Wageningen University and Research Centre

About: Wageningen University and Research Centre is a education organization based out in Wageningen, Netherlands. It is known for research contribution in the topics: Population & Sustainability. The organization has 23474 authors who have published 54833 publications receiving 2608897 citations.

A computational framework to explore large-scale biosynthetic diversity

Abstract: Genome mining has become a key technology to exploit natural product diversity. Although initially performed on a single-genome basis, the process is now being scaled up to mine entire genera, strain collections and microbiomes. However, no bioinformatic framework is currently available for effectively analyzing datasets of this size and complexity. In the present study, a streamlined computational workflow is provided, consisting of two new software tools: the ‘biosynthetic gene similarity clustering and prospecting engine’ (BiG-SCAPE), which facilitates fast and interactive sequence similarity network analysis of biosynthetic gene clusters and gene cluster families; and the ‘core analysis of syntenic orthologues to prioritize natural product gene clusters’ (CORASON), which elucidates phylogenetic relationships within and across these families. BiG-SCAPE is validated by correlating its output to metabolomic data across 363 actinobacterial strains and the discovery potential of CORASON is demonstrated by comprehensively mapping biosynthetic diversity across a range of detoxin/rimosamide-related gene cluster families, culminating in the characterization of seven detoxin analogues. Two bioinformatic tools, BiG-SCAPE and CORASON, enable sequence similarity network and phylogenetic analysis of gene clusters and their families across hundreds of strains and in large datasets, leading to the discovery of new natural products.

Lipid Oxidation in Oil‐in‐Water Emulsions: Involvement of the Interfacial Layer

Abstract: More polyunsaturated fats in processed foods and fewer additives are a huge demand of public health agencies and consumers. Consequently, although foods have an enhanced tendency to oxidize, the usage of antioxidants, especially synthetic antioxidants, is restrained. An alternate solution is to better control the localization of reactants inside the food matrix to limit oxidation. This review establishes the state-of-the-art on lipid oxidation in oil-in-water (O/W) emulsions, with an emphasis on the role of the interfacial region, a critical area in the system in that respect. We first provide a summary on the essential basic knowledge regarding (i) the structure of O/W emulsions and interfaces and (ii) the general mechanisms of lipid oxidation. Then, we discuss the factors involved in the development of lipid oxidation in O/W emulsions with a special focus on the role played by the interfacial region. The multiple effects that can be attributed to emulsifiers according to their chemical structure and their location, and the interrelationships between the parameters that define the physicochemistry and structure of emulsions are highlighted. This work sheds new light on the interpretation of reported results that are sometimes ambiguous or contradictory.

Gain and Loss of Fruit Flavor Compounds Produced by Wild and Cultivated Strawberry Species

Abstract: The blends of flavor compounds produced by fruits serve as biological perfumes used to attract living creatures, including humans. They include hundreds of metabolites and vary in their characteristic fruit flavor composition. The molecular mechanisms by which fruit flavor and aroma compounds are gained and lost during evolution and domestication are largely unknown. Here, we report on processes that may have been responsible for the evolution of diversity in strawberry (Fragaria spp) fruit flavor components. Whereas the terpenoid profile of cultivated strawberry species is dominated by the monoterpene linalool and the sesquiterpene nerolidol, fruit of wild strawberry species emit mainly olefinic monoterpenes and myrtenyl acetate, which are not found in the cultivated species. We used cDNA microarray analysis to identify the F. ananassa Nerolidol Synthase1 (FaNES1) gene in cultivated strawberry and showed that the recombinant FaNES1 enzyme produced in Escherichia coli cells is capable of generating both linalool and nerolidol when supplied with geranyl diphosphate (GPP) or farnesyl diphosphate (FPP), respectively. Characterization of additional genes that are very similar to FaNES1 from both the wild and cultivated strawberry species (FaNES2 and F. vesca NES1) showed that only FaNES1 is exclusively present and highly expressed in the fruit of cultivated (octaploid) varieties. It encodes a protein truncated at its N terminus. Green fluorescent protein localization experiments suggest that a change in subcellular localization led to the FaNES1 enzyme encountering both GPP and FPP, allowing it to produce linalool and nerolidol. Conversely, an insertional mutation affected the expression of a terpene synthase gene that differs from that in the cultivated species (termed F. ananassa Pinene Synthase). It encodes an enzyme capable of catalyzing the biosynthesis of the typical wild species monoterpenes, such as α-pinene and β-myrcene, and caused the loss of these compounds in the cultivated strawberries. The loss of α-pinene also further influenced the fruit flavor profile because it was no longer available as a substrate for the production of the downstream compounds myrtenol and myrtenyl acetate. This phenomenon was demonstrated by cloning and characterizing a cytochrome P450 gene (Pinene Hydroxylase) that encodes the enzyme catalyzing the C10 hydroxylation of α-pinene to myrtenol. The findings shed light on the molecular evolutionary mechanisms resulting in different flavor profiles that are eventually selected for in domesticated species.

Vitamin G: effects of green space on health, well-being, and social safety

Abstract: Background: Looking out on and being in the green elements of the landscape around us seem to affect health, well-being and feelings of social safety. This article discusses the design of a research program on the effects of green space in the living environment on health, well-being and social safety. Methods/design: The program consists of three projects at three different scales: at a macro scale using data on the Netherlands as a whole, at an intermediate scale looking into the specific effect of green space in the urban environment, and at micro scale investigating the effects of allotment gardens. The projects are observational studies, combining existing data on land use and health interview survey data, and collecting new data through questionnaires and interviews. Multilevel analysis and GIS techniques will be used to analyze the data. Discussion: Previous (experimental) research in environmental psychology has shown that a natural environment has a positive effect on well-being through restoration of stress and attentional fatigue. Descriptive epidemiological research has shown a positive relationship between the amount of green space in the living environment and physical and mental health and longevity. The program has three aims. First, to document the relationship between the amount and type of green space in people's living environment and their health, well-being, and feelings of safety. Second, to investigate the mechanisms behind this relationship. Mechanisms relate to exposure (leading to stress reduction and attention restoration), healthy behavior and social integration, and selection. Third, to translate the results into policy on the crossroads of spatial planning, public health, and safety. Strong points of our program are: we study several interrelated dependent variables, in different ordinary settings (as opposed to experimental or extreme settings), focusing on different target groups, using appropriate multilevel methods.

Short-term cold acclimation improves insulin sensitivity in patients with type 2 diabetes mellitus

Abstract: Cold exposure may be a potential therapy for diabetes by increasing brown adipose tissue (BAT) mass and activity. Here we report that 10 d of cold acclimation (14-15 °C) increased peripheral insulin sensitivity by ∼43% in eight type 2 diabetes subjects. Basal skeletal muscle GLUT4 translocation markedly increased, without effects on insulin signaling or AMP-activated protein kinase (AMPK) activation and only a minor increase in BAT glucose uptake.