Showing papers by "Agrocampus Ouest published in 2014"

A standardised static in vitro digestion method suitable for food – an international consensus

Abstract: Simulated gastro-intestinal digestion is widely employed in many fields of food and nutritional sciences, as conducting human trials are often costly, resource intensive, and ethically disputable. As a consequence, in vitro alternatives that determine endpoints such as the bioaccessibility of nutrients and non-nutrients or the digestibility of macronutrients (e.g. lipids, proteins and carbohydrates) are used for screening and building new hypotheses. Various digestion models have been proposed, often impeding the possibility to compare results across research teams. For example, a large variety of enzymes from different sources such as of porcine, rabbit or human origin have been used, differing in their activity and characterization. Differences in pH, mineral type, ionic strength and digestion time, which alter enzyme activity and other phenomena, may also considerably alter results. Other parameters such as the presence of phospholipids, individual enzymes such as gastric lipase and digestive emulsifiers vs. their mixtures (e.g. pancreatin and bile salts), and the ratio of food bolus to digestive fluids, have also been discussed at length. In the present consensus paper, within the COST Infogest network, we propose a general standardised and practical static digestion method based on physiologically relevant conditions that can be applied for various endpoints, which may be amended to accommodate further specific requirements. A frameset of parameters including the oral, gastric and small intestinal digestion are outlined and their relevance discussed in relation to available in vivo data and enzymes. This consensus paper will give a detailed protocol and a line-by-line, guidance, recommendations and justifications but also limitation of the proposed model. This harmonised static, in vitro digestion method for food should aid the production of more comparable data in the future.

Environmental DNA surveillance for invertebrate species: advantages and technical limitations to detect invasive crayfish Procambarus clarkii in freshwater ponds.

Abstract: 1. The introduction of non-native species is a major threat to biodiversity. While eradication programs of well-established invaders are costly and hazardous for non-target species, the early detection of a non-native species at low density is critical for preventing biological invasions in recipient ecosystems. Recent studies reveal that environmental DNA (eDNA) is a powerful tool for detecting target species in aquatic ecosystems, but these studies focus mostly on fish and amphibians.2. We examine the reliability of using eDNA to detect the presence of an invasive freshwater crustacean species, the red swamp crayfish Procambarus clarkii. Species-specific primers and probes were designed; their specificity was tested using in silico PCR simulations and against tissues of other crayfish species. Limits of detection and quantification were specified for the target DNA sequence by means of quantitative PCR amplifications on dilution series of known amount of P. clarkii DNA.3. The method was applied to water samples collected in 158 ponds in a French Nature Park, and results were compared to a traditional method using food-baited funnel traps. Environmental DNA had a better detection efficiency but predominantly led to divergent results compared with the trapping method. While habitat features partly explained the failure of crayfish detection by trapping, detection by eDNA was problematic at low crayfish abundances. When P. clarkii was detected, the estimated concentrations of crayfish DNA in water samples were always below the limit of quantification for the target DNA sequence.4. Synthesis and applications. The combination of environmental DNA (eDNA) and conventional trapping methods is recommended to monitor the invasion by P. clarkii in small waterbodies such as ponds. However, the risk of mortality for non-target species, notably amphibians, has to be carefully evaluated before large-scale deployment of traps. Contrary to fish and amphibians, a low amount of extracellular DNA in water is suspected to be the major limitation for crayfish detection by molecular approaches. Current advancements in PCR technology, together with optimization of the water sampling method, promise upcoming developments of eDNA detection for aquatic invertebrate species.

Specificity of Infant Digestive Conditions: Some Clues for Developing Relevant In Vitro Models

Abstract: Digestion of nutrients is an essential function of the newborn infant gut to allow growth and development and understanding infant digestive function is essential to optimize nutrition and oral drug delivery. Ethical considerations prohibit invasive in vivo trials and as a consequence in vitro assays are often conducted. However, the choice of in vitro model parameters are not supported by an exhaustive analysis of the literature and do not mimic precisely the digestive conditions of the infant. This review contains a compilation of the studies which characterized the gastroduodenal conditions in full-term or preterm infants of variable postnatal age from birth up to six months. Important data about healthy full-term infants are reported. The enzymatic (type of enzymes and level of activity) and nonenzymatic (milk-based diet, frequency of feeding, bile salt concentrations) conditions of digestion in infants are shown to differ significantly from those in adults. In addition, the interindividual and developmental variability of the digestive conditions in infants is also highlighted.

Process Consistency in Models: the Importance of System Signatures, Expert Knowledge and Process Complexity

Abstract: Hydrological models frequently suffer from limited predictive power despite adequate calibration performances. This can indicate insufficient representations of the underlying processes. Thus, ways are sought to increase model consistency while satisfying the contrasting priorities of increased model complexity and limited equifinality. In this study, the value of a systematic use of hydrological signatures and expert knowledge for increasing model consistency was tested. It was found that a simple conceptual model, constrained by four calibration objective functions, was able to adequately reproduce the hydrograph in the calibration period. The model, however, could not reproduce a suite of hydrological signatures, indicating a lack of model consistency. Subsequently, testing 11 models, model complexity was increased in a stepwise way and counter-balanced by “prior constraints,” inferred from expert knowledge to ensure a model which behaves well with respect to the modeler's perception of the system. We showed that, in spite of unchanged calibration performance, the most complex model setup exhibited increased performance in the independent test period and skill to better reproduce all tested signatures, indicating a better system representation. The results suggest that a model may be inadequate despite good performance with respect to multiple calibration objectives and that increasing model complexity, if counter-balanced by prior constraints, can significantly increase predictive performance of a model and its skill to reproduce hydrological signatures. The results strongly illustrate the need to balance automated model calibration with a more expert-knowledge-driven strategy of constraining models.

Milk proteins as encapsulation devices and delivery vehicles: Applications and trends

Abstract: Increasing the shelf-life of sensitive substances and targeting the release of nutritional/bioactive molecules are among the great challenges for the food industry. The development of food products with embedded encapsulation devices used to reach these objectives, constitutes a growing market. Milk proteins are biopolymers that are chemically and structurally versatile and are well adapted to several encapsulation purposes. Therefore, in this paper, the strategies, techniques, advantages and trends associated with the use of milk proteins as encapsulating device are reviewed. Special attention is given to the novel potential of reversibly co-assembled protein structures as encapsulating devices.

The Ubiquitous Distribution of Late Embryogenesis Abundant Proteins across Cell Compartments in Arabidopsis Offers Tailored Protection against Abiotic Stress

Abstract: Late embryogenesis abundant (LEA) proteins are hydrophilic, mostly intrinsically disordered proteins, which play major roles in desiccation tolerance. In Arabidopsis thaliana, 51 genes encoding LEA proteins clustered into nine families have been inventoried. To increase our understanding of the yet enigmatic functions of these gene families, we report the subcellular location of each protein. Experimental data highlight the limits of in silico predictions for analysis of subcellular localization. Thirty-six LEA proteins localized to the cytosol, with most being able to diffuse into the nucleus. Three proteins were exclusively localized in plastids or mitochondria, while two others were found dually targeted to these organelles. Targeting cleavage sites could be determined for five of these proteins. Three proteins were found to be endoplasmic reticulum (ER) residents, two were vacuolar, and two were secreted. A single protein was identified in pexophagosomes. While most LEA protein families have a unique subcellular localization, members of the LEA_4 family are widely distributed (cytosol, mitochondria, plastid, ER, and pexophagosome) but share the presence of the class A α-helix motif. They are thus expected to establish interactions with various cellular membranes under stress conditions. The broad subcellular distribution of LEA proteins highlights the requirement for each cellular compartment to be provided with protective mechanisms to cope with desiccation or cold stress.

Evolutionary impact assessment: accounting for evolutionary consequences of fishing in an ecosystem approach to fisheries management.

Abstract: Managing fisheries resources to maintain healthy ecosystems is one of the main goals of the ecosystem approach to fisheries (EAF). While a number of international treaties call for the implementation of EAF, there are still gaps in the underlying methodology. One aspect that has received substantial scientific attention recently is fisheries-induced evolution (FIE). Increasing evidence indicates that intensive fishing has the potential to exert strong directional selection on life-history traits, behaviour, physiology, and morphology of exploited fish. Of particular concern is that reversing evolutionary responses to fishing can be much more difficult than reversing demographic or phenotypically plastic responses. Furthermore, like climate change, multiple agents cause FIE, with effects accumulating over time. Consequently, FIE may alter the utility derived from fish stocks, which in turn can modify the monetary value living aquatic resources provide to society. Quantifying and predicting the evolutionary effects of fishing is therefore important for both ecological and economic reasons. An important reason this is not happening is the lack of an appropriate assessment framework. We therefore describe the evolutionary impact assessment (EvoIA) as a structured approach for assessing the evolutionary consequences of fishing and evaluating the predicted evolutionary outcomes of alternative management options. EvoIA can contribute to EAF by clarifying how evolution may alter stock properties and ecological relations, support the precautionary approach to fisheries management by addressing a previously overlooked source of uncertainty and risk, and thus contribute to sustainable fisheries.

Bayesian QTL analyses using pedigreed families of an outcrossing species, with application to fruit firmness in apple

Abstract: Bayesian QTL linkage mapping approaches offer the flexibility to study multiple full sib families with known pedigrees simultaneously. Such a joint analysis increases the probability of detecting these quantitative trait loci (QTL) and provide insight of the magnitude of QTL across different genetic backgrounds. Here, we present an improved Bayesian multi-QTL pedigree-based approach on an outcrossing species using progenies with different (complex) genetic relationships. Different modeling assumptions were studied in the QTL analyses, i.e., the a priori expected number of QTL varied and polygenic effects were considered. The inferences include number of QTL, additive QTL effect sizes and supporting credible intervals, posterior probabilities of QTL genotypes for all individuals in the dataset, and QTL-based as well as genome-wide breeding values. All these features have been implemented in the FlexQTL™ software. We analyzed fruit firmness in a large apple dataset that comprised 1,347 individuals forming 27 full sib families and their known ancestral pedigrees, with genotypes for 87 SSR markers on 17 chromosomes. We report strong or positive evidence for 14 QTL for fruit firmness on eight chromosomes, validating our approach as several of these QTL were reported previously, though dispersed over a series of studies based on single mapping populations. Interpretation of linked QTL was possible via individuals’ QTL genotypes. The correlation between the genomic breeding values and phenotypes was on average 90 %, but varied with the number of detected QTL in a family. The detailed posterior knowledge on QTL of potential parents is critical for the efficiency of marker-assisted breeding.

Bovine β-lactoglobulin/fatty acid complexes: binding, structural, and biological properties.

Abstract: Ligand-binding properties of β-lactoglobulin (β-lg) are well documented, but the subsequent biological functions are still unclear. Focusing on fatty acids/β-lg complexes, the structure-function relationships are reviewed in the light of the structural state of the protein (native versus non-native aggregated proteins). After a brief description of β-lg native structure, the review takes an interest in the binding properties of native β-lg (localization of binding sites, stoichiometry, and affinity) and the way the interaction affects the biological properties of the protein and the ligand. The binding properties of non-native aggregated forms of β-lg that are classically generated during industrial processing are also related. Structural changes modify the stoichiometry and the affinity of β-lg for fatty acids and consequently the biological functions of the complex. Finally, the fatty acid-binding properties of other whey proteins (α-lactalbumin, bovine serum albumin) and some biological properties of the complexes are also addressed. These proteins affect β-lg/fatty acids complex in whey given their competition with β-lg for fatty acids.

Carotene Hydroxylase Activity Determines the Levels of Both α-Carotene and Total Carotenoids in Orange Carrots

Abstract: The typically intense carotenoid accumulation in cultivated orange-rooted carrots (Daucus carota) is determined by a high protein abundance of the rate-limiting enzyme for carotenoid biosynthesis, phytoene synthase (PSY), as compared with white-rooted cultivars. However, in contrast to other carotenoid accumulating systems, orange carrots are characterized by unusually high levels of α-carotene in addition to β-carotene. We found similarly increased α-carotene levels in leaves of orange carrots compared with white-rooted cultivars. This has also been observed in the Arabidopsis thaliana lut5 mutant carrying a defective carotene hydroxylase CYP97A3 gene. In fact, overexpression of CYP97A3 in orange carrots restored leaf carotenoid patterns almost to those found in white-rooted cultivars and strongly reduced α-carotene levels in the roots. Unexpectedly, this was accompanied by a 30 to 50% reduction in total root carotenoids and correlated with reduced PSY protein levels while PSY expression was unchanged. This suggests a negative feedback emerging from carotenoid metabolites determining PSY protein levels and, thus, total carotenoid flux. Furthermore, we identified a deficient CYP97A3 allele containing a frame-shift insertion in orange carrots. Association mapping analysis using a large carrot population revealed a significant association of this polymorphism with both α-carotene content and the α-/β-carotene ratio and explained a large proportion of the observed variation in carrots.

The use of free amino acids allows formulating very low crude protein diets for piglets.

Abstract: Reducing the dietary CP level with free AA supplementation allows reduction of N excretion and the risk of gut disorders while maintaining performance of pigs. We have recently reevaluated the Val, Ile, His, and Leu requirements in pigs, which enables formulating very low CP diets. However, requirements for undifferentiated N, and thus the extent to which the dietary CP content can be reduced, are unknown. Two experiments were conducted to test the effect of reducing the dietary CP content to meet an ideal AA profile on N retention and performance in 10- to 20-kg pigs. In the first experiment, we measured N retention in 6 blocks of 4 pigs each, all receiving diets with 1.15% standardized ileal digestible (SID) Lys. Each pig within a block was allotted to different levels of dietary CP (19.7%, 16.8%, 14.0%, and 12.7%). The reduction of CP content from 19.7% to 16.8% had no impact on N retention and decreased N excretion by 29%. A further decrease in CP content to 14.0% and 12.7% resulted in a reduced N retention (P < 0.01). In the second experiment, we measured performance in 14 groups of 6 pigs each, allotted to 6 levels of dietary CP with 1.00% SID Lys with soybean meal (17.6%, 15.6%, 13.5%, and 11.8%) or without soybean meal (14.0% and 13.0%). Decreasing the dietary CP content from 17.6% to 13.5% had no effect on performance. Daily gain was reduced in pigs receiving the 11.8% CP diet (P < 0.01). Feeding the diet formulated without soybean meal with 13.0% CP content resulted in reduced feed efficiency, but the addition of Glu to increase the CP content from 13.0% to 14.0% restored performance (P < 0.01). In conclusion, the use of L-Val, L-Leu, L-Ile, L-His, and L-Phe enables a 4% unit reduction in the CP content relative to SID Lys in diets for pigs. Soybean meal can be totally replaced using cereals and free AA. However, a further reduction in dietary CP:Lys level below 13.5% reduces feed efficiency, indicating that the supply of N for the synthesis of dispensable AA may be a limiting factor for the performance of pigs.

Coalescence 2.0: a multiple branching of recent theoretical developments and their applications.

Abstract: Population genetics theory has laid the foundations for genomic analyses including the recent burst in genome scans for selection and statistical inference of past demographic events in many prokaryote, animal and plant species. Identifying SNPs under natural selection and underpinning species adaptation relies on disentangling the respective contribution of random processes (mutation, drift, migration) from that of selection on nucleotide variability. Most theory and statistical tests have been developed using the Kingman coalescent theory based on the Wright-Fisher population model. However, these theoretical models rely on biological and life history assumptions which may be violated in many prokaryote, fungal, animal or plant species. Recent theoretical developments of the so-called multiple merger coalescent models are reviewed here (Λ-coalescent, beta-coalescent, Bolthausen-Sznitman, Ξ-coalescent). We explain how these new models take into account various pervasive ecological and biological characteristics, life history traits or life cycles which were not accounted in previous theories such as (i) the skew in offspring production typical of marine species, (ii) fast adapting microparasites (virus, bacteria and fungi) exhibiting large variation in population sizes during epidemics, (iii) the peculiar life cycles of fungi and bacteria alternating sexual and asexual cycles and (iv) the high rates of extinction-recolonization in spatially structured populations. We finally discuss the relevance of multiple merger models for the detection of SNPs under selection in these species, for population genomics of very large sample size and advocate to potentially examine the conclusion of previous population genetics studies.

An ecological cost associated with protective symbionts of aphids.

Abstract: Beneficial symbioses are widespread and diverse in the functions they provide to the host ranging from nutrition to protection. However, these partnerships with symbionts can be costly for the host. Such costs, so called “direct costs”, arise from a trade-off between allocating resources to symbiosis and other functions such as reproduction or growth. Ecological costs may also exist when symbiosis negatively affects the interactions between the host and other organisms in the environment. Although ecological costs can deeply impact the evolution of symbiosis, they have received little attention. The pea aphid Acyrthosiphon pisum benefits a strong protection against its main parasitoids from protective bacterial symbionts. The ecological cost of symbiont-mediated resistance to parasitism in aphids was here investigated by analyzing aphid behavior in the presence of predatory ladybirds. We showed that aphids harboring protective symbionts expressed less defensive behaviors, thus suffering a higher predation than symbiont-free aphids. Consequently, our study indicates that this underlined ecological cost may affect both the coevolutionary processes between symbiotic partners and the prevalence of such beneficial bacterial symbionts in host natural populations.

Light Signaling in Bud Outgrowth and Branching in Plants.

Abstract: Branching determines the final shape of plants, which influences adaptation, survival and the visual quality of many species. It is an intricate process that includes bud outgrowth and shoot extension, and these in turn respond to environmental cues and light conditions. Light is a powerful environmental factor that impacts multiple processes throughout plant life. The molecular basis of the perception and transduction of the light signal within buds is poorly understood and undoubtedly requires to be further unravelled. This review is based on current knowledge on bud outgrowth-related mechanisms and light-mediated regulation of many physiological processes. It provides an extensive, though not exhaustive, overview of the findings related to this field. In parallel, it points to issues to be addressed in the near future.

Effect of digestive enzymes on antimicrobial, radical scavenging and angiotensin I-converting enzyme inhibitory activities of camel colostrum and milk proteins

Abstract: Camel milk and colostrum are known to be a rich source of bioactive proteins. Camel milk, colostrum and colostral whey proteins were successively hydrolysed by pepsin and pancreatin using an in vitro protocol mimicking gastro-intestinal digestion. The degradation of proteins was characterised by electrophoresis and reversed-phase ultra-high performance liquid chromatography. Two whey proteins, α-lactalbumin and immunoglobulins G, were more resistant to the digestive proteolytic enzymes than other camel milk and colostrum proteins. Undigested and digested samples were assayed for their antioxidant, angiotensin I-converting enzyme inhibitory and antimicrobial properties. Camel colostrum, colostral whey and milk proteins had unveiled angiotensin I-converting enzyme (ACE) inhibitory activity following in vitro enzymatic digestion and a higher free radical scavenging activity than before their digestion. Moreover, Escherichia coli XL1 blue and Listeria innocua LRGIA01 cells growth were both inhibited by undigested and digested samples, suggesting that antimicrobial proteins resisted to the action of digestive enzymes or that antimicrobial fragments of camel milk and colostrum proteins were released or both. After pepsin and pancreatin hydrolysis, camel milk and colostrum proteins digests still had an antibacterial activity and their antioxidative and ACE-inhibitory activity even increased, suggesting that bioactive fragments of camel milk and colostrum proteins such as antioxidative and ACE-inhibitory peptides were released. Among 181 peptides identified by tandem mass spectrometry, 25 were homologous to known bioactive peptides, particularly with ACE inhibitors and free radical scavengers.