Chlortetracycline and related tetracyclines: detection in wheat and rye grain.

BACKGROUND: Antibiotic drugs are excreted to a large proportion by livestock. Thus, antibiotics are distributed on fields with slurry and can be taken up by plants. In the present study, hydroponic experiments were performed to reveal whether the widely administered chlortetracycline is taken up into wheat grain in a concentration-dependent manner. A further goal was to determine (chlor)tetracyclines in wheat and rye grain from agricultural practice. RESULTS: Increasing chlortetracycline deposition in wheat grain was observed with a rising chlortetracycline spiking level in the hydroponic solution. In 371 selected wheat and rye samples from three growing years of agricultural practice, the overall detection frequency was 21% for tetracyclines. In the most highly contaminated sample, tetracyclines occurred at 18.2 µg kg-1 . Tetracycline residues were also found in rye grain. Conversion and degradation products of (chlor)tetracycline such as tetracycline, doxycycline and demeclocycline were detected in grains from hydroponic experiments and from agricultural practice. CONCLUSION: Concentrations of tetracyclines found in wheat and rye grains were of no concern with respect to toxicity regarding human consumption. However, antibiotic concentrations below the minimum inhibitory concentration can select for antibiotic resistance in bacteria. Thus, low levels of different tetracycline residues contained in food should be taken into account regarding risk assessment. © 2018 Society of Chemical Industry.

Learning to Classify Organic and Conventional Wheat - A Machine Learning Driven Approach Using the MeltDB 2.0 Metabolomics Analysis Platform.

We present results of our machine learning approach to the problem of classifying GC-MS data originating from wheat grains of different farming systems. The aim is to investigate the potential of learning algorithms to classify GC-MS data to be either from conventionally grown or from organically grown samples and considering different cultivars. The motivation of our work is rather obvious nowadays: increased demand for organic food in post-industrialized societies and the necessity to prove organic food authenticity. The background of our data set is given by up to 11 wheat cultivars that have been cultivated in both farming systems, organic and conventional, throughout 3 years. More than 300 GC-MS measurements were recorded and subsequently processed and analyzed in the MeltDB 2.0 metabolomics analysis platform, being briefly outlined in this paper. We further describe how unsupervised (t-SNE, PCA) and supervised (SVM) methods can be applied for sample visualization and classification. Our results clearly show that years have most and wheat cultivars have second-most influence on the metabolic composition of a sample. We can also show that for a given year and cultivar, organic and conventional cultivation can be distinguished by machine-learning algorithms.

Metabolite profiling on wheat grain to enable a distinction of samples from organic and conventional farming systems.

BACKGROUND: Identification of biomarkers capable of distinguishing organic and conventional products would be highly welcome to improve the strength of food quality assurance. Metabolite profiling was used for biomarker search in organic and conventional wheat grain (Triticum aestivum L.) of 11 different old and new bread wheat cultivars grown in the DOK system comparison trial. Metabolites were extracted using methanol and analysed by gas chromatography-mass spectrometry. RESULTS: Altogether 48 metabolites and 245 non-identified metabolites (TAGs) were detected in the cultivar Runal. Principal component analysis showed a sample clustering according to farming systems and significant differences in peak areas between the farming systems for 10 Runal metabolites. Results obtained from all 11 cultivars indicated a greater influence of the cultivar than the farming system on metabolite concentrations. Nevertheless, a t-test on data of all cultivars still detected 5 metabolites and 11 TAGs with significant differences between the farming systems. CONCLUSION: Based on individual cultivars, metabolite profiling showed promising results for the categorization of organic and conventional wheat. Further investigations are necessary with wheat from more growing seasons and locations before definite conclusions can be drawn concerning the feasibility to evolve a combined set of biomarkers for organically grown wheat using metabolite profiles.

MeltDB 2.0-advances of the metabolomics software system.

MOTIVATION: The research area metabolomics achieved tremendous popularity and development in the last couple of years. Owing to its unique interdisciplinarity, it requires to combine knowledge from various scientific disciplines. Advances in the high-throughput technology and the consequently growing quality and quantity of data put new demands on applied analytical and computational methods. Exploration of finally generated and analyzed datasets furthermore relies on powerful tools for data mining and visualization. RESULTS: To cover and keep up with these requirements, we have created MeltDB 2.0, a next-generation web application addressing storage, sharing, standardization, integration and analysis of metabolomics experiments. New features improve both efficiency and effectivity of the entire processing pipeline of chromatographic raw data from pre-processing to the derivation of new biological knowledge. First, the generation of high-quality metabolic datasets has been vastly simplified. Second, the new statistics tool box allows to investigate these datasets according to a wide spectrum of scientific and explorative questions. AVAILABILITY: The system is publicly available at https://meltdb.cebitec.uni-bielefeld.de. A login is required but freely available.

Search for diagnostic proteins to prove authenticity of organic wheat grains (Triticum aestivum L.).

Research comparing the biochemical composition of wheat grains from organic or conventional agriculture has used the targeted analytical approach. To obtain a more comprehensive record of the food's composition, we employed protein profiling techniques. Levels of 1049 proteins were recorded in wheat grains (Triticum aestivum L., cv. Titlis) of two growing seasons from a rigorously controlled field trial in Switzerland, containing organic and conventional plots. Levels of 25 proteins were different between organic and conventional wheat in both years. Storage proteins, enzymes of carbohydrate metabolism, a peroxidase, and proteins of unknown function were affected by the agricultural regime. Total protein content was lower in organic wheat. We consider these differences negligible with regard to nutrition in an average diet and propose that food quality of conventional and organic wheat grown in the field trial was equal. Applying various filters and calculations, one of which takes seasonal influences into account, 16 of the 25 proteins with different levels in organic and conventional wheat were retained. These 16 "diagnostic" proteins have the potential to afford a signature to prove authenticity of organic wheat.

Quantitative protein composition and baking quality of winter wheat as affected by late sulfur fertilization.

Increasing prices for wheat products and fertilizers, as well as reduced sulfur (S) contributions from the atmosphere, call for an improvement of product quality and agricultural management. To detect the impact of a time-dependent S fertilization, the quantitative protein composition and the baking quality of two different wheat cultivars, Batis and Turkis, were evaluated. The glutathione concentration in grains serves as a reliable marker of the need for added S fertilizer. The quantitation of gliadins and glutenin subunits by reversed-phase high-performance liquid chromatography confirmed that S-rich proteins significantly increased with S fertilization, whereas the S-poor proteins significantly decreased. Proteome analysis by means of high-resolution protein profiles detected 55 and 37 proteins from Batis and Turkis changed by late S fertilization. A microscale baking test using wholemeal flour was implemented for the evaluation of baking quality, and late S fertilization was found to improve the composition of gluten proteins and baking quality.

Levels of compounds and metabolites in wheat ears and grains in organic and conventional agriculture.

In this work, wheat from two farming systems, organic and conventional, was analyzed. Organic agriculture is one of the fastest growing sectors in the food industry of Europe and the United States. It is an open question, whether organic or conventional agricultural management influences variables such as metabolism, nutrient supply, seed loading and metabolite composition of wheat. Our aim was to detect if organic or conventional farming systems would affect concentrations of metabolites and substances in developing ears and in corresponding matured grain. Therefore, broadband metabolite profiles together with lipids, cations, starch and protein concentrations of wheat ears in the last phase of grain development and of matured grain from organic and conventional agriculture of a rigorously controlled field trial with two organic and two conventional systems were examined. It appears that seed metabolism and supply of developing ears differ in organic and conventional agriculture. However, the differences in 62 metabolite concentrations become marginal or disappear in the matured grains, indicating an adjustment of nutrients in the matured grain from organic agriculture. This result suggests a high degree of homeostasis in the final seed set independent of the growing regime.

Metabolite profiling of wheat grains (Triticum aestivum L.) from organic and conventional agriculture.

In some European community countries up to 8% of the agricultural area is managed organically. The aim was to obtain a metabolite profile for wheat (Triticum aestivum L.) grains grown under comparable organic and conventional conditions. These conditions cannot be found in plant material originating from different farms or from products purchased in supermarkets. Wheat grains from a long-term biodynamic, bioorganic, and conventional farming system from the harvest 2003 from Switzerland were analyzed. The presented data show that using a high throughput GC-MS technique, it was possible to determine relative levels of a set of 52 different metabolites including amino acids, organic acids, sugars, sugar alcohols, sugar phosphates, and nucleotides from wheat grains. Within the metabolites from all field trials, there was at the most a 50% reduction comparing highest and lowest mean values. The statistical analysis of the data shows that the metabolite status of the wheat grain from organic and mineralic farming did not differ in concentrations of 44 metabolites. This result indicates no impact or a small impact of the different farming systems. In consequence, we did not detect extreme differences in metabolite composition and quality of wheat grains.

Sucrose phosphate synthase genes in plants belong to three different families.

We present phylogenetic analyses to demonstrate that there are three families of sucrose phosphate synthase (SPS) genes present in higher plants. Two data sets were examined, one consisting of full-length proteins and a second larger set that covered a highly conserved region including the 14-3-3 binding region and the UDPGlu active site. Analysis of both datasets showed a well supported separation of known genes into three families, designated A, B, and C. The genomic sequences of Arabidopsis thaliana include a member in each family: two genes on chromosome 5 belong to Family A, one gene on chromosome 1 to Family B, and one gene on chromosome 4 to Family C. Each of three Citrus genes belong to one of the three families. Intron/exon organization of the four Arabidopsis genes differed according to phylogenetic analysis, with members of the same family from different species having similar genomic organization of their SPS genes. The two Family A genes on Arabidopsis chromosome 5 appear to be due to a recent duplication. Analysis of published literature and ESTs indicated that functional differentiation of the families was not obvious, although B family members appear not to be expressed in roots. B family genes were cloned from two Actinidia species and southern analysis indicated the presence of a single gene family, which contrasts to the multiple members of Family A in Actinidia. Only two family C genes have been reported to date.