Showing papers by "University of Avignon published in 2016"

Stabilizing and Modulating Color by Copigmentation: Insights from Theory and Experiment

Abstract: Natural anthocyanin pigments/dyes and phenolic copigments/co-dyes form noncovalent complexes, which stabilize and modulate (in particular blue, violet, and red) colors in flowers, berries, and food products derived from them (including wines, jams, purees, and syrups). This noncovalent association and their electronic and optical implications constitute the copigmentation phenomenon. Over the past decade, experimental and theoretical studies have enabled a molecular understanding of copigmentation. This review revisits this phenomenon to provide a comprehensive description of the nature of binding (the dispersion and electrostatic components of π-π stacking, the hydrophobic effect, and possible hydrogen-bonding between pigment and copigment) and of spectral modifications occurring in copigmentation complexes, in which charge transfer plays an important role. Particular attention is paid to applications of copigmentation in food chemistry.

Effects of dietary polyphenols on metabolic syndrome features in humans: a systematic review

Abstract: Dietary polyphenols constitute a large family of bioactive substances potential beneficial effect on metabolic syndrome (MetS). This review summarizes the results of clinical studies on patients with MetS involving the chronic supplementation of a polyphenol-rich diet, foods, extracts or with single phenolics on the features of MetS (obesity, dyslipidemia, blood pressure and glycaemia) and associated complications (oxidative stress and inflammation). Polyphenols were shown to be efficient, especially at higher doses, and there were no specific foods or extracts able to alleviate all the features of MetS. Green tea, however, significantly reduced body mass index and waist circumference and improved lipid metabolism. Cocoa supplementation reduced blood pressure and blood glucose. Soy isoflavones, citrus products, hesperidin and quercetin improved lipid metabolism, whereas cinnamon reduced blood glucose. In numerous clinical studies, antioxidative and anti-inflammatory effects were not significant after polyphenol supplementation in patients with MetS. However, some trials pointed towards an improvement of endothelial function in patients supplemented with cocoa, anthocyanin-rich berries, hesperidin or resveratrol. Therefore, diets rich in polyphenols, such as the Mediterranean diet, which promote the consumption of diverse polyphenol-rich products could be an effective nutritional strategy to improve the health of patients with MetS. © 2016 The Authors. Obesity Reviews published by John Wiley & Sons Ltd on behalf of World Obesity.

Lycopene and Its Antioxidant Role in the Prevention of Cardiovascular Diseases-A Critical Review.

Abstract: The present review is based mainly on papers published between 2000 and 2011 and gives information about the properties of the carotenoid lycopene in chemical and biological systems and its possible role in preventing cardiovascular diseases (CVD). The main aim of this report is to highlight its role as an antioxidant, also reported are bioactive properties that may influence the development of foam cells and protection against endothelial cell damage. The paper will also examine recent observations that lycopene may improve blood flow and reduce inflammatory responses. Lycopene possesses antioxidant properties in vitro, and some epidemiological studies have reported protective effects against the progression of CVD. The oxidation of human low density lipoproteins (LDL) is a fundamental mechanism in the initiation of atherosclerosis. A beneficial role of lycopene as antioxidant in the prevention of CVD is suggested but the data are still controversial. Lycopene is believed to be the most potent carotenoid antioxidant in vitro. Tissue culture experiments and animal studies support potential cardioprotective effects for lycopene and other carotenoids in the blood. Most studies showed beneficial effects of lycopene to individuals who are antioxidant-deficient like elderly patients, or humans exposed to higher levels of oxidative stress like smokers, diabetics, hemodialysis patients and acute myocardial infarction patients. By defining the right population and combining antioxidant potentials of lycopene with vitamins and other bioactive plant compounds, the beneficial role of lycopene in CVD can be clarified in future studies.

Is it possible to substitute hexane with green solvents for extraction of carotenoids? A theoretical versus experimental solubility study

Abstract: The present study was designed to evaluate five green solvents, i.e. 2-methyltetrahydrofuran (2-MeTHF), dimethyl carbonate (DMC), cyclopentyl methyl ether (CPME), isopropyl alcohol (IPA) and ethyl acetate, for the substitution of n-hexane in the extraction of carotenoids from carrots. Initially, solvent selection was made through the theoretical physicochemical solvent properties and solubility results obtained using two simulation programs, Hansen Solubility Parameters (HSPs) and Conductor-like Screening Model for Realistic Solvation (COSMO-RS) which use a statistical thermodynamics approach based on the result of quantum chemical calculation, for comprehension of the dissolving mechanism. On the basis of the HSPs analysis, non-polar or slightly polar solvents were the most suitable solvents for extraction of carotenoids. COSMO-RS analysis showed a higher probability of solubility for all the carotenoids from carrot in CPME, 2-MeTHF and ethyl acetate compared with n-hexane. The experimental results using a conventional solid–liquid extraction by maceration showed that the best green solvents were CPME, 2-MeTHF and ethyl acetate in accordance with the predictive results from COSMO-RS. The highest carotenoid content (78.4 mg 100 g−1 DM) was observed in CPME where 66% was represented by β-carotene and 34% was α-carotene. These results support the potential of CPME and 2-MeTHF as alternative green solvents for extraction of carotenoids.

Bio-Based Solvents for Green Extraction of Lipids from Oleaginous Yeast Biomass for Sustainable Aviation Biofuel.

Abstract: Lipid-based oleaginous microorganisms are potential candidates and resources for the sustainable production of biofuels. This study was designed to evaluate the performance of several alternative bio-based solvents for extracting lipids from yeasts. We used experimental design and simulation with Hansen solubility simulations and the conductor-like screening model for realistic solvation (COSMO-RS) to simulate the solubilization of lipids in each of these solvents. Lipid extracts were analyzed by high performance thin-layer chromatography (HPTLC) to obtain the distribution of lipids classes and gas chromatography coupled with a flame ionization detector (GC/FID) to obtain fatty acid profiles. Our aim was to correlate simulation with experimentation for extraction and solvation of lipids with bio-based solvents in order to make a preliminary evaluation for the replacement of hexane to extract lipids from microorganisms. Differences between theory and practice were noted for several solvents, such as CPME, MeTHF and ethyl acetate, which appeared to be good candidates to replace hexane.

Comparative Study of Essential Oils Extracted from Egyptian Basil Leaves (Ocimum basilicum L.) Using Hydro-Distillation and Solvent-Free Microwave Extraction.

Abstract: Solvent-free microwave extraction (SFME) and conventional hydro-distillation (HD) were used for the extraction of essential oils (EOs) from Egyptian sweet basil (Ocimum basilicum L.) leaves. The two resulting EOs were compared with regards to their chemical composition, antioxidant, and antimicrobial activities. The EO analyzed by GC and GC-MS, presented 65 compounds constituting 99.3% and 99.0% of the total oils obtained by SFME and HD, respectively. The main components of both oils were linalool (43.5% SFME; 48.4% HD), followed by methyl chavicol (13.3% SFME; 14.3% HD) and 1,8-cineole (6.8% SFME; 7.3% HD). Their antioxidant activity were studied with the 2,2-diphenyl-1-picrylhydrazyl (DPPH(•)) radical scavenging method. The heating conditions effect was evaluated by the determination of the Total Polar Materials (TPM) content. The antimicrobial activity was investigated against five microorganisms: two Gram-positive bacteria, Staphylococcus aureus and Bacillus subtilis, two Gram-negative bacteria, Escherichia coli and Pseudomonas aeruginosa, and one yeast, Candida albicans. Both EOs showed high antimicrobial, but weak antioxidant, activities. The results indicated that the SFME method may be a better alternative for the extraction of EO from O. basilicum since it could be considered as providing a richer source of natural antioxidants, as well as strong antimicrobial agents for food preservation.

Herbicides do not ensure for higher wheat yield, but eliminate rare plant species.

Abstract: Weed control is generally considered to be essential for crop production and herbicides have become the main method used for weed control in developed countries. However, concerns about harmful environmental consequences have led to strong pressure on farmers to reduce the use of herbicides. As food demand is forecast to increase by 50% over the next century, an in-depth quantitative analysis of crop yields, weeds and herbicides is required to balance economic and environmental issues. This study analysed the relationship between weeds, herbicides and winter wheat yields using data from 150 winter wheat fields in western France. A Bayesian hierarchical model was built to take account of farmers’ behaviour, including implicitly their perception of weeds and weed control practices, on the effectiveness of treatment. No relationship was detected between crop yields and herbicide use. Herbicides were found to be more effective at controlling rare plant species than abundant weed species. These results suggest that reducing the use of herbicides by up to 50% could maintain crop production, a result confirmed by previous studies, while encouraging weed biodiversity. Food security and biodiversity conservation may, therefore, be achieved simultaneously in intensive agriculture simply by reducing the use of herbicides.

Pollution-induced community tolerance (PICT): towards an ecologically relevant risk assessment of chemicals in aquatic systems

Abstract: A major challenge in environmental risk assessment of pollutants is establishing a causal relationship between field exposure and community effects that integrates both structural and functional complexity within ecosystems. Pollution-induced community tolerance (PICT) is a concept that evaluates whether pollutants have exerted a selection pressure on natural communities. PICT detects whether a pollutant has eliminated sensitive species from a community and thereby increased its tolerance. PICT has the potential to link assessments of the ecological and chemical status of ecosystems by providing causal analysis for effect-based monitoring of impacted field sites. Using PICT measurements and microbial community endpoints in environmental assessment schemes could give more ecological relevance to the tools that are now used in environmental risk assessment. Here, we propose practical guidance and a list of research issues that should be further considered to apply the PICT concept in the field.

Modeling soil evaporation efficiency in a range of soil and atmospheric conditions using a meta‐analysis approach

Abstract: A meta-analysis data-driven approach is developed to represent the soil evaporative efficiency (SEE) defined as the ratio of actual to potential soil evaporation. The new model is tested across a bare soil database composed of more than 30 sites around the world, a clay fraction range of 0.02-0.56, a sand fraction range of 0.05-0.92, and about 30,000 acquisition times. SEE is modeled using a soil resistance ($r_{ss}$) formulation based on surface soil moisture ($\theta$) and two resistance parameters $r_{ss,ref}$ and $\theta_{efolding}$. The data-driven approach aims to express both parameters as a function of observable data including meteorological forcing, cut-off soil moisture value $\theta_{1/2}$ at which SEE=0.5, and first derivative of SEE at $\theta_{1/2}$, named $\Delta\theta_{1/2}^{-1}$. An analytical relationship between $(r_{ss,ref};\theta_{efolding})$ and $(\theta_{1/2};\Delta\theta_{1/2}^{-1})$ is first built by running a soil energy balance model for two extreme conditions with $r_{ss} = 0$ and $r_{ss}\sim\infty$ using meteorological forcing solely, and by approaching the middle point from the two (wet and dry) reference points. Two different methods are then investigated to estimate the pair $(\theta_{1/2} ; \Delta\theta_{1/2}^{-1})$ either from the time series of SEE and $\theta$ observations for a given site, or using the soil texture information for all sites. The first method is based on an algorithm specifically designed to accomodate for strongly nonlinear $\text{SEE}(\theta)$ relationships and potentially large random deviations of observed SEE from the mean observed $\text{SEE}(\theta)$. The second method parameterizes $\theta_{1/2}$ as a multi-linear regression of clay and sand percentages, and sets $\Delta\theta_{1/2}^{-1}$ to a constant mean value for all sites. The new model significantly outperformed the evaporation modules of ISBA (Interaction Sol-Biosph\`{e}re-Atmosph\`{e}re), H-TESSEL (Hydrology-Tiled ECMWF Scheme for Surface Exchange over Land), and CLM (Community Land Model). It has potential for integration in various land-surface schemes, and real calibration capabilities using combined thermal and microwave remote sensing data.

Investigating the inclusion of ecosystem services in biodiversity offsetting

Abstract: In response to growing international interest regarding the consideration of ecosystem services (ES) in the framework of biodiversity offsetting (BO) and the current lack of guidelines on the subject, we investigated the potential inclusion of ES in BO, highlighting the risks and opportunities. Our argument is premised on the assumption that a practical link already exists between the two and that most of the tools required to make this approach operational are available. But so far, ES are not explicitly taken into account when calculating and designing offsets (whether regulatory or voluntary). One way to integrate ES in BO is to use the Environmental Impact Assessments' framework, here we propose a logical way to integrate ES at each step of the implementation of the mitigation hierarchy and provide details on the links with existing practice. In our proposal, the inclusion of ES is presented as a way to complement current approaches based on the assessment of habitats/species/ecological functions rather than to replace them. We argue that measures proposed to offset biodiversity losses, in addition to respecting ecological performance standards, should equally be chosen to minimize residual losses of ES. The latter require offsetting by different types of complementary measures. Implementing these recommendations as good practice should strengthen the weight of biodiversity, demonstrate consideration of social equity, and result in better acceptance of development projects and the measures proposed to offset them.

The Network of Knowledge approach: improving the science and society dialogue on biodiversity and ecosystem services in Europe

Abstract: The absence of a good interface between scientific and other knowledge holders and decision-makers in the area of biodiversity and ecosystem services has been recognised for a long time. Despite recent advancements, e.g. with the Intergovernmental Platform on Biodiversity and Ecosystem Services (IPBES), challenges remain, particularly concerning the timely provision of consolidated views from different knowledge domains. To address this challenge, a strong and flexible networking approach is needed across knowledge domains and institutions. Here, we report on a broad consultation process across Europe to develop a Network of Knowledge on biodiversity and ecosystem services (NoK), an approach aiming at (1) organising institutions and knowledge holders in an adaptable and responsive framework and (2) informing decision-makers with timely and accurate biodiversity knowledge. The consultation provided a critical analysis of the needs that should be addressed by a NoK and how it could complement existing European initiatives and institutions at the interface between policy and science. Among other functions, the NoK provides consolidated scientific views on contested topics, identification of research gaps to support relevant policies, and horizon scanning activities to anticipate emerging issues. The NoK includes a capacity building component on interfacing activities and contains mechanisms to ensure its credibility, relevance and legitimacy. Such a network would need to ensure credibility, relevance and legitimacy of its work by maximizing transparency and flexibility of processes, quality of outputs, the link to data and knowledge provision, the motivation of experts for getting involved and sound communication and capacity building.

Scale- and taxon-dependent patterns of plant diversity in steppes of Khakassia, South Siberia (Russia)

Abstract: The drivers of plant richness at fine spatial scales in steppe ecosystems are still not sufficiently understood. Our main research questions were: (i) How rich in plant species are the natural steppes of Southern Siberia compared to natural and semi-natural grasslands in other regions of the Palaearctic? (ii) What are the main environmental drivers of the diversity patterns in these steppes? (iii) What are the diversity–environment relationships and do they vary between spatial scales and among different taxonomic groups? We sampled the steppe vegetation (vascular plants, bryophytes and lichens) in Khakassia (Russia) with 39 nested-plot series (0.0001–100-m2 plot size) and 54 additional 10-m2 quadrats across the regional range of steppe types and measured various environmental variables. We measured β-diversity using z-values of power-law species–area relationships. GLM analyses were performed to assess the importance of environmental variables as predictors of species richness and z-value. Khakassian steppes showed both high α- and β-diversity. We found significant scale dependence for the z-values, which had their highest values at small spatial scales and then decreased exponentially. Total species richness was controlled predominantly by heat load index, mean annual precipitation, humus content and soil skeleton content. The positive role of soil pH was evident only for vascular plant species richness. Similar to other studies, we found that the importance of environmental factors strongly differed among taxonomic groups and across spatial scales, thus highlighting the need to study more than one taxon and more than one plot size to get a reliable picture.

Unraveling the pectinolytic function of Bacteroides xylanisolvens using a RNA-seq approach and mutagenesis

Abstract: Diet and particularly dietary fibres have an impact on the gut microbiome and play an important role in human health and disease. Pectin is a highly consumed dietary fibre found in fruits and vegetables and is also a widely used additive in the food industry. Yet there is no information on the effect of pectin on the human gut microbiome. Likewise, little is known on gut pectinolytic bacteria and their enzyme systems. This study was undertaken to investigate the mechanisms of pectin degradation by the prominent human gut symbiont Bacteroides xylanisolvens. Transcriptomic analyses of B. xylanisolvens XB1A grown on citrus and apple pectins at mid- and late-log phases highlighted six polysaccharide utilization loci (PUL) that were overexpressed on pectin relative to glucose. The PUL numbers used in this report are those given by Terrapon et al. (Bioinformatics 31(5):647-55, 2015) and found in the PUL database: http://www.cazy.org/PULDB/ . Based on their CAZyme composition, we propose that PUL 49 and 50, the most overexpressed PULs on both pectins and at both growth phases, are involved in homogalacturonan (HG) and type I rhamnogalacturonan (RGI) degradation, respectively. PUL 13 and PUL 2 could be involved in the degradation of arabinose-containing side chains and of type II rhamnogalacturonan (RGII), respectively. Considering that HG is the most abundant moiety (>70 %) within pectin, the importance of PUL 49 was further investigated by insertion mutagenesis into the susC-like gene. The insertion blocked transcription of the susC-like and the two downstream genes (susD-like/FnIII). The mutant showed strong growth reduction, thus confirming that PUL 49 plays a major role in pectin degradation. This study shows the existence of six PULs devoted to pectin degradation by B. xylanisolvens, one of them being particularly important in this function. Hence, this species deploys a very complex enzymatic machinery that probably reflects the structural complexity of pectin. Our findings also highlight the metabolic plasticity of B. xylanisolvens towards dietary fibres that contributes to its competitive fitness within the human gut ecosystem. Wider functional and ecological studies are needed to understand how dietary fibers and especially plant cell wall polysaccharides drive the composition and metabolism of the fibrolytic and non-fibrolytic community within the gut microbial ecosystem.

Root age distribution: how does it matter in plant processes? A focus on water uptake

Abstract: Root growth creates a gradient in age at both the scale of the single root, from distal to proximal parts, but also at the root system level when young branch roots emerge from the axis or new nodal roots are emitted that may reach same soil domain as older roots. It is known that a number of root functions will vary with root type and root tissue age (e.g. respiration, exudation, ion uptake, root hydraulic conductance, mucilage release…) and so will the resulting rhizosphere properties. The impact of the distribution of root demography with depth, and related functions, on the overall functioning of the root system is fundamental for an integration of processes at the root system scale. Starting from methods for measuring root demography, we discuss the availability of data related to root age and its spatial distribution, considering plant types (monocot/dicot, perennial/annuals) which may exhibit different patterns. We then give a detailed review of variation of root/rhizosphere properties related to root age, focusing on root water uptake processes. We examine the type of response of certain properties to changes in age and whether a functional relationship can be derived. Integration of changing root properties with age into modelling approaches is shown from 3D models at the single plant scale to approaches at the field scale based on integrated root system age. Functional structural modelling combined with new development in non-invasive imaging of roots show promises for integrating influence of age on root properties, from the local to whole root system scales. However, experimental quantification of these properties, such as hydraulic conductance variation with root age and root types, or impact of mucilage and its degradation products on rhizosphere hydraulic properties, presently lag behind the theoretical developments and increase in computational power.

The role of porous matrix in water flow regulation within a karst unsaturated zone: an integrated hydrogeophysical approach

Abstract: Some portions of the porous rock matrix in the karst unsaturated zone (UZ) can contain large volumes of water and play a major role in water flow regulation. The essential results are presented of a local-scale study conducted in 2011 and 2012 above the Low Noise Underground Laboratory (LSBB – Laboratoire Souterrain a Bas Bruit) at Rustrel, southeastern France. Previous research revealed the geological structure and water-related features of the study site and illustrated the feasibility of specific hydrogeophysical measurements. In this study, the focus is on hydrodynamics at the seasonal and event timescales. Magnetic resonance sounding (MRS) measured a high water content (more than 10 %) in a large volume of rock. This large volume of water cannot be stored in fractures and conduits within the UZ. MRS was also used to measure the seasonal variation of water stored in the karst UZ. A process-based model was developed to simulate the effect of vegetation on groundwater recharge dynamics. In addition, electrical resistivity tomography (ERT) monitoring was used to assess preferential water pathways during a rain event. This study demonstrates the major influence of water flow within the porous rock matrix on the UZ hydrogeological functioning at both the local (LSBB) and regional (Fontaine de Vaucluse) scales. By taking into account the role of the porous matrix in water flow regulation, these findings may significantly improve karst groundwater hydrodynamic modelling, exploitation, and sustainable managementme portions of the porous rock matrix in the karst unsaturated zone (UZ) can contain large volumes of water and play a major role in water flow regulation. The essential results are presented of a local-scale study conducted in 2011 and 2012 above the Low Noise Underground Laboratory (LSBB – Laboratoire Souterrain a Bas Bruit) at Rustrel, southeastern France. Previous research revealed the geological structure and water-related features of the study site and illustrated the feasibility of specific hydrogeophysical measurements. In this study, the focus is on hydrodynamics at the seasonal and event timescales. Magnetic resonance sounding (MRS) measured a high water content (more than 10 %) in a large volume of rock. This large volume of water cannot be stored in fractures and conduits within the UZ. MRS was also used to measure the seasonal variation of water stored in the karst UZ. A process-based model was developed to simulate the effect of vegetation on groundwater recharge dynamics. In addition, electrical resistivity tomography (ERT) monitoring was used to assess preferential water pathways during a rain event. This study demonstrates the major influence of water flow within the porous rock matrix on the UZ hydrogeological functioning at both the local (LSBB) and regional (Fontaine de Vaucluse) scales. By taking into account the role of the porous matrix in water flow regulation, these findings may significantly improve karst groundwater hydrodynamic modelling, exploitation, and sustainable management.

Topology Optimization of Electric Motor Using Topological Derivative for Nonlinear Magnetostatics

Abstract: We aim at finding an optimal design for an interior permanent magnet electric motor by means of a sensitivity-based topology optimization method. The gradient-based ON/OFF method has been successfully applied to optimization problems of this form. We show that this method can be improved by considering the mathematical concept of topological derivatives (TDs). TDs for optimization problems constrained by linear partial differential equations (PDEs) are well understood, whereas little is known about TDs in combination with nonlinear PDE constraints. We derive the TD for an optimization problem constrained by the equation of nonlinear 2-D magnetostatics, illustrate its advantages over the sensitivities used in the ON/OFF method, and show numerical results for the optimization of an interior permanent magnet electric motor obtained by a level-set algorithm, which is based on the TD.