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High-throughput (HTP) plant phenotyping approaches are developing rapidly and are already helping to bridge the genotype-phenotype gap. However, technologies should be developed beyond current physico-spectral evaluations to extend our analytical capacities to the subcellular level. Metabolites define and determine many key physiological and agronomic features in plants and an ability to integrate a metabolomics approach within current HTP phenotyping platforms has huge potential for added value. While key challenges remain on several fronts, novel technological innovations are upcoming yet under-exploited in a phenotyping context. In this review, we present an overview of the state of the art and how current limitations might be overcome to enable full integration of metabolomics approaches into a generic phenotyping pipeline in the near future.

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The present work shows key possibilities in modelling the kinetics of phenylacetaldehyde formation as a function of sugar, phenolic compounds, metals and sulphur dioxide. The release kinetics were measured online by proton transfer reaction-mass spectrometry (PTR-MS). Phenylacetaldehyde formation was fitted using Weibull models and an activation energy of 73 kJ/mol estimated. Also, a confirmation that glucose can inhibit the aldehyde formation was demonstrated, and the sequential additions in real time showed that the inhibition level was dependent on metal ions presence. Moreover, for the first time it was observed in real time the capacity of SO2 to bind with phenylacetaldehyde, and by trapping it, lowering its release. Finally, the impact of pH and temperature in the stability of the formed adducts and underling release mechanism is also elucidated.

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A response surface methodology was applied to study the effect of precursors on o-quinone and phenylacetaldehyde formation in wine model systems stored at 40 °C during 24 h. The results confirmed that glucose plays an important role in reducing aldehyde formation by inhibiting the formation of o-quinone. The regression equations showed that oxygen consumption followed a 2nd polynomial equation whereas phenylacetaldehyde and o-quinone were best fit with a polynomial function containing quadratic terms. These behaviors indicate that different pathways are involved in the respective aldehyde formation and oxygen consumption. RSM has been shown to be a powerful tool to better understand key chemical reactions. By considering a number of factors, individually and in combinations, the derived equations predicted that the best combination to minimize phenylacetaldehyde was achieved for high glucose levels and low amounts of gallic acid and metals. This is valuable information when trying to improve wines sensorial properties during shelf-life.

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Strecker degradation (SD) leading to the formation of phenylacetaldehyde (PA) was studied in wine systems. New insights were gained by using two full factorial designs focusing on the effects of (1) pH and (2) temperature. In each design of experiments (DoE) three factors, glucose, gallic acid, and metals at two levels (present or absence), were varied while phenylalanine was kept constant. The obtained results gave a clear indication, with statistical significance, that in wine conditions, the SD occurs in the presence of metals preferentially via the phenolic oxidation independent of the temperature (40 or 80 °C). The reaction of the amino acid with the o-quinone formed by the oxidation of the gallic acid seems to be favored when compared with the SD promoted by the reaction with α-dicarbonyls formed by MR between glucose and phenylalanine. In fact, kinetics results showed that the presence of glucose had an inhibitory effect on PA rate of formation. PA formation was 4 times higher in the control wine when compared to the same wine with 10 g/L glucose added. By gallic acid quinone quantitation it is shown that glucose affects directly the concentration of the quinone. decreasing the rate of quinone formation. This highlights the role of sugar in o-quinone concentration and consequently in the impact on Strecker aldehyde formation, a promising new perspective regarding wine shelf-life understanding.

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Succinic acid is a platform chemical that plays an important role as precursor for the synthesis of many valuable bio-based chemicals. Its microbial production from renewable resources has seen great developments, specially exploring the use of yeasts to overcome the limitations of using bacteria. The objective of the present work was to screen for succinate-producing isolates, using a yeast collection with different origins and characteristics. Four strains were chosen, two as promising succinic acid producers, in comparison with two low producers. Genome of these isolates was analysed, and differences were found mainly in genes SDH1, SDH3, MDH1 and the transcription factor HAP4, regarding the number of single nucleotide polymorphisms and the gene copy-number profile. Real-time PCR was used to study gene expression of 10 selected genes involved in the metabolic pathway of succinic acid production. Results show that for the non-producing strain, higher expression of genes SDH1, SDH2, ADH1, ADH3, IDH1 and HAP4 was detected, together with lower expression of ADR1 transcription factor, in comparison with the best producer strain. This is the first study showing the capacity of natural yeast isolates to produce high amounts of succinic acid, together with the understanding of the key factors associated, giving clues for strain improvement.

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The effect of repetitive controlled oxidation on the chemical and sensory composition of a fresh and fruity style Sauvignon blanc wine was investigated. Chemical analyses were conducted together with extensive sensory profiling. A decrease in volatile thiols responsible for the fruity nuances and an increase in oxidation-related compounds, such as acetaldehyde, during the course of the oxidation was observed. The wine evolved from a fresh and fruity one to one with slight oxidation and then developed extreme oxidative characteristics. The control samples (no oxygen added) developed a "cooked" character that could indicate the formation of "reductive" compounds in these wines. Conversely, the wines that received a single dose of oxygen did not develop this flavor and were perceived to be fresher and fruitier than the control samples. The color of the wine evolved before the disappearance of the pleasant aroma.

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During must fermentation by Saccharomyces cerevisiae strains thousands of volatile aroma compounds are formed. The objective of the present work was to adapt computational approaches to analyze pheno-metabolomic diversity of a S. cerevisiae strain collection with different origins. Phenotypic and genetic characterization together with individual must fermentations were performed, and metabolites relevant to aromatic profiles were determined. Experimental results were projected onto a common coordinates system, revealing 17 statistical-relevant multi-dimensional modules, combining sets of most-correlated features of noteworthy biological importance. The present method allowed, as a breakthrough, to combine genetic, phenotypic and metabolomic data, which has not been possible so far due to difficulties in comparing different types of data. Therefore, the proposed computational approach revealed as successful to shed light into the holistic characterization of S. cerevisiae pheno-metabolome in must fermentative conditions. This will allow the identification of combined relevant features with application in selection of good winemaking strains.

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In this paper, computational means were used to explain and predict the interaction of several odorant molecules, including three haloanisoles, 2,4,6-trichloroanisole (TCA), 2,4,6-tribromoanisole (TBA), and 2,4,6-trichlorophenol (TCP), with three olfactory receptors (ORs): OR1A1, OR1A2, and OR3A1. As the X-ray structure of these ORs is not known, the three-dimensional structure of each OR was modeled by homology modeling. The structures of these ORs were stabilized by molecular dynamic simulations and the complexes of the odorant molecules with each ORs were generated by molecular docking. The theoretical results have shown that each OR has distinct but well-defined binding regions for each type of odorant molecules (aldehydes and alcohols). In OR3A1, the aldehydes bind in the bottom region of the binding pocket nearby Ser257 and Thr249. In the paralogues OR1A1 and OR1A2, the aldehydes tend to interact in the top region of the binding pocket and close to a positively charged lysine. On the other hand, the alcohols interact in the bottom region of the active site and close to a negatively charged aspartate. These results indicate that when aldehydes and alcohols odorants compete in these two ORs, the aldehydes can block the access of the alcohols odorants to their specific binding site. This observation goes in line with the experimental data that reveals that when the odorant is an aldehyde, a lower quantity of ligand is needed to cause 50% of the maximum response (lower EC50), when compared with the alcohols. The theoretical results have also allowed to explain the differences in the activity of (S)-(-)-citronellol in the wild-type and mutated OR1A1. The theoretical results show that Asn109 has a preponderant role in this matter, since when it is mutated, it leads to a conformational rearrangement of the binding pocket that prevents the interaction of (S)-(-)-citronellol with Asp111 that was shown to be important for the OR activation. The good agreement between the theoretical and experimental results also lead us to study the potential interaction of the haloanisoles, TCA, TBA, and TCP with these ORs. The results have shown that these compounds can compete with other known agonists/antagonists for the access to the binding regions of ORs. These results may partially explain the capability of these compounds to give a musty odor to food and beverages at very low concentrations.

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Although neglected by science for a long time, the olfactory sense is now the focus of a panoply of studies that bring new insights and raises interesting questions regarding its functioning. The importance in the clarification of this process is of interest for science, but also motivated by the food and perfume industries boosted by a consumer society with increasingly demands for higher quality standards. In this review, a general overview of the state of art of science regarding the olfactory sense is presented with the main focus on the peripheral olfactory system. Special emphasis will be given to the deorphanization of the olfactory receptors (ORs), a critical issue because the specificity and functional properties of about 90% of human ORs remain unknown mainly due to the difficulties associated with the functional expression of ORs in high yields.

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Although phenolics are recognized to be related with health benefits by limiting lipid oxidation, in wine, they are the primary substrates for oxidation resulting in the quinone by-products with the participation of transition metal ions. Nevertheless, high quality Port wines require a period of aging in either bottle or barrels. During this time, a modification of sensory properties of wines such as the decrease of astringency or the stabilization of color is recognized to phenolic compounds, mainly attributed to anthocyanins and derived pigments. The present work aims to illustrate the oxidation of red Port wine based on its phenolic composition by the effect of both thermal and oxygen exposures. A kinetic approach toanthocyanins degradation was also achieved. For this purpose a forced red Port wine aging protocol was performed at four different storage temperatures, respectively, 20, 30, 35 and 40°C, and two adjusted oxygen saturation levels, no oxygen addition (treatment I), and oxygen addition (treatment II). Three hydroxycinnamic esters, three hydroxycinnamic acids, three hydroxybenzoic acids, two flavan-3-ols, and six anthocyanins were quantitated weekly during 63days, along with oxygen consumption. The most relevant phenolic oxidation markers were anthocyanins and catechin-type flavonoids, which had the highest decreases during the thermal and oxidative red Port wine process. Both temperature and oxygen treatments affected the rate of phenolic degradation. In addition, temperature seems to influence mostly the phenolics kinetic degradation.

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Mushrooms are known all over the world both due to the remarkable gastronomic value of some species and for severe intoxications mediated by other species that are frequently difficult to distinguish from the edible ones, by the common user. Therefore, it is important to develop strategies to discover molecules that can identify mushroom species. In the present work, two GC-MS methodologies were applied in the chemical characterization of 22 mushroom species (12 edible, 3 toxic and 7 potentially toxic) - a multi-target procedure to simultaneously determine amino acids (AA), fatty acids (FA) and sterols by previous derivatization procedure with MSTFA, and a Head Space-Solid Phase Microextraction method to determine volatiles. For both methods, two approaches to data analysis were used: (I) targeted analysis, to identify and quantify AA, FA sterols and volatiles; (II) untargeted analysis, including Principal Component Analysis and Partial Least Square Discriminant Analysis, in order to identify metabolites/metabolite pattern with potential species identification and/or differentiation. Multi-target experiment allowed the identification and quantification of twenty one primary metabolites (9 AA, 11 FA and 1 sterol). Furthermore, through untargeted data analysis, it was possible to identify a 5-carbon sugar alcohol structure molecule, which was tentatively identified as xylitol or adonitol, with potential to be a species-marker of the edible Suillus bovinus mushrooms. Volatile profiling studies resulted in the identification of the main volatiles in mushrooms. Untargeted analysis allowed the identification of 6 molecules that can be species- or genus-specific: one secondary metabolite specific to the edible species Lycoperdon perlatum, an ester of hexanoic acid, tentatively identified as allyl or vinyl caproate; and five other secondary metabolites, whose identification was not achieved, which were only detected in Lactarius aurantiacus specimens (edibility/toxicity unknown).

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Metabolomics aims at gathering the maximum amount of metabolic information for a total interpretation of biological systems. A process analytical technology pipeline, combining gas chromatography-mass spectrometry data preprocessing with multivariate analysis, was applied to a Port wine "forced ageing" process under different oxygen saturation regimes at 60°C. It was found that extreme "forced ageing" conditions promote the occurrence of undesirable chemical reactions by production of dioxane and dioxolane isomers, furfural and 5-hydroxymethylfurfural, which affect the quality of the final product through the degradation of the wine aromatic profile, colour and taste. Also, were found high kinetical correlations between these key metabolites with benzaldehyde, sotolon, and many other metabolites that contribute for the final aromatic profile of the Port wine. The use of the kinetical correlations in time-dependent processes as wine ageing can further contribute to biological or chemical systems monitoring, new biomarkers discovery and metabolic network investigations.

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Port wine is a flagship fortified wine of Portugal, which undergoes a particularly long aging period, developing a dynamic sensory profile over time, responsible for several wine categories, which is dependent upon the type of aging (bottle or barrel). Therefore, the quality of the product is dependent upon the chemical mechanisms occurring during the aging process, such as oxidation or Maillard reactions. To attain the desired quality management, it is necessary to understand how technological parameters, such as temperature or oxygen exposure, affect the kinetics of the formation of key odorants, such as sotolon. There is a lack of information about the impact of the storage conditions (oxygen and temperature) on Port wine quality. In this study, the effect of these two parameters were investigated to increase the knowledge database concerning aging management of Port wines. It was found that sotolon formation is highly dependent upon oxygen and temperature. There is however a synergistic effect between these two parameters that could significantly increase the concentration. The kinetic parameters of oxygen, sotolon, and other compounds related to Port aging (cis- and trans-5-hydroxy-2-methyl-1,3-dioxan, 2-furfural, 5-hydroxy-methyl-furfural, and 5-methyl-furfural) are also reported. Kinetic models with Monte Carlo simulations, where the oxygen permeability dispersion and temperature are the parameters under evaluation, were applied. On the basis of the modeling predictions, it would seem that the temperature of a cellar would have a more significant impact on the Port wines stored in containers where the oxygen intake is higher (barrels) when compared to containers with low oxygen permeability (bottles using cork stoppers).

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Chromatography separates the different components of complex mixtures and generates a fingerprint representing the chemical composition of the sample. The resulting data structure depends on the characteristics of the detector used, univariate for devices such as a flame ionization detector (FID) or multivariate for mass spectroscopy (MS). This study addresses the potential use of a univariate signal for a nontargeted approach to (i) classify samples according to a given process or perturbation, (ii) evaluate the feasibility of developing a screening procedure to select candidates related to the process, and (iii) provide insight into the chemical mechanisms that are affected by the perturbation. To achieve this, it was necessary to use and develop methods for data preprocessing and visualization tools to assist an analytical chemist to view and interpret complex multidimensional data sets. Dichloromethane Port wine extracts were collected using GC-FID; the chromatograms were then aligned with correlation optimized warping (COW) and subsequently analyzed with multivariate statistics (MVA) by principal component analysis (PCA) and partial least-squares regression (PLS-R). Furthermore, wavelets were used for peak calling and alignment refinement, and the resulting matrix was used to perform kinetic network reconstruction via correlation networks and maximum spanning trees. Network-target correlation projections were used to screen for potential chromatographic regions/peaks related to aging mechanisms. Results from PLS between aligned chromatograms and target molecules showed high X to Y correlations of 0.91, 092, and 0.89 with 5-hydroxymethylfurfural (HMF) (Maillard), acetaldehyde (oxidation), and 4,5-dimethyl-(5H)-3-hydroxy-2-furanone, respectively. The context of the correlation (and therefore likely kinetic) relationships among compounds detected by GC-FID and the relationships between target compounds within different regions of the network can be clearly seen.

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The development of a fingerprinting strategy capable to evaluate the "oxidation status" of white wines based on cyclic voltammetry is proposed here. It is known that the levels of specific antioxidants and redox mechanisms may be evaluated by cyclic voltammetry. This electrochemical technique was applied on two sets of samples. One group was composed of normal aged white wines and a second group obtained from a white wine forced aging protocol with different oxygen, SO(2), pH, and temperature regimens. A study of antioxidant additions, namely ascorbic acid, was also made in order to establish a statistical link between voltammogram fingerprints and chemical antioxidant substances. It was observed that the oxidation curve presented typical features, which enables sample discrimination according to age, oxygen consumption, and antioxidant additions. In fact, it was possible to place the results into four significant orthogonal directions, compressing 99.8% of nonrandom features. Attempts were made to make voltammogram fingerprinting a tool for monitoring oxidation management. For this purpose, a supervised multivariate control chart was developed using a control sample as reference. When white wines are plotted onto the chart, it is possible to monitor the oxidation status and to diagnose the effects of oxygen regimes and antioxidant activity. Finally, quantification of substances implicated in the oxidation process as reagents (antioxidants) and products (off-flavors) was tried using a supervised algorithmic the partial least square regression analysis. Good correlations (r > 0.93) were observed for ascorbic acid, Folin-Ciocalteu index, total SO(2), methional, and phenylacetaldehyde. These results show that cyclic voltammetry fingerprinting can be used to monitor and diagnose the effects of wine oxidation.

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Two gas chromatography-olfactometry (GC-O) techniques were used to screen targeting compounds with an impact on the perceived quality of Sherry vinegar: detection frequency and aroma extract dilution analysis (AEDA). The GC-O study revealed the presence of 108 aromatic notes, of which 64 were identified. Diacetyl, isoamyl acetate, acetic acid, and sotolon reached the highest frequency and flavor dilution (FD) factors. Ethyl acetate accounted for the maximum frequency but only a FD factor of 4. To test the sensory impact of these odorants, they were added to a 7% (w/v) acetic acid solution. We determined similarity values (SV) between solutions and the Sherry vinegar. The highest value from the similarity test was observed when diacetyl, ethyl acetate, and sotolon were added simultaneously. The profile of this model solution and a representative Sherry vinegar showed good similarity in the general impression descriptor, which emphasizes the important contribution of these three compounds to the global aroma of this vinegar.

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The carotenoids degradation and the formation of volatiles were examined by simulating Port wine aging. A two year old red Port wine was saturated with oxygen, supplemented with lutein and ß-carotene and kept at 60°C during 87h. A similar study was performed in a model wine solution. Results showed that the percentage decrease in lutein levels was, respectively, 79% and 95%, in the wine model solution and in the Port wine, and 55% and 10% for ß-carotene, indicating that lutein was more sensitive to degradation than ß-carotene. Two other unknown degradation carotenoid compounds were identified by HPLC/DAD (reverse phase λmax: 422; 445; 475 and 422; 445; 472) in the lutein supplemented wine. Levels of ß-ionone and ß-cyclocitral increased (2.5 times) in both, wine and wine model solution, supplemented with ß-carotene. Along with these compounds, the same behaviour was observed in ß-damascenone in the supplemented lutein wine and wine model solution. New insights were provided into the understanding of aroma modifications occurring during Port wine aging. The relationship between carotenoid molecules (ß-carotene and lutein) and some volatiles has also been provided.

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The aim of this work was the simultaneous determination of both ketoacids and dicarbonyl compounds in wine. To detect ketoacid compounds in wine, a method based on the quinoxaline derivatives by the reaction with diaminobenzene, currently employed to detect alpha-dicarbonyl compounds, was developed. The quinoxaline derivatives were detected by RP-HPLC with UV detection, which allows the determination of the major dicarbonyl compounds in wine: glyoxal, methylglyoxal, diacetyl and pentane-2,6-dione, and the quinoxaline/quinoxalinol derivatives of alpha-keto-gamma-(methylthio)butyric acid and beta-phenylpyruvic acid (intermediate ketoacid compounds of methional and phenylacetaldehyde) were simultaneously detected by a fluorescence detector. The identification was performed by comparison with standards and also by using LC-MSMS. The levels found in 15 wines analyzed (white wines, Madeira wines, and Port wines) diverge according to the type and the age of the wine. The ketoacid compounds ranged from 0.2 to 5.7 mg/L for alpha-keto-gamma-(methylthio)butyric acid and 0.1 to 9.6 mg/L for beta-phenylpyruvic acid. The quantities observed for dicarbonyl compounds were similar to those already reported.

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Carotenoids and chlorophyll-derived compounds in grapes and Port wines were investigated by HPLC-DAD and HPLC-DAD-MS (ESP+) analysis. A total of 13 carotenoid and chlorophyll-derived compounds are formally reported in grapes, 3 are identified for the first time, pheophytins a and b and (13Z)-beta-carotene, and 3 others remain unknown. In Port wines 19 compounds with carotenoid or chlorophyll-like structures are present, 8 still unidentified. The young wines showed higher total carotenoid content and chlorophyll-like compounds compared to aged Ports, with lutein and beta-carotene as major carotenoids. Among samples analyzed of monovarietal Vitis vinifera L. cultivar wines produced with the five most important Douro varieties, Tinta Roriz contained the highest levels of carotenoids and Touriga Franca the lowest. The forced-aging study indicated that lutein was more sensitive to temperature than beta-carotene. Additionally, aged wines showed higher ratios of beta-carotene/lutein concentrations compared to new Ports. Rates of degradation of chlorophyll derivative compounds were higher than those for carotene and lutein.

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This study was designed to monitor molinate losses in surface and underground waters during Ordram application in a rice field situated in central Portugal. Water samples were collected from different sites, before, during and about one month and a half after Ordram application. Molinate quantification was based on a solid-phase microextraction (SPME) method followed by gas chromatography with flame photometric detector (GC-FPD) analysis, and led to the conclusion that the herbicide was dissipated in the environment, reaching levels as high as 3.9 microgl(-1) in underground water and 15.8 microgl(-1) in the river receiving tail waters. The feasibility of the application of treatment methodologies based on adsorption or biodegradation as processes to remove molinate from real-world waters was assessed. These methods seem suitable to reduce molinate concentrations to values in the range of the legally recommended limits (<0.5 microgl(-1)).

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