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The production of fine-flavor cocoa represents a promising avenue to enhance socioeconomic development in Colombia and Latin America. Premium chocolate is obtained through a post-harvesting process, which relies on semi-standardized techniques. The change in the metabolic profile during cocoa processing considerably impacts flavor and nutraceutical properties of the final product. Understanding this impact considering both volatiles and non-volatile compounds is crucial for process and product re-engineering of cocoa post-harvesting. Consequently, this work studied the metabolic composition of cocoa liquor by untargeted metabolomics and lipidomics. This approach offered a comprehensive view of cocoa biochemistry, considering compounds associated with bioactivity and flavor in cocoa liquor. Their variations were traced back over the cocoa processing (i.e., drying, and roasting), highlighting their impact on flavor development and the nutraceutical properties. These results represent the basis for future studies aimed to re-engineer cocoa post-harvesting considering the variation of key flavor and bioactive compounds over processing.

Transient expression in Nicotiana benthamiana offers a robust platform for the rapid production of complex secondary metabolites. It has proven highly effective in helping identify genes associated with pathways responsible for synthesizing various valuable natural compounds. While this approach has seen considerable success, it has yet to be applied to uncovering genes involved in anthocyanin biosynthetic pathways. This is because only a single anthocyanin, delphinidin 3‐O‐rutinoside, can be produced in N. benthamiana by activation of anthocyanin biosynthesis using transcription factors. The production of other anthocyanins would necessitate the suppression of certain endogenous flavonoid biosynthesis genes while transiently expressing others. In this work, we present a series of tools for the reconstitution of anthocyanin biosynthetic pathways in N. benthamiana leaves. These tools include constructs for the expression or silencing of anthocyanin biosynthetic genes and a mutant N. benthamiana line generated using CRISPR. By infiltration of defined sets of constructs, the basic anthocyanins pelargonidin 3‐O‐glucoside, cyanidin 3‐O‐glucoside and delphinidin 3‐O‐glucoside could be obtained in high amounts in a few days. Additionally, co‐infiltration of supplementary pathway genes enabled the synthesis of more complex anthocyanins. These tools should be useful to identify genes involved in the biosynthesis of complex anthocyanins. They also make it possible to produce novel anthocyanins not found in nature. As an example, we reconstituted the pathway for biosynthesis of Arabidopsis anthocyanin A5, a cyanidin derivative and achieved the biosynthesis of the pelargonidin and delphinidin variants of A5, pelargonidin A5 and delphinidin A5.

Tomatoes show diverse phytochemical attributes that contribute to their nutritive and health values. This study comprehensively dissects primary and secondary metabolite profiles of seven tomato varieties. UHPLC-qTOF-MS assisted molecular networking was used to monitor 206 metabolites, 30 of which were first-time to be reported. Flavonoids, as valuable antioxidants, were enriched in light-colored tomatoes (golden sweet, sun gold, and yellow plum) versus high tomatoside A, an antihyperglycemic saponin, in cherry bomb and red plum varieties. UV–Vis analysis revealed similar results with a strong absorbance corresponding to rich phenolic content in light varieties. GC–MS unveiled monosaccharides as the main contributors to samples’ segregation, found abundant in San Marzano tomato accounting for its sweet flavor. Fruits also demonstrated potential antioxidant activities in correlation to their flavonoids and phospholipids. This work provides a complete map of tomatoes’ metabolome heterogeneity for future breeding programs and a comparative approach utilizing different metabolomic platforms for tomato analysis.

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M. oleifera known as “miracle tree” is increasingly used in nutraceuticals for the reported health effects and nutritional value of its leaves. This study presents the first metabolome profiling of M. oleifera leaves of African origin using different solvent polarities via HR-UPLC/MS based molecular networking followed by multivariate data analyses for samples classification. 119 Chemicals were characterized in both positive and negative modes belonging to 8 classes viz. phenolic acids, flavonoids, peptides, fatty acids/amides, sulfolipids, glucosinolates and carotenoids. New metabolites i.e., polyphenolics, fatty acids, in addition to a new class of sulfolipids were annotated for the first time in Moringa leaves. In vitro anti-inflammatory and anti-aging bioassays of the leaf extracts were assessed and in correlation to their metabolite profile via multivariate data analyses. Kaempferol, quercetin and apigenin-O/C-glycosides, fatty acyl amides and carotenoids appeared crucial for biological activities and leaves origin discrimination.

With a favored taste and various bioactivities, coffee has been consumed as a daily beverage worldwide. The current study presented a multi-faceted comparative metabolomics approach dissecting commercially available coffee products in the Middle East region for quality assessment and functional food purposes using NMR and GC/MS platforms. NMR metabolites fingerprinting led to identification of 18 metabolites and quantification (qNMR) of six prominent markers for standardization purposes. An increase of β-ethanolamine (MEA) reported for the first time, 5-(hydroxymethyl) furfural (5-HMF), concurrent with a reduction in chlorogenic acid, kahweol, and sucrose levels post roasting as revealed using multivariate data analyses (MVA). The diterpenes kahweol and cafestol were identified in green and roasted Coffea arabica, while 16-O-methyl cafestol in roasted C. robusta. Moreover, GC/MS identified a total of 143 metabolites belonging to 15 different chemical classes, with fructose found enriched in green C. robusta versus fatty acids abundance, i.e., palmitic and stearic acids in C. arabica confirming NMR results. These potential results aided to identify novel quality control attributes, i.e., ethanolamine, for coffee in the Middle East region and have yet to be confirmed in other coffee specimens.

The impact of cocoa lipid content on chocolate quality has been extensively described. Nevertheless, few studies have elucidated the cocoa lipid composition and their bioactive properties, focusing only on specific lipids. In the present study the lipidome of fine-flavor cocoa fermentation was analyzed using LC-MS-QTOF and a Machine Learning model to assess potential bioactivity was developed. Our results revealed that the cocoa lipidome, comprised mainly of fatty acyls and glycerophospholipids, remains stable during fine-flavor cocoa fermentations. Also, several Machine Learning algorithms were trained to explore potential biological activity among the identified lipids. We found that K-Nearest Neighbors had the best performance. This model was used to classify the identified lipids as bioactive or non-bioactive, nominating 28 molecules as potential bioactive lipids. None of these compounds have been previously reported as bioactive. Our work is the first untargeted lipidomic study and systematic effort to investigate potential bioactivity in fine-flavor cocoa lipids.

Saffron is a spice revered for its unique flavor and health attributes often subjected to fraudulence. In this study, molecular networking as a visualization tool for UPLC/MS dataset of saffron and its common substitutes i.e. safflower and calendula (n = 21) was employed for determining genuineness of saffron and detecting its common substitutes i.e. safflower and calendula. Saffron was abundant in flavonol-O-glycosides and crocetin esters versus richness of flavanones/chalcones glycosides in safflower and cinnamates/terpenes in calendula. OPLS-DA identified differences in UPLC/MS profiles of different saffron accessions where oxo-hydroxy-undecenoic acid-O-hexoside was posed as saffron authentication marker and aided in discrimination between Spanish saffron of high quality from its inferior grade i.e. Iranian saffron along with crocetin di-O-gentiobiosyl ester and kaempferol-O-sophoroside. Kaempferol-O-neohesperidoside and N,N,N,-p-coumaroyl spermidine were characteristic safflower metabolites, whereas, calendulaglycoside C and di-O-caffeoyl quinic acid were unique to calendula. UV/VIS fingerprint spectral regions of picrocrocin (230–260 nm) and crocin derivatives (400–470 nm) were posed as being discriminatory of saffron authenticity and suggestive it can replace UPLC/MS in saffrom quality determination.

In biological discovery and engineering research, there is a need to spatially and/or temporally regulate transgene expression. However, the limited availability of promoter sequences that are uniquely active in specific tissue-types and/or at specific times often precludes co-expression of >multiple transgenes in precisely controlled developmental contexts. Here, we developed a system for use in rice that comprises synthetic designer transcription activator-like effectors (dTALEs) and cognate synthetic TALE-activated promoters (STAPs). The system allows multiple transgenes to be expressed from different STAPs, with the spatial and temporal context determined by a single promoter that drives expression of the dTALE. We show that two different systems—dTALE1-STAP1 and dTALE2-STAP2—can activate STAP-driven reporter gene expression in stable transgenic rice lines, with transgene transcript levels dependent on both dTALE and STAP sequence identities. The relative strength of individual STAP sequences is consistent between dTALE1 and dTALE2 systems but differs between cell-types, requiring empirical evaluation in each case. dTALE expression leads to off-target activation of endogenous genes but the number of genes affected is substantially less than the number impacted by the somaclonal variation that occurs during the regeneration of transformed plants. With the potential to design fully orthogonal dTALEs for any genome of interest, the dTALE-STAP system thus provides a powerful approach to fine-tune the expression of multiple transgenes, and to simultaneously introduce different synthetic circuits into distinct developmental contexts.