PathwayNexus: a tool for interactive metabolic data analysis.

MOTIVATION: High-throughput omics methods increasingly result in large datasets including metabolomics data, which are often difficult to analyse. RESULT: To help researchers to handle and analyse those datasets by mapping and investigating metabolomics data of multiple sampling conditions (e. g., different time points or treatments) in the context of pathways, PathwayNexus has been developed, which presents the mapping results in a matrix format, allowing users to easily observe the relations between the compounds and the pathways. It also offers functionalities like ranking, sorting, clustering, pathway views and further analytical tools. Its primary objective is to condense large sets of pathways into smaller, more relevant subsets that align with the specific interests of the user. AVAILABILITY AND IMPLEMENTATION: The methodology presented here is implemented in PathwayNexus, an open-source add-on for Vanted available at www.cls.uni-konstanz.de/software/pathway-nexus. SUPPLEMENTARY INFORMATION: Website: www.cls.uni-konstanz.de/software/pathway-nexus.

APL@voro-interactive visualization and analysis of cell membrane simulations.

SUMMARY: Molecular dynamics (MD) simulations of cell membranes allow for a better understanding of complex processes such as changing membrane dynamics, lipid rafts and the incorporation/passing of macromolecules into/through membranes. To explore and understand cell membrane compositions, dynamics and processes, visual analytics can help to interpret MD simulation data. APL@Voro is a software for the interactive visualization and analysis of cell membrane simulations. Here, we present the new APL@Voro, which has been continuously developed since its initial release in 2013. We discuss newly implemented algorithms, methodologies and features, such as the interactive comparison of related simulations and methods to assign lipids to either the upper or lower leaflet. AVAILABILITY AND IMPLEMENTATION: The current open-source version of APL@Voro can be downloaded from http://aplvoro.com.

A cross-cultural perspective on feeling good in the context of foods and beverages.

The aim of the present research was to explore consumers' conceptualization of feeling good in relation to food and beverages from a cross-cultural perspective. Participants from 14 countries across 5 continents and covering 10 languages (N = 8325) responded to an online survey including word association and free listing tasks related to feeling good in the context of food and beverages. Results were analyzed using inductive coding: a list of main codes was generated in English for each of the tasks, after which native speakers for each language coded the responses. Codes were grouped into categories reflecting common themes from which eight dimensions were identified. Results showed that in the context of foods and beverages, feeling good was mainly associated with specific foods and sensory and hedonic properties. Across the 14 countries, 'Sweet and fat food', 'Fruit and vegetables', and 'Protein food' were the three food categories most associated with feeling good. Emotional aspects of food consumption ('Taste good' and emotions) were also relevant. Health and nutrition-related aspects were more relevant for consumers when they were asked to think about how foods and beverages would make them feel good in the future. In other words, food-related feeling good seems to be mainly driven by sensory pleasure at present, but it is also related to nutrition and health in the future. Differences in the strength of the associations between feeling good and the identified categories were found between countries, in line with the existence of cultural differences in food habits, as well as in the importance people attach to the characteristics of foods and beverages. Results from the present work provide insights on the impact of eating and drinking on feeling good in terms of emotional, physical and social aspects, and increase knowledge about the way food and drink can contribute to general well-being.

15N-nitrate and 34S-sulfate isotopic fractionation reflects electron acceptor 'recycling' during hydrocarbon biodegradation.

The analysis of stable carbon isotopes for the assessment of contaminant fate in the aquifer is impeded in the case of petroleum hydrocarbons (TPH) by their chain length. Alternatively, the coupled nitrogen-sulfur-carbon cycles involved into TPH biodegradation under sulfate- and nitrate reducing conditions can be investigated using nitrogen (δ15N) and sulfur (δ34S) isotopic shifts in terminal electron acceptors (TEA) involved in anaerobic TPH oxidation. Biodegradation of a paraffin-rich crude oil was studied in anaerobic aquifer microcosms with nitrate (NIT), sulfate (SUL), nitrate plus sulfate (MIX) and nitrate under sulfate reduction suppression by molybdate (MOL) as TEA. After 8 months, TPH biodegradation was not different (around 33%) in experiments receiving only nitrate (NIT, MOL) versus under mixed TEA-conditions (MIX), despite higher biodiversity under mixed conditions (H'NIT and H'MOL≈5.9, H'MIX=8.0). Molybdate addition effected higher nitrate depletion, possibly by increasing the production of nitrate reductase. Additional sulfate depletion under mixed conditions suggested bioconversion of polar intermediates. Microcosms only receiving sulfate (SUL) showed no significant TEA and TPH decrease. A Rayleigh kinetic isotope enrichment model for isotopic 15N/14N and 34S/32S shifts in residual TEA gave apparent enrichment factors ɛN,NIT and ɛN,MOL values of -16.7 to -18.0‰ for nitrate as sole TEA and ɛN,MIX of -6.0‰ and ɛS,MIX of -4.1‰ under mixed electron accepting conditions. The low isotopic fractionation under mixed terminal electron accepting conditions was attributed to lithotrophic, sulfide-dependent denitrification by Thiobacillus species, while it was hypothesized that Desulfovibrio replenished the reduced sulfur pool via oxidation of polar hydrocarbon metabolites. Concurrently, organotrophic denitrification was performed by Pseudomonas species, with isotopic fractionation expressed by ɛN,MIX representing the superposition of both denitrification processes. This is, to our knowledge, the first characterization of sulfur and nitrogen isotopic shifts associated to concurrent organotrophic and lithotrophic denitrification in a hydrocarbon-contaminated environment, and offers the prospect of improved understanding of biogeochemical cycles including in situ hydrocarbon biotransformation.