Metabolic profiling of root exudates of Arabidopsis thaliana

In addition to accumulating biologically active chemicals, plant roots continuously produce and secrete compounds into their immediate rhizosphere. However, the mechanisms that drive and regulate root secretion of secondary metabolites are not fully understood. To enlighten two neglected areas of root biology, root secretion and secondary metabolism, an in vitro system implementing root-specific elicitation over a 48-day time course was developed. After roots of Arabidopsis thaliana had been elicited with salicylic acid, jasmonic acid, chitosan, and two fungal cell wall elicitors, the secondary metabolites subsequently secreted were profiled. High-performance liquid chromatography was used to metabolically profile compounds in the root exudates, and 289 possible secondary metabolites were quantified. The chemical structures of 10 compounds were further characterized by (1)H and (13)C NMR: butanoic acid, trans-cinnamic acid, o-coumaric acid, p-coumaric acid, ferulic acid, p-hydroxybenzamide, methyl p-hydroxybenzoate, 3-indolepropanoic acid, syringic acid, and vanillic acid. Several of these compounds exhibited a wide range of antimicrobial activity against both soil-borne bacteria and fungi at the concentration detected in the root exudates.     

Concurrent phenomena contributing to the formation of the aroma of wine during aging in oak wood: an analytical study

Red wine was stored in different oak barrels or in stainless steel, and samples were taken for two years to determine 79 aroma compounds. Aging in oak affects 41 compounds. The type of wood affects 11 compounds. At least seven different processes seem to take place concurrently in aroma evolution, and five such processes, affecting 37 compounds, are linked to the oak cask. These are extraction from the wood, oxidation of wine alcohols and amino acids, microbiological formation of ethyl phenols, sorption processes, and condensation of acetaldehyde with polyphenols. The wood can release linear gamma- and delta-lactones, beta-damascenone, and ionones. Some compounds are released very fast from wood, which suggests they lie in the external part of the wood. Some extraction profiles are too complex to be explained by physical processes. Finally, the levels of 2,5-dimethyl-4-hydroxy-3(2H)-furanone and 2-ethyl-5-methyl-4-hydroxy-3(2H)-furanone increase even in the reference wine, which suggests the presence of a precursor.     

Metabolic profiling reveals a functional succession of active fungi during the decay of Mediterranean plant litter

We evaluated the relationship between the potential activity shown by pure fungal isolates (in vitro) and their ecological role in the field. Fungal species frequency and occurrence during trophic succession on a natural resource were studied and used as a tool to gain a better understanding of the metabolic profiles obtained in vitro, thus permitting clarification of the role played by some of the key fungal species involved in the decomposition process within a Mediterranean natural ecosystem. Litter bags containing pure (homogeneous) and mixed leaves of low maquis plant species were incubated for one year in a field experiment. Functional diversity of a representative pool of fungal communities was analysed and compared using a “phenotype microarray” technique. Taking as its basis the screening of metabolic profiles using culturable isolates, this investigation showed that there was a high potentiality of functional redundancy between low, intermediate and high frequency taxa, and potential niche overlap during the different phases that occur during leaf litter decomposition. The early stages of decomposition appeared to be characterized by the presence of rare taxa (“Low” species), with a significantly higher functional potential, especially for sugar compounds. Conversely, the later phases of decomposition appeared to be characterized by species of intermediate frequency, while rare taxa at these stages seem to lose their dominant role. The importance of the different groups of substrates found across the decomposition phases also represented a key factor. For example, redundancy in the utilization of N-related compounds indicated a high potential for overlapping between species, especially in the early phases of the decomposition process, suggesting that the capacity for interspecific competition on some substrates can be considerable, particularly at the start of substrate exploitation.     

Semicarbazide formation in azodicarbonamide-treated flour: a model study

Semicarbazide was previously found in foods that were in contact with rubber gaskets foamed at high temperatures with a blowing agent azodicarbonamide. Because azodicarbonamide is an approved flour additive in certain countries, we set out to ascertain if semicarbazide is formed during the baking process from flours containing that additive. The levels of semicarbazide in baking flour treated with azodicarbonamide and bread baked from such flours were determined by isotope dilution (13C15N2-semicarbazide) liquid chromatography electrospray tandem mass spectrometry (LC-MS/MS). The samples were homogenized with HCl, extracted with n-pentane, derivatized with 2-nitrobenzaldehyde, and the derivative was extracted with ethyl acetate. After solvent exchange to 10% acetonitrile in water containing 0.1% acetic acid, the samples were analyzed using a 2.1 mm x 150 mm C18 column eluted with 2 mM ammonium formate in water/methanol (40:60). Semicarbazide was formed during the dry heating of commercial azodicarbonamide-containing flours at temperatures of 150-200 degrees C reaching levels of 0.2 mg/kg. Similar levels of semicarbazide were found in the crusts of breads made from azodicarbonamide-treated flour.     

Exploring the predictability of soil texture and organic matter content with a commercial integrated soil profiling tool

In soil mapping, combining information from conceptually different proximal soil sensors can increase the accuracy of prediction and robustness of the model when compared with using individual sensors. In this study the predictability of soil texture (clay, silt and sand fractions) and soil organic matter (SOM) content was tested with a commercial integrated soil profiling tool that included sensors for measuring apparent electrical conductivity (EC_a), reflectance in the visible and near‐infrared (vis‐NIR) parts of the electromagnetic spectrum and insertion force (IF). The measurements were made at 20 locations on each of two Swedish farms. At every location, sensor measurements were made at 1.5‐cm intervals from the soil surface to a depth of 0.8 m. Soil samples were collected close to the sensor measurement points and analysed for texture and SOM content. Farm‐specific calibrations were developed for texture and SOM with each sensor separately and with combinations of all three sensors. The calibrations were made using both partial least squares regression (PLSR) and simple linear regression. The results for the two farms were quite consistent in terms of rank in prediction performance between the individual sensors and the sensor combinations. The vis‐NIR spectrometer was the best individual sensor for predicting the soil properties tested on both farms, with root mean square error of cross‐validation (RMSECV) of 0.3–0.5% for SOM, about 6% for clay and silt and 10–11% for sand. The inclusion of IF reduced the RMSECV for predictions of SOM content by about 10%. For soil texture, including EC_a reduced the RMSECV on average for all particle size fractions by 5–10%. However, the small improvements obtained by combining sensors do not provide strong support for combining vis‐NIR sensor measurements with measurements of EC_a and or IF.     

Preliminary study of oaklins, a new class of brick-red catechinpyrylium pigments resulting from the reaction between catechin and wood aldehydes

Several structurally related pigments were found to result from the reaction between catechin and coniferaldehyde/sinapaldehyde extracted from oak wood. Their structures were tentatively identified by mass spectrometry, and their formation was studied in different pH and temperature conditions for several days. They were all found to have a characteristic catechinpyrylium core, thereby constituting a new class of compounds named as oaklins. One of the main oaklins was also detected in a commercial table red wine aged in oak barrels.     

Metabolic dependence of green tea on plucking positions revisited: a metabolomic study

The dependence of global green tea metabolome on plucking positions was investigated through (1)H nuclear magnetic resonance (NMR) analysis coupled with multivariate statistical data set. Pattern recognition methods, such as principal component analysis (PCA) and orthogonal projection on latent structure-discriminant analysis (OPLS-DA), were employed for a finding metabolic discrimination among fresh green tea leaves plucked at different positions from young to old leaves. In addition to clear metabolic discrimination among green tea leaves, elevations in theanine, caffeine, and gallic acid levels but reductions in catechins, such as epicatechin (EC), epigallocatechin (EGC), epicatechin-3-gallate (ECG), and epigallocatechin-3-gallate (EGCG), glucose, and sucrose levels were observed, as the green tea plant grows up. On the other hand, the younger the green tea leaf is, the more theanine, caffeine, and gallic acid but the lesser catechins accumlated in the green tea leaf, revealing a reverse assocation between theanine and catechins levels due to incorporaton of theanine into catechins with growing up green tea plant. Moreover, as compared to the tea leaf, the observation of marked high levels of theanine and low levels of catechins in green tea stems exhibited a distinct tea plant metabolism between the tea leaf and the stem. This metabolomic approach highlights taking insight to global metabolic dependence of green tea leaf on plucking position, thereby providing distinct information on green tea production with specific tea quality.     

Quercetin exhibits a specific fluorescence in cellular milieu: a valuable tool for the study of its intracellular distribution

The elaboration of novel techniques for flavonoid intracellular tracing would elucidate the compounds' absorption and bioavailability and assist molecular and pharmacological approaches, as they are promising candidates for drug development. This study exploited the properties of quercetin (3,3',4',5,7-pentahydroxyflavone), found in high concentrations in the majority of edible plants. Through the use of UV-vis spectroscopy, confocal microscopy, and HPLC-ESI-MS, native quercetin, at physiologically relevant concentrations, was found to exhibit a specific fluorescence (488 nmex/500-540 nmem) upon internalization. This fluorescence shift is due to a non-covalent binding to intracellular targets (probably proteins) and compatible with the settings applied in confocal microscopy. This property provides a valuable, selective alternative technique for quercetin tracing in cellular systems, permitting the quantitative evaluation of its transit at pharmacologically relevant concentrations and the validation of a number of already described molecular functions.     

Metabolic profiling of flavonol metabolites in human urine by liquid chromatography and tandem mass spectrometry

Twenty-one flavonol metabolites have been identified by LC/ESI-MS/MS in human urine, including isomers, after the consumption of cooked onions. Metabolites identified include quercetin monoglucuronides, methyl quercetin monoglucuronides, a quercetin monoglucuronide sulfate, quercetin diglucuronides, a methyl quercetin diglucuronide, quercetin glucoside sulfates, methyl quercetin, quercetin, and kaempferol monoglucuronides. The fragmentation patterns of flavonol metabolites obtained by MS/MS were distinctive for some isomers, indicating that fragmentation patterns may be useful predictors of conjugation position. Two isomers of sulfate quercetin glucosides were also found in urine, suggesting that many of the quercetin glucosides in onion are absorbed intact and undergo metabolism to the sulfate conjugate. Additionally, the interindividual variation in urinary quercetin metabolite profiles was determined by comparing the relative level of six different quercetin metabolites excreted in the urine of healthy volunteers. The ranges of quercetin metabolites excreted were similar among volunteers, yet notable differences in the levels of metabolites among individuals were observed. This study demonstrates the potential of monitoring the range of quercetin metabolites to reveal information on interindividual biotransformation capacity in response to dietary manipulations and as a biomarker for flavonol consumption.     

Cleanup of atrazine-contaminated soils: ecotoxicological study on the efficacy of a bioremediation tool with Pseudomonas sp. ADP

Journal of Soils and Sediments - To mitigate the environmental effects of atrazine, one of the cleanup strategies available is based on the use of atrazine-degrading bacteria. This work aimed to...     

Sugar fragmentation in the maillard reaction cascade: formation of short-chain carboxylic acids by a new oxidative alpha-dicarbonyl cleavage pathway

The formation of short-chain carboxylic acids was studied in Maillard model systems (90 degrees C, pH 6-10) with emphasis on the role of oxygen and water. The total amount of acetic acid formed did not depend on the reaction atmosphere. In the presence of labeled dioxygen or water (18O2, H2 17O), labeled oxygen was partially incorporated into acetic acid. Thermal treatment of 1-deoxy-d-erythro-2,3-hexodiulose (1) and 3-deoxy-d-erythro-hexos-2-ulose in the presence of 17O-enriched water under alkaline conditions led to acetic and formic acid, respectively, as indicated by 17O NMR spectroscopy. The suggested mechanism involves an oxidative alpha-dicarbonyl cleavage leading to an intermediary mixed acid anhydride that releases the acids, e.g., acetic and erythronic acid, from 1. Similarly, glyceric and lactic acids were formed from 1-deoxy-3,4-hexodiuloses, corroborated by complementary analytical techniques. This paper provides for the first time evidence for the direct formation of acids from C6-alpha-dicarbonyls by an oxidative mechanism and incorporation of a 17OH group into the carboxylic moiety. The experimental data obtained support the coexistence of at least two newly described reaction mechanisms leading to carboxylic acids, i.e., (i) a hydrolytic beta-dicarbonyl cleavage as a major pathway and (ii) an alternative minor pathway via oxidative alpha-dicarbonyl cleavage induced by oxidizing species.     

Deforesting the riverscape: the effects of wood on fish diversity in a Venezuelan piedmont stream

While deforestation of tropical ecosystems has been shown to have significant impacts on terrestrial habitats, its effects on aquatic habitats are poorly studied. Deforestation dramatically reduces the input of woody debris to streams, and given the importance of large woody debris to fish communities in temperate streams, this might be one mechanism by which logging could affect aquatic ecosystems in the tropics. To examine the effects of large woody debris on the diverse fish assemblage of a tropical stream, we surveyed pools with and without wood at Rio Las Marias, Venezuela. Pools containing wood contained greater numbers of individuals and more species of fish than pools without wood, and the two types of pools differed in their composition. To test whether these results were due to the presence of woody debris, we conducted an experimental wood addition. Pools to which wood was added showed marked increases in both fish abundance and species richness relative to wood-free pools, and the composition of the fish assemblage in experimental pools approached that of pools with naturally occurring woody debris. These results demonstrate that large woody debris plays a major role in structuring fish communities in tropical streams. As a consequence, logging practices that reduce the input of woody debris to tropical streams or directly remove wood from streams could have serious impacts on aquatic habitats, affecting both the diverse fish communities and local economies dependent on stream fisheries.     

Metabolic profiling of potential probiotic or synbiotic cheeses by nuclear magnetic resonance (NMR) spectroscopy

To assess ripening of potential probiotic cheeses (containing either Lactobacillus casei -01 or Bifidobacterium lactis B94) or synbiotic cheeses with fructooligosaccharides (FOS) or a 50:50 mix of FOS/inulin, metabolic profiles have been obtained via classical biochemical analyses and by NMR spectroscopy. The addition of prebiotics to the cheeses resulted in lower proteolysis indices, especially in those synbiotic cheeses inoculated with B. lactis B94. Among synbiotic cheeses the combination of FOS and inulin resulted in an increase in lipolytic activity. The metabolic profiles of the cheeses analyzed by NMR spectroscopy, combined with multivariate statistics, allowed profiles to be distinguished by maturation time, added probiotic bacteria, or, in the case of B. lactis B94 cheese, added prebiotic. The NMR results are in agreement with the biochemical analyses and demonstrate the potential of NMR for the study of metabolic processes in probiotic/synbiotic food matrices.     

The multispecies freshwater biomonitor a potential new tool for sediment biotests and biomonitoring

Behavioural changes are used as early warning systems for water quality monitoring or as rapid and sensitive endpoints in toxicity bioassays. In this study, the automated measurement of behavioural patterns of the thrichopteranHydropsyche angustipennis (Curtis 1834) has been recorded for the first time in sediment with the Multispecies Freshwater Biomonitor, MFB. The MFB recorded different types of behaviour in sediment with the same accuracy as in water. Behavioural differences of the larvae exposed to ‘water only’ and ‘sediment only’ have been described. In ‘choice’ experiments, the larvae preferred the ‘water only’ compartment.     

Evolution of wheat gliadins conformation during film formation: a fourier transform infrared study

The secondary structures of wheat gliadins (a major storage protein fraction from gluten) in film-forming solutions and their evolution during film formation were investigated by Fourier transform infrared spectroscopy. In the film-forming solution, wheat gliadins presented a mixture of different secondary structures, with an important contribution of beta-turns induced by proline residues. The presence of plasticizer did not have any influence on protein secondary structure in the film-forming solution. The evolution of protein conformation was followed during drying; the major feature of this evolution was a clear growing of the infrared band at 1622 cm(-1), characteristic of intermolecular hydrogen-bonded beta-sheets. This revealed the formation of protein aggregates during film drying. The influence of the drying temperature on film properties and gliadin secondary structures was also investigated. Higher drying temperatures induced an increase of both the tensile strength of the films and the amount of beta-sheets aggregates. Although the appearance of heat-induced disulfide bridge cross-links has already been described, there is clear evidence that hydrogen-bonded beta-sheets aggregates are also induced by thermal treatment. It was not possible, however, to determine whether there is a direct relationship between the occurrence of these aggregates and the increase of the tensile strength of the films.     

Microbial activities in a histosol: Effects of wood ash and NPK fertilizers

Mineralization of organic matter and microbial activities in an intensively cultivated acid, N-rich peat soil planted with Salix sp. cv. aquatica were examined for 3 yr. The soil was amended with wood ash or NPK fertilizers providing N as ammonium nitrate or urea. The wood ash amendment (10 tons ha^?1) increased soil pH from 4.6 to 5.5 and increased markedly all microbial activities measured, resulting in increased mineralization and N availability, and in loss of 9% total soil N during the first year. The addition of ammonium nitrate caused a corresponding though less pronounced increase in N mineralization. Cellulose decomposition increased in all amended soils, reaching rates 53–86% higher than in non-amended soil. Potential N₂ fixation (C₂H₂ reduction) by free-living organisms was increased by the ash-amendment. Potential denitrification rates were positively correlated (r = 0.98) with the presence of water-soluble organic-C, which was more abundant in ash-amended and non-amended soils than in the soils fertilized with N.     

Metabolic profiling of turmeric (Curcuma longa L.) plants derived from in vitro micropropagation and conventional greenhouse cultivation

Turmeric (Curcuma longa) was considered only a culinary spice in many parts of the world until the notable anti-inflammation curcuminoids were discovered from this herb. Because it is a sterile triploid and is propagated vegetatively by rhizome division, turmeric is susceptible to pathogens that accumulate and are transmitted from generation to generation, and amplification of particularly useful stocks is a slow process. An in vitro propagation method has been developed to alleviate these problems. Metabolic profiling, using GC-MS and LC-ESI-MS, was used to determine if chemical differences existed between greenhouse-grown and in vitro micropropagation derived plants. The major chemical constituent curcuminoids, a group of diarylheptanoid compounds, as well as major mono- and sesquiterpenoids were identified and quantified. Principal component analysis and hierarchical cluster analysis revealed chemical differences between lines (T3C turmeric vs Hawaiian red turmeric) and tissues (rhizome, root, leaf, and shoot). However, this analysis indicated that no significant differences existed between growth treatments (conventional greenhouse-grown vs in vitro propagation derived plants).