Special Issue on “fruit metabolism and metabolomics”

Over the past 10 years, knowledge about several aspects of fruit metabolism has been greatly improved. Notably, high-throughput metabolomic technologies have allowed quantifying metabolite levels across various biological processes, and identifying the genes that underly fruit development and ripening. This Special Issue is designed to exemplify the current use of metabolomics studies of temperate and tropical fruit for basic research as well as practical applications. It includes articles about different aspects of fruit biochemical phenotyping, fruit metabolism before and after harvest, including primary and specialized metabolisms, and bioactive compounds involved in growth and environmental responses. The effect of genotype, stages of development or fruit tissue on metabolomic profiles and corresponding metabolism regulations are addressed, as well as the combination of other omics with metabolomics for fruit metabolism studies. © 2020 by the authors. Licensee MDPI, Basel, Switzerland.partly funded by MetaboHUB (ANR‐11‐INBS‐0010) and PHENOME (ANR‐11‐ INBS‐0012) French Agence Nationale de la Recherche projects. S.O. was parcially supported by grants RTI2018‐ 099797‐B‐100 (Ministerio de ciencia, Innovación y Universidades, Spain) and UMA18‐DEDERJA‐179 (Consejería de Economía, Conocimiento, Empresas y Universidades, Junta de Andalucía, Spain).Peer reviewe

Special Issue on “fruit metabolism and metabolomics”

Over the past 10 years, knowledge about several aspects of fruit metabolism has been greatly improved. Notably, high-throughput metabolomic technologies have allowed quantifying metabolite levels across various biological processes, and identifying the genes that underly fruit development and ripening. This Special Issue is designed to exemplify the current use of metabolomics studies of temperate and tropical fruit for basic research as well as practical applications. It includes articles about different aspects of fruit biochemical phenotyping, fruit metabolism before and after harvest, including primary and specialized metabolisms, and bioactive compounds involved in growth and environmental responses. The effect of genotype, stages of development or fruit tissue on metabolomic profiles and corresponding metabolism regulations are addressed, as well as the combination of other omics with metabolomics for fruit metabolism studies. © 2020 by the authors. Licensee MDPI, Basel, Switzerland.partly funded by MetaboHUB (ANR‐11‐INBS‐0010) and PHENOME (ANR‐11‐ INBS‐0012) French Agence Nationale de la Recherche projects. S.O. was parcially supported by grants RTI2018‐ 099797‐B‐100 (Ministerio de ciencia, Innovación y Universidades, Spain) and UMA18‐DEDERJA‐179 (Consejería de Economía, Conocimiento, Empresas y Universidades, Junta de Andalucía, Spain).Peer reviewe

Correlation Network Analysis reveals a sequential reorganization of metabolic and transcriptional states during germination and gene-metabolite relationships in developing seedlings of Arabidopsis

<p>Abstract</p> <p>Background</p> <p>Holistic profiling and systems biology studies of nutrient availability are providing more and more insight into the mechanisms by which gene expression responds to diverse nutrients and metabolites. Less is known about the mechanisms by which gene expression is affected by endogenous metabolites, which can change dramatically during development. Multivariate statistics and correlation network analysis approaches were applied to non-targeted profiling data to investigate transcriptional and metabolic states and to identify metabolites potentially influencing gene expression during the heterotrophic to autotrophic transition of seedling establishment.</p> <p>Results</p> <p>Microarray-based transcript profiles were obtained from extracts of Arabidopsis seeds or seedlings harvested from imbibition to eight days-old. ¹H-NMR metabolite profiles were obtained for corresponding samples. Analysis of transcript data revealed high differential gene expression through seedling emergence followed by a period of less change. Differential gene expression increased gradually to day 8, and showed two days, 5 and 7, with a very high proportion of up-regulated genes, including transcription factor/signaling genes. Network cartography using spring embedding revealed two primary clusters of highly correlated metabolites, which appear to reflect temporally distinct metabolic states. Principle Component Analyses of both sets of profiling data produced a chronological spread of time points, which would be expected of a developmental series. The network cartography of the transcript data produced two distinct clusters comprising days 0 to 2 and days 3 to 8, whereas the corresponding analysis of metabolite data revealed a shift of day 2 into the day 3 to 8 group. A metabolite and transcript pair-wise correlation analysis encompassing all time points gave a set of 237 highly significant correlations. Of 129 genes correlated to sucrose, 44 of them were known to be sucrose responsive including a number of transcription factors.</p> <p>Conclusions</p> <p>Microarray analysis during germination and establishment revealed major transitions in transcriptional activity at time points potentially associated with developmental transitions. Network cartography using spring-embedding indicate that a shift in the state of nutritionally important metabolites precedes a major shift in the transcriptional state going from germination to seedling emergence. Pair-wise linear correlations of transcript and metabolite levels identified many genes known to be influenced by metabolites, and provided other targets to investigate metabolite regulation of gene expression during seedling establishment.</p

Metabolite modifications in Solanum lycopersicum roots and leaves under cadmium stress

The effects of cadmium (Cd) were investigated on growth and metabolite profiling in roots and leaves of tomato (Solanum lycopersicum L., Var. Ibiza F1) plants exposed for 3 and 10 days to various CdCl2 concentrations (0 - 300 ìM). The aim of this study was to describe metabolite modifications in response to Cd stress and to identify Cd stress markers in the roots and leaves of tomato plants. During the treatment, Cd accumulated  significantly in the roots compared to stems and leaves. Plant growth (root, stem and leaf) decreased when Cd concentration increased. The analysis of 1H-NMR spectra of polar extracts showed clear differences between metabolites amounts (soluble sugars, organic and amino acids) in 30 and 300 ìM Cd-treated plants versus control ones. Among soluble sugars and organic acids, glucose, fructose and citrate contents significantly increased, by a factor 2 to 5 in both leaves and roots of Cd treated plants during the first three days of the treatment and then only in roots. In addition, Cd induced qualitative and quantitative changes in amino acid contents in the roots. Asparagine, glutamine and branched chain amino acids (valine, isoleucine, phenylalanine and tryptophane) significantly accumulated after 10 days of Cd exposure. Asparagine content which increased by 26 fold in the roots of 300 ìM Cd treated plants when compared with control ones, was found to be a good marker for Cd stress. In contrast, few modifications occurred in the leaves in response to Cd, except for tyrosine which content was highly increased (by 10 fold) after three days of treatment with 30 ìM. Taken together, our results show that, the exposure of tomato plants to various Cd concentrations results in significant changes in primary metabolism compounds, especially in the accumulation of some amino and organic acids involved in cellular compartmentation and detoxification of Cd.Key words: Cadmium, sugars, organic acids, amino acids, tomato (Solanum lycopersicum)

Integrating Technical Standards into ET Curricula to Meet ABET Standards and Industry Needs

With technical standards affecting nearly every aspect of our daily lives, from computers to the components and materials used in car engines, it is critical that undergraduate students are educated on the importance of standards and provided with opportunities to locate and apply relevant technical standards to real world situations. In addition, with ABET accreditation requiring students to have a “basic understanding and familiarity with,” and experience “using” codes and standards, faculty need to consider how such material can be naturally integrated into the curriculum. At Purdue University, education about codes and standards has been integrated into the mechanical engineering technology (MET) curriculum for decades with significant success. This paper discusses how standards are incorporated into mechanical design and quality control courses, as well as strategies for integrating standards into more courses in an MET curriculum. In addition, a discussion of standards resources that are freely available is included. Finally, a call to action for industry is presented, explaining the need and potential areas where industry can increase involvement in teaching students about technical standards

Nrf2-interacting nutrients and COVID-19: time for research to develop adaptation strategies.

There are large between- and within-country variations in COVID-19 death rates. Some very low death rate settings such as Eastern Asia, Central Europe, the Balkans and Africa have a common feature of eating large quantities of fermented foods whose intake is associated with the activation of the Nrf2 (Nuclear factor (erythroid-derived 2)-like 2) anti-oxidant transcription factor. There are many Nrf2-interacting nutrients (berberine, curcumin, epigallocatechin gallate, genistein, quercetin, resveratrol, sulforaphane) that all act similarly to reduce insulin resistance, endothelial damage, lung injury and cytokine storm. They also act on the same mechanisms (mTOR: Mammalian target of rapamycin, PPARγ:Peroxisome proliferator-activated receptor, NFκB: Nuclear factor kappa B, ERK: Extracellular signal-regulated kinases and eIF2α:Elongation initiation factor 2α). They may as a result be important in mitigating the severity of COVID-19, acting through the endoplasmic reticulum stress or ACE-Angiotensin-II-AT1R axis (AT1R) pathway. Many Nrf2-interacting nutrients are also interacting with TRPA1 and/or TRPV1. Interestingly, geographical areas with very low COVID-19 mortality are those with the lowest prevalence of obesity (Sub-Saharan Africa and Asia). It is tempting to propose that Nrf2-interacting foods and nutrients can re-balance insulin resistance and have a significant effect on COVID-19 severity. It is therefore possible that the intake of these foods may restore an optimal natural balance for the Nrf2 pathway and may be of interest in the mitigation of COVID-19 severity

CD4 cell count and the risk of AIDS or death in HIV-Infected adults on combination antiretroviral therapy with a suppressed viral load: a longitudinal cohort study from COHERE.

BACKGROUND: Most adults infected with HIV achieve viral suppression within a year of starting combination antiretroviral therapy (cART). It is important to understand the risk of AIDS events or death for patients with a suppressed viral load. METHODS AND FINDINGS: Using data from the Collaboration of Observational HIV Epidemiological Research Europe (2010 merger), we assessed the risk of a new AIDS-defining event or death in successfully treated patients. We accumulated episodes of viral suppression for each patient while on cART, each episode beginning with the second of two consecutive plasma viral load measurements 500 copies/µl, the first of two consecutive measurements between 50-500 copies/µl, cART interruption or administrative censoring. We used stratified multivariate Cox models to estimate the association between time updated CD4 cell count and a new AIDS event or death or death alone. 75,336 patients contributed 104,265 suppression episodes and were suppressed while on cART for a median 2.7 years. The mortality rate was 4.8 per 1,000 years of viral suppression. A higher CD4 cell count was always associated with a reduced risk of a new AIDS event or death; with a hazard ratio per 100 cells/µl (95% CI) of: 0.35 (0.30-0.40) for counts <200 cells/µl, 0.81 (0.71-0.92) for counts 200 to <350 cells/µl, 0.74 (0.66-0.83) for counts 350 to <500 cells/µl, and 0.96 (0.92-0.99) for counts ≥500 cells/µl. A higher CD4 cell count became even more beneficial over time for patients with CD4 cell counts <200 cells/µl. CONCLUSIONS: Despite the low mortality rate, the risk of a new AIDS event or death follows a CD4 cell count gradient in patients with viral suppression. A higher CD4 cell count was associated with the greatest benefit for patients with a CD4 cell count <200 cells/µl but still some slight benefit for those with a CD4 cell count ≥500 cells/µl

H-NMR metabolic profiling of wines from three cultivars, three soil types and two contrasting vintages

Differences in wine flavour proceed primarily from grape quality. Environmental factors (climate, soil), cultivars and training systems modify many grape and wine quality traits. Metabolic profiling based on proton nuclear magnetic resonance (1H-NMR) spectra has been proved to be useful to study multifactorial effects of the vine environment on intricate grape quality traits. The capacity of this method to discriminate the environmental effects on wine has to be demonstrate

Subcellular concentrations of sugar alcohols and sugars in relation to phloem translocation in Plantago major, Plantago maritima, Prunus persica, and Apium graveolens

Sugar and sugar alcohol concentrations were analyzed in subcellular compartments of mesophyll cells, in the apoplast, and in the phloem sap of leaves of Plantago major (common plantain), Plantago maritima (sea plantain), Prunus persica (peach) and Apium graveolens (celery). In addition to sucrose, common plantain, sea plantain, and peach also translocated substantial amounts of sorbitol, whereas celery translocated mannitol as well. Sucrose was always present in vacuole and cytosol of mesophyll cells, whereas sorbitol and mannitol were found in vacuole, stroma, and cytosol in all cases except for sea plantain. The concentration of sorbitol, mannitol and sucrose in phloem sap was 2- to 40-fold higher than that in the cytosol of mesophyll cells. Apoplastic carbohydrate concentrations in all species tested were in the low millimolar range versus high millimolar concentrations in symplastic compartments. Therefore, the concentration ratios between the apoplast and the phloem were very strong, ranging between 20- to 100-fold for sorbitol and mannitol, and between 200- and 2000-fold for sucrose. The woody species, peach, showed the smallest concentration ratios between the cytosol of mesophyll cells and the phloem as well as between the apoplast and the phloem, suggesting a mixture of apoplastic and symplastic phloem loading, in contrast to the herbal plant species (common plantain, sea plantain, celery) which likely exhibit an active loading mode for sorbitol and mannitol as well as sucrose from the apoplast into the phloem