Tissue biochemical diversity of 20 gooseberry cultivars and the effect of ethylene supplementation on postharvest life

The European gooseberry (Ribes uva-crispa) is still an understudied crop with limited data available on its biochemical profile and postharvest life. A variety of polyphenols were detected in the skin and flesh of 20 gooseberry cvs, representing mainly flavonol glycosides, anthocyanins and flavan-3-ols. In contrast, gooseberry seeds were for the first time characterised by the presence of considerable amounts of hydroxycinnamic acid glycosides tentatively identified by UPLC-QToF/MS. All cvs examined represented a good source of vitamin C while being low in sugar. Furthermore, the postharvest stability of bioactives was explored by supplementation of exogenous ethylene in air at 5 °C. Results suggest a low sensitivity of gooseberries to ethylene. The overall quality of gooseberries remained stable over two weeks, showing potential for extended bioactive life

Simultaneous quantification of antioxidants paraxanthine and caffeine in human saliva by electrochemical sensing for CYP1A2 phenotyping

The enzyme CYP1A2 is responsible for the metabolism of numerous antioxidants in the body, including caffeine, which is transformed into paraxanthine, its main primary metabolite. Both molecules are known for their antioxidant and pro-oxidant characteristics, and the paraxanthine-to-caffeine molar ratio is a widely accepted metric for CYP1A2 phenotyping, to optimize dose\u2013 response effects in individual patients. We developed a simple, cheap and fast electrochemical based method for the simultaneous quantification of paraxanthine and caffeine in human saliva, by differential pulse voltammetry, using an anodically pretreated glassy carbon electrode. Cyclic voltammetry experiments revealed for the first time that the oxidation of paraxanthine is diffusion controlled with an irreversible peak at ca. +1.24 V (vs. Ag/AgCl) in a 0.1 M H2 SO4 solution, and that the mechanism occurs via the transfer of two electrons and two protons. The simultaneous quantification of paraxanthine and caffeine was demonstrated in 0.1 M H2 SO4 and spiked human saliva samples. In the latter case, limits of detection of 2.89 \ub5M for paraxanthine and 5.80 \ub5M for caffeine were obtained, respectively. The sensor is reliable, providing a relative standard deviation within 7% (n = 6). Potential applicability of the sensing platform was demonstrated by running a small scale trial on five healthy volunteers, with simultaneous quantification by differential pulse voltammetry (DPV) of paraxanthine and caffeine in saliva samples collected at 1, 3 and 6 h postdose administration. The results were validated by ultra-high pressure liquid chromatography and shown to have a high correlation factor (r = 0.994)

Covalently Crosslinked Nanogels: An NMR Study of the Effect of Monomer Reactivity on Composition and Structure

Covalently crosslinked nanogels are widely explored as drug delivery systems and sensors. Radical polymerization provides a simple, inexpensive, and broadly applicable approach for their preparation, although the random nature of the reaction requires careful study of the final chemical composition. We demonstrate how the different reactivities of the monomers influence the total degree of incorporation into the polymer matrix and the role played by the experimental parameters in maximizing polymerization efficiency. Nanogels based on N-isopropylacrylamide, N-n-propylacrylamide, and acrylamide crosslinked with N,N’-methylenebisacrylamide were included in this study, in combination with functional monomers N-acryloyl-l-proline, 2-acrylamido-2-methyl-1-propanesulfonic acid, and 4-vinyl-1H-imidazole. Total monomer concentration and initiator quantities are determining parameters for maximizing monomer conversions and chemical yields. The results show that the introduction of functional monomers, changes in the chemical structure of the polymerizable unit, and the addition of templating molecules can all have an effect on the polymerization kinetics. This can significantly impact the final composition of the matrices and their chemical structure, which in turn influence the morphology and properties of the nanogels

Prediction of self-assembly of adenosine analogues in solution: a computational approach validated by isothermal titration calorimetry.

The recent discovery of the role of adenosine-analogues as neuroprotectants and cognitive enhancers has sparked interest in these molecules as new therapeutic drugs. Understanding the behavior of these molecules in solution and predicting their ability to self-assemble will accelerate new discoveries. We propose a computational approach based on density functional theory, a polarizable continuum solvation description of the aqueous environment, and an efficient search procedure to probe the potential energy surface, to determine the structure and thermodynamic stability of molecular clusters of adenosine analogues in solution, using caffeine as a model. The method was validated as a tool for the prediction of the impact of small structural variations on self-assembly using paraxanthine. The computational results were supported by isothermal titration calorimetry experiments. The thermodynamic parameters enabled the quantification of the actual percentage of dimer present in solution as a function of concentration. The data suggest that both caffeine and paraxanthine are present at concentrations comparable to the ones found in biological samples

Covalently crosslinked nanogels: an NMR study of the effect of monomer reactivity on composition and structure

Covalently crosslinked nanogels are widely explored as drug delivery systems and sensors. Radical polymerization provides a simple, inexpensive, and broadly applicable approach for their preparation, although the random nature of the reaction requires careful study of the final chemical composition. We demonstrate how the different reactivities of the monomers influence the total degree of incorporation into the polymer matrix and the role played by the experimental parameters in maximizing polymerization efficiency. Nanogels based on N-isopropylacrylamide, N-n-propylacrylamide, and acrylamide crosslinked with N,N’-methylenebisacrylamide were included in this study, in combination with functional monomers N-acryloyl-l-proline, 2-acrylamido-2-methyl-1-propanesulfonic acid, and 4-vinyl-1H-imidazole. Total monomer concentration and initiator quantities are determining parameters for maximizing monomer conversions and chemical yields. The results show that the introduction of functional monomers, changes in the chemical structure of the polymerizable unit, and the addition of templating molecules can all have an effect on the polymerization kinetics. This can significantly impact the final composition of the matrices and their chemical structure, which in turn influence the morphology and properties of the nanogels

Transcriptome and phytohormone changes associated with ethylene-induced onion bulb dormancy

Control of dormancy and sprouting in onion bulbs is commercially important for postharvest management. Although ethylene application is sometimes used to extend dormancy, the underlying mechanisms regulating dormancy transition remain unclear. Since the sprout leaves emerge from the bulb baseplate, we used this tissue to assess the impact of ethylene treatment and storage time on the hormone profile and the transcriptome. Reads from 30 libraries were assembled and annotated, with 94,840 unigenes retained after filtering. The de novo transcriptome assembly was of high quality and continuity (N50: 1809 bp, GC content: 36.21 %), and was used to analyse differential expression and Gene Onotologies. Across two years, applied ethylene resulted in delayed dormancy break and reduced post-dormancy sprout vigour. Ethylene supplementation enhanced endogenous ethylene production and caused a transient climacteric-like increase in respiration. Significant changes in hormone and associated transcript profiles occurred through storage and in response to ethylene. In particular, abscisic acid (ABA) and its metabolite phaseic acid (PA) increased under ethylene during the longer dormancy period; however, cytokinin increases observed during storage appeared largely independent of ethylene treatment. Several hormone-related transcripts showed differential expression over time and/or in response to ethylene. Expression of ethylene biosynthesis (ACO), receptor (EIN4) and transcription factor (EIL3) genes were modified by ethylene, as were ABA biosynthesis genes such NCED, and cytokinin biosynthesis genes such as LOG and CKX. We conclude that ethylene substantially modifies expression of genes in several phytohormone pathways, and some of these changes may underlie the dormancy-extending effects of exogenous ethylene

The first comprehensive chemical profiling of Vachellia gummifera (Willd.) Kyal. & Boatwr., a plant with medicinal value

Vachellia gummifera (Willd.) Kyal. & Boatwr. is a medicinal plant endemic to Morocco that has no documented studies on its chemical composition. In this study, the chemical composition of the water/methanol (4 : 1) extracts of air-dried leaf and stem samples of Moroccan V. gummifera was determined using UHPLC-MS and NMR. In total, over 100 metabolites were identified in our study. Pinitol was the major compound in both the leaf and stem extracts, being significantly more abundant in the former. Asparagine and 3-hydroxyheteroendrin were the second most abundant compounds in the stem and leaf extracts, respectively, though both compounds were present in each tissue. The other compounds included flavonoids based on quercetin, and phenolic derivatives. Eucomic acid, only identified in the stems and was the major aromatic compound distinguishing the leaf and stem profiles. Quercetin 3-O-(6′′-O-malonyl)-β-D-glucopyranoside was identified as the major flavonoid in the leaves but was also present in the stems. Other malonylated derivatives that were all flavonol glycosides based on myricetin, kaempferol, and isorhamnetin in addition to quercetin were also identified. This is the first report of eucomic acid and malonylated compounds in Vachellia species. This report provides valuable insights into the chemotaxonomic significance of the Vachellia genus.OCP Morocco.FP05is a collaboration between Mohammed VI Polytechnic University, Rothamsted Research and Cranfield Universit

CRAMER: A lightweight, highly customisable web-based genome browser supporting multiple visualisation instances

In recent years the ability to generate genomic data has increased dramatically along with the demand for easily personalised and customisable genome browsers for effective visualisation of diverse types of data. Despite the large number of web-based genome browsers available nowadays, none of the existing tools provide means for creating multiple visualisation instances without manual set up on the deployment server side. The Cranfield Genome Browser (CRAMER) is an open-source, lightweight and highly customisable web application for interactive visualisation of genomic data. Once deployed, CRAMER supports seamless creation of multiple visualisation instances in parallel while allowing users to control and customise multiple tracks. The application is deployed on a Node.js server and is supported by a MongoDB database which stored all customisations made by the users allowing quick navigation between instances. Currently, the browser supports visualising a large number of file formats for genome annotation, variant calling, reads coverage and gene expression. Additionally, the browser supports direct Javascript coding for personalised tracks, providing a whole new level of customisation both functionally and visually. Tracks can be added via direct file upload or processed in real-time via links to files stored remotely on an FTP repository. Furthermore, additional tracks can be added by users via simple drag and drop to an existing visualisation instance

Metabolic characterization of Palatinate German white wines according to sensory attributes, varieties, and vintages using NMR spectroscopy and multivariate data analyses

1H NMR (nuclear magnetic resonance spectroscopy) has been used for metabolomic analysis of ‘Riesling’ and ‘Mueller-Thurgau’ white wines from the German Palatinate region. Diverse two-dimensional NMR techniques have been applied for the identification of metabolites, including phenolics. It is shown that sensory analysis correlates with NMR-based metabolic profiles of wine. 1H NMR data in combination with multivariate data analysis methods, like principal component analysis (PCA), partial least squares projections to latent structures (PLS), and bidirectional orthogonal projections to latent structures (O2PLS) analysis, were employed in an attempt to identify the metabolites responsible for the taste of wine, using a non-targeted approach. The high quality wines were characterized by elevated levels of compounds like proline, 2,3-butanediol, malate, quercetin, and catechin. Characterization of wine based on type and vintage was also done using orthogonal projections to latent structures (OPLS) analysis. ‘Riesling’ wines were characterized by higher levels of catechin, caftarate, valine, proline, malate, and citrate whereas compounds like quercetin, resveratrol, gallate, leucine, threonine, succinate, and lactate, were found discriminating for ‘Mueller-Thurgau’. The wines from 2006 vintage were dominated by leucine, phenylalanine, citrate, malate, and phenolics, while valine, proline, alanine, and succinate were predominantly present in the 2007 vintage. Based on these results, it can be postulated the NMR-based metabolomics offers an easy and comprehensive analysis of wine and in combination with multivariate data analyses can be used to investigate the source of the wines and to predict certain sensory aspects of wine

Establishing a generalized polyepigenetic biomarker for tobacco smoking

Large-scale epigenome-wide association meta-analyses have identified multiple 'signatures'' of smoking. Drawing on these findings, we describe the construction of a polyepigenetic DNA methylation score that indexes smoking behavior and that can be utilized for multiple purposes in population health research. To validate the score, we use data from two birth cohort studies: The Dunedin Longitudinal Study, followed to age-38 years, and the Environmental Risk Study, followed to age-18 years. Longitudinal data show that changes in DNA methylation accumulate with increased exposure to tobacco smoking and attenuate with quitting. Data from twins discordant for smoking behavior show that smoking influences DNA methylation independently of genetic and environmental risk factors. Physiological data show that changes in DNA methylation track smoking-related changes in lung function and gum health over time. Moreover, DNA methylation changes predict corresponding changes in gene expression in pathways related to inflammation, immune response, and cellular trafficking. Finally, we present prospective data about the link between adverse childhood experiences (ACEs) and epigenetic modifications; these findings document the importance of controlling for smoking-related DNA methylation changes when studying biological embedding of stress in life-course research. We introduce the polyepigenetic DNA methylation score as a tool both for discovery and theory-guided research in epigenetic epidemiology.This article is freely available via Open Access. Click on the Publisher URL to access it via the publisher's site.The Dunedin Longitudinal Study is funded by the New Zealand Health Research Council, the New Zealand Ministry of Business, Innovation, and Employment, the National Institute on Aging (AG032282), and the Medical Research Council (MR/P005918/1). The E-Risk Study is funded by the Medical Research Council (G1002190) and the National Institute of Child Health and Human Development (HD077482). Additional support was provided by a Distinguished Investigator Award from the American Asthma Foundation to Dr. Mill, and by the Jacobs Foundation and the Avielle Foundation. Dr. Arseneault is the Mental Health Leadership Fellow for the U.K. Economic and Social Research Council. Dr. Belsky is a Jacobs Foundation Fellow. This work used a high-performance computing facility partially supported by grant 2016-IDG-1013 (“HARDAC + : Reproducible HPC for Next-generation Genomics”) from the North Carolina Biotechnology Center. Illumina DNA methylation data are accessible from the Gene Expression Omnibus (accession code: GSE105018).pre-print, post-print, publisher's PD