conventional soybean (BRS Sambaíba) and genetically modified (GM) [Msoy 9144 Roundup Ready (RR)] cultivars and varying doses of phosphorus fertilizer (0, 60, 120, and 240 kg/ha P2O5). Soybeans were evaluated for chemical composition, total phenols, phytic acid content, individual isoflavone content, antioxidant activity, oil quality, fatty acid profile, total carotenoid content, and individual tocopherol contents. Multivariate analysis facilitated reduction in the number of variables with respect to soybean genotype (conventional BRS Sambaíba and GM Msoy 9144 RR), dose of P2O5 fertilizer, and place of cultivation (microregion I and II). BRS Sambaíba had higher concentrations of β-glucosides, malonylglucosides, glycitein, and genistein than Msoy 9144 RR, which showed a higher concentration of daidzein. The highest concentrations of isoflavones and fatty acids were observed in soybeans treated with 120 and 240 kg/ha P2O5, regardless of the location and cultivar.

Application of self-organising maps towards segmentation of soybean samples by determination of amino acids concentration

Soybeans are widely used both for human nutrition and animal feed, since they are an important source of protein, and they also provide components such as phytosterols, isoflavones, and amino acids. In this study, were determined the concentrations of the amino acids lysine, histidine, arginine, asparagine, glutamic acid, glycine, alanine, valine, isoleucine, leucine, tyrosine, phenylalanine present in 14 samples of conventional soybeans and 6 transgenic, cultivated in two cities of the state of Paraná, Londrina and Ponta Grossa. The results were tabulated and presented to a self-organising map for segmentation according planting regions and conventional or transgenic varieties. A network with 7000 training epochs and a 10 × 10 topology was used, and it proved appropriate in the segmentation of the samples using the data analysed. The weight maps provided by the network, showed that all the amino acids were important in targeting the samples, especially isoleucine. Three clusters were formed, one with only Ponta Grossa samples (including transgenic (PGT) and common (PGC)), a second group with Londrina transgenic (LT) samples and the third with Londrina common (LC) samples.

Flavonoid glycosides from Persea caerulea. Unraveling their interactions with SDS-micelles through matrix-assisted DOSY, PGSE, mass spectrometry, and NOESY

Two flavonoid glycosides derived from rhamnopyranoside (1) and arabinofuranoside (2) have been isolated from leaves of Persea caerulea for the first time. The structures of 1 and 2 have been established by ¹ H NMR, ¹³ C NMR, and IR spectroscopy, together with LC-ESI-TOF and LC-ESI-IT MS spectrometry. From the MS and MS/MS data, the molecular weights of the intact molecules as well as those of quercetin and kaempferol together with their sugar moieties were deduced. The NMR data provided information on the identity of the compounds, as well as the α and β configurations and the position of the glycosides on quercetin and kaempferol. We have also explored the application of sodium dodecyl sulfate (SDS) normal micelles in binary aqueous solution, at a range of concentrations, to the diffusion resolution of these two glycosides, by the application of matrix-assisted diffusion ordered spectroscopy (DOSY) and pulse field gradient spin echo (PGSE) methodologies, showing that SDS micelles offer a significant resolution which can, in part, be rationalized in terms of differing degrees of hydrophobicity, amphiphilicity, and steric effects. In addition, intra-residue and inter-residue proton-proton distances using nuclear Overhauser effect build-up curves were used to elucidate the conformational preferences of these two flavonoid glycosides when interacting with the micelles. By the combination of both diffusion and nuclear Overhauser spectroscopy techniques, the average location site of kaempferol and quercetin glycosides has been postulated, with the former exhibiting a clear insertion into the interior of the SDS-micelle, whereas the latter is placed closer to the surface. Copyright © 2016 John Wiley & Sons, Ltd.

Volatile Organic Compounds Induced by Herbivory of the Soybean Looper Chrysodeixis includens in Transgenic Glyphosate-Resistant Soybean and the Behavioral Effect on the Parasitoid, Meteorus rubens

Transgenic soybean plants (RR) engineered to express resistance to glyphosate harbor a variant of the enzyme EPSPS (5-enolpyruvylshikimate-3-phosphate synthase) involved in the shikimic acid pathway, the biosynthetic route of three aromatic amino acids: phenylalanine, tyrosine, and tryptophan. The insertion of the variant enzyme CP4 EPSPS confers resistance to glyphosate. During the process of genetic engineering, unintended secondary effects are likely to occur. In the present study, we quantified volatile organic compounds (VOCs) emitted constitutively or induced in response to herbivory by the soybean looper Chrysodeixis includens in transgenic soybean and its isogenic (untransformed) line. Since herbivore-induced plant volatiles (HIPVs) are known to play a role in the recruitment of natural enemies, we assessed whether changes in VOC profiles alter the foraging behavior of the generalist endoparasitic larval parasitoid, Meteorus rubens in the transgenic line. Additionally, we assessed whether there was a difference in plant quality by measuring the weight gain of the soybean looper. In response to herbivory, several VOCs were induced in both the conventional and the transgenic line; however, larger quantities of a few compounds were emitted by transgenic plants. Meteorus rubens females were able to discriminate between the odors of undamaged and C. includens-damaged plants in both lines, but preferred the odors emitted by herbivore-damaged transgenic plants over those emitted by herbivore-damaged conventional soybean plants. No differences were observed in the weight gain of the soybean looper. Our results suggest that VOC-mediated tritrophic interactions in this model system are not negatively affected. However, as the preference of the wasps shifted towards damaged transgenic plants, the results also suggest that genetic modification affects that tritrophic interactions in multiple ways in this model system.

Fate of transgenic deoxyribonucleic acid fragments in digesta and tissues of rabbits fed genetically modified soybean meal

Numerous animal feeding studies have investigated the presence of DNA from transgenic plants in tissues from different animal species, but the data reported are sometimes controversial. The aim of this study was to investigate the presence of transgenic DNA (tDNA) in the digesta and tissues of a meat rabbit breed fed genetically modified (GM) soybean meal. Fifteen male New Zealand White rabbits were used for the experimental trial. Ten rabbits (treated group [TG]) were fed a mixed feed containing 10% GM soybean meal and 5 rabbits (control group [CG]) received a mixed feed containing conventional soybean meal, both from weaning (28 d of age) to slaughter (80 ± 3 d). Samples of blood, liver, kidney, heart, stomach, intestine (jejunum), lateral quadricep muscle, longissimus muscle, and perirenal adipose tissue were collected to assess the possible DNA transfer from GM feed to animal tissues. Samples of stomach contents and feces were also taken to study the degradability of ingested tDNA from feed in the digestive tract of rabbit. Moreover, samples of hair were collected to determine the possible environmental contamination from feed powders present on the farm. The DNA extraction was performed using specific genomic DNA kits. All samples were monitored, by using real-time PCR, for oligonucleotide primers and probes specific for the transgenic Roundup Ready soybean 40-3-2 and for the endogenous () gene. As an internal control of rabbit tissues, the presence of the () gene was used. In this study, no fragments of tDNA were detectable in tissue DNA samples of rabbits except in the extracted DNA from stomach digesta, feces, and hair of rabbits fed with GM soybean. Similar results were found for the reference gene, whereas the presence of the gene was detected in all rabbit tissues. The lack of tDNA of soybean in rabbit tissues represents an important result, which demonstrates that meat from rabbits fed a diet containing GM feed is as that derived from rabbits fed conventional crops. The recombinant DNA recovered in the stomach digesta and in feces indicates an incomplete digestion of the soybean DNA in the gastrointestinal tract of the rabbit, whereas the presence of trace soybean transgene in the hair of the TG rabbits is suggestive of an environmental contamination.

Culturable endophytic bacterial communities associated with field-grown soybean

AIMS

Assess the diversity of the culturable endophytic bacterial population associated with transgenic and nontransgenic soybean grown in field trial sites in Brazil and characterize them phenotypically and genotypically focusing on characteristics related to plant growth promotion.

METHODS AND RESULTS

Endophytic bacteria were isolated from roots, stems and leaves of soybean cultivars (nontransgenic (C) and glyphosate-resistant (GR) transgenic soybean), including the isogenic BRS133 and BRS245RR. Significant differences were observed in bacterial densities in relation to genotype and tissue from which the isolates were obtained. The highest number of bacteria was observed in roots and in GR soybean. Based on characteristics related to plant growth promotion, 54 strains were identified by partial 16S rRNA sequence analysis, with most of the isolates belonging to the species Enterobacter ludwigii and Variovorax paradoxus. Among the isolates, 44·4% were able to either produce indoleacetic acid (IAA) or solubilize phosphates, and 9·2% (all from GR soybean) presented both plant growth-promoting activities.

CONCLUSIONS

The results from this study indicate that the abundance of endophytic bacterial communities of soybean differs between cultivars and in general it was higher in the transgenic cultivars than in nontransgenic cultivars. BRS 245 RR exhibited no significant difference in abundance compared to nontransgenic BRS133. This suggests that the impact of the management used in the GR soybean fields was comparable with the impacts of some enviromental factors. However, the bacterial endophytes associated to GR and nontransgenic soybean were different. The soybean-associated bacteria showing characteristics related to plant growth promotion were identified as belonging to the species Pantoea agglomerans and Variovorax paradoxus.

SIGNIFICANCE AND IMPACT OF THE STUDY

Our study demonstrated differences concerning compostion of culturable endophytic bacterial population in nontransgenic and transgenic soybean.

Metabolomic changes in grains of well-watered and drought-stressed transgenic rice

BACKGROUND

Drought induces a number of physiological and biochemical responses in cereals. This study was designed to examine the metabolite changes in grains of drought-tolerant transgenic rice (Oryza sativa L.) that overexpresses AtCYP78A7 encoding cytochrome P450 protein using proton nuclear magnetic resonance ((1)H-NMR) and gas chromatography/mass spectrometry.

RESULTS

Principal component analysis showed that the (1)H-NMR-based profile was clearly separated by soil water status of well-watered and water-deficit. A discrimination of metabolites between transgenic and non-transgenic grains appeared under both watering regimes. Variations in the levels of amino acids and sugars led to the discrimination of metabolites among genotypes. In particular, drought significantly enhanced the levels of γ-aminobutyric acid (GABA, 244.6%), fructose (155.7%), glucose (211.0%), glycerol (57.2%), glycine (65.8%) and aminoethanol (192.4%) in the transgenic grains compared with the non-transgenic control grains.

CONCLUSION

These changes in amounts of metabolites may assist in improving drought tolerance in transgenic rice by playing crucial roles in stress-responsive pathways including GABA biosynthesis, sucrose metabolism and antioxidant defenses.

Proteomics and Metabolomics: Two Emerging Areas for Legume Improvement

The crop legumes such as chickpea, common bean, cowpea, peanut, pigeonpea, soybean, etc. are important sources of nutrition and contribute to a significant amount of biological nitrogen fixation (>20 million tons of fixed nitrogen) in agriculture. However, the production of legumes is constrained due to abiotic and biotic stresses. It is therefore imperative to understand the molecular mechanisms of plant response to different stresses and identify key candidate genes regulating tolerance which can be deployed in breeding programs. The information obtained from transcriptomics has facilitated the identification of candidate genes for the given trait of interest and utilizing them in crop breeding programs to improve stress tolerance. However, the mechanisms of stress tolerance are complex due to the influence of multi-genes and post-transcriptional regulations. Furthermore, stress conditions greatly affect gene expression which in turn causes modifications in the composition of plant proteomes and metabolomes. Therefore, functional genomics involving various proteomics and metabolomics approaches have been obligatory for understanding plant stress tolerance. These approaches have also been found useful to unravel different pathways related to plant and seed development as well as symbiosis. Proteome and metabolome profiling using high-throughput based systems have been extensively applied in the model legume species, Medicago truncatula and Lotus japonicus, as well as in the model crop legume, soybean, to examine stress signaling pathways, cellular and developmental processes and nodule symbiosis. Moreover, the availability of protein reference maps as well as proteomics and metabolomics databases greatly support research and understanding of various biological processes in legumes. Protein-protein interaction techniques, particularly the yeast two-hybrid system have been advantageous for studying symbiosis and stress signaling in legumes. In this review, several studies on proteomics and metabolomics in model and crop legumes have been discussed. Additionally, applications of advanced proteomics and metabolomics approaches have also been included in this review for future applications in legume research. The integration of these "omics" approaches will greatly support the identification of accurate biomarkers in legume smart breeding programs.

Metabolic Profiling and Enzyme Analyses Indicate a Potential Role of Antioxidant Systems in Complementing Glyphosate Resistance in an Amaranthus palmeri Biotype

Metabolomics and biochemical assays were employed to identify physiological perturbations induced by a commercial formulation of glyphosate in susceptible (S) and resistant (R) biotypes of Amaranthus palmeri. At 8 h after treatment (HAT), compared to the respective water-treated control, cellular metabolism of both biotypes were similarly perturbed by glyphosate, resulting in abundance of most metabolites including shikimic acid, amino acids, organic acids and sugars. However, by 80 HAT the metabolite pool of glyphosate-treated R-biotype was similar to that of the control S- and R-biotypes, indicating a potential physiological recovery. Furthermore, the glyphosate-treated R-biotype had lower reactive oxygen species (ROS) damage, higher ROS scavenging activity, and higher levels of potential antioxidant compounds derived from the phenylpropanoid pathway. Thus, metabolomics, in conjunction with biochemical assays, indicate that glyphosate-induced metabolic perturbations are not limited to the shikimate pathway, and the oxidant quenching efficiency could potentially complement the glyphosate resistance in this R-biotype.

Impact of the ahas transgene for herbicides resistance on biological nitrogen fixation and yield of soybean

Studies on the effects of transgenes in soybean [Glycine max (L.) Merr.] and the associated use of specific herbicides on biological nitrogen fixation (BNF) are still few, although it is important to ensure minimal impacts on benefits provided by the root-nodule symbiosis. Cultivance CV127 transgenic soybean is a cultivar containing the ahas gene, which confers resistance to herbicides of the imidazolinone group. The aim of this study was to assess the effects of the ahas transgene and of imidazolinone herbicide on BNF parameters and soybean yield. A large-scale set of field experiments was conducted, for three cropping seasons, at nine sites in Brazil, with a total of 20 trials. The experiment was designed as a completely randomized block with four replicates and the following treatments: (T1) near isogenic transgenic soybean (Cultivance CV127) + herbicide of the imidazolinone group (imazapyr); (T2) near isogenic transgenic soybean + conventional herbicides; and (T3) parental conventional soybean (Conquista) + conventional herbicides; in addition, two commercial cultivars were included, Monsoy 8001 (M-SOY 8001) (T4), and Coodetec 217 (CD 217) (T5). At the R2 growth stage, plants were collected and BNF parameters evaluated. In general, there were no effects on BNF parameters due to the transgenic trait or associated with the specific herbicide. Similarly, at the final harvest, no grain-yield effects were detected related to the ahas gene or to the specific herbicide. However, clear effects on BNF and grain yield were attributed to location and cropping season.

Expanding Omics Resources for Improvement of Soybean Seed Composition Traits

Food resources of the modern world are strained due to the increasing population. There is an urgent need for innovative methods and approaches to augment food production. Legume seeds are major resources of human food and animal feed with their unique nutrient compositions including oil, protein, carbohydrates, and other beneficial nutrients. Recent advances in next-generation sequencing (NGS) together with "omics" technologies have considerably strengthened soybean research. The availability of well annotated soybean genome sequence along with hundreds of identified quantitative trait loci (QTL) associated with different seed traits can be used for gene discovery and molecular marker development for breeding applications. Despite the remarkable progress in these technologies, the analysis and mining of existing seed genomics data are still challenging due to the complexity of genetic inheritance, metabolic partitioning, and developmental regulations. Integration of "omics tools" is an effective strategy to discover key regulators of various seed traits. In this review, recent advances in "omics" approaches and their use in soybean seed trait investigations are presented along with the available databases and technological platforms and their applicability in the improvement of soybean. This article also highlights the use of modern breeding approaches, such as genome-wide association studies (GWAS), genomic selection (GS), and marker-assisted recurrent selection (MARS) for developing superior cultivars. A catalog of available important resources for major seed composition traits, such as seed oil, protein, carbohydrates, and yield traits are provided to improve the knowledge base and future utilization of this information in the soybean crop improvement programs.

Metabolomics of genetically modified crops

Metabolomic-based approaches are increasingly applied to analyse genetically modified organisms (GMOs) making it possible to obtain broader and deeper information on the composition of GMOs compared to that obtained from traditional analytical approaches. The combination in metabolomics of advanced analytical methods and bioinformatics tools provides wide chemical compositional data that contributes to corroborate (or not) the substantial equivalence and occurrence of unintended changes resulting from genetic transformation. This review provides insight into recent progress in metabolomics studies on transgenic crops focusing mainly in papers published in the last decade.

Evaluation of Fe uptake and translocation in transgenic and non-transgenic soybean plants using enriched stable (57)Fe as a tracer

A tracer experiment is carried out with transgenic T (variety M 7211 RR) and non-transgenic NT (variety MSOY 8200) soybean plants to evaluate if genetic modification can influence the uptake and translocation of Fe. A chelate of EDTA with enriched stable (57)Fe is applied to the plants cultivated in vermiculite plus substrate and the (57)Fe acts as a tracer. The exposure of plants to enriched (57)Fe causes the dilution of the natural previously existing Fe in the plant compartments and then the changed Fe isotopic ratio ((57)Fe/(56)Fe) is measured using a quadrupole-based inductively coupled plasma mass spectrometer equipped with a dynamic reaction cell (DRC). Mathematical calculations based on the isotope dilution methodology allow distinguishing the natural abundance Fe from the enriched Fe (incorporated during the experiment). The NT soybean plants acquire higher amounts of Fe from natural abundance (originally present in the soil) and from enriched Fe (coming from the (57)Fe-EDTA during the experiment) than T soybean ones, demonstrating that the NT soybean plants probably absorb higher amounts of Fe, independently of the source. The percentage of newly incorporated Fe (coming from the treatment) was approximately 2.0 and 1.1% for NT and T soybean plants, respectively. A higher fraction (90.1%) of enriched Fe is translocated to upper parts, and a slightly lower fraction (3.8%) is accumulated in the stems by NT plants than by T ones (85.1%; 5.1%). Moreover, in both plants, the Fe-EDTA facilitates the transport and translocation of Fe to the leaves. The genetic modification is probably responsible for differences observed between T and NT soybean plants.

Prevalence and impacts of genetically engineered feedstuffs on livestock populations

Globally, food-producing animals consume 70 to 90% of genetically engineered (GE) crop biomass. This review briefly summarizes the scientific literature on performance and health of animals consuming feed containing GE ingredients and composition of products derived from them. It also discusses the field experience of feeding GE feed sources to commercial livestock populations and summarizes the suppliers of GE and non-GE animal feed in global trade. Numerous experimental studies have consistently revealed that the performance and health of GE-fed animals are comparable with those fed isogenic non-GE crop lines. United States animal agriculture produces over 9 billion food-producing animals annually, and more than 95% of these animals consume feed containing GE ingredients. Data on livestock productivity and health were collated from publicly available sources from 1983, before the introduction of GE crops in 1996, and subsequently through 2011, a period with high levels of predominately GE animal feed. These field data sets, representing over 100 billion animals following the introduction of GE crops, did not reveal unfavorable or perturbed trends in livestock health and productivity. No study has revealed any differences in the nutritional profile of animal products derived from GE-fed animals. Because DNA and protein are normal components of the diet that are digested, there are no detectable or reliably quantifiable traces of GE components in milk, meat, and eggs following consumption of GE feed. Globally, countries that are cultivating GE corn and soy are the major livestock feed exporters. Asynchronous regulatory approvals (i.e., cultivation approvals of GE varieties in exporting countries occurring before food and feed approvals in importing countries) have resulted in trade disruptions. This is likely to be increasingly problematic in the future as there are a large number of "second generation" GE crops with altered output traits for improved livestock feed in the developmental and regulatory pipelines. Additionally, advanced techniques to affect targeted genome modifications are emerging, and it is not clear whether these will be encompassed by the current GE process-based trigger for regulatory oversight. There is a pressing need for international harmonization of both regulatory frameworks for GE crops and governance of advanced breeding techniques to prevent widespread disruptions in international trade of livestock feedstuffs in the future.