Showing papers by "Agrocampus Ouest published in 2010"

Exploratory Multivariate Analysis by Example Using R

Abstract: Principal Component Analysis (PCA) Data - Notation - Examples Objectives Studying Individuals Studying Variables Relationships between the Two Representations NI and NK Interpreting the Data Implementation with FactoMineR Additional Results Example: The Decathlon Dataset Example: The Temperature Dataset Example of Genomic Data: The Chicken Dataset Correspondence Analysis (CA) Data - Notation - Examples Objectives and the Independence Model Fitting the Clouds Interpreting the Data Supplementary Elements (= Illustrative) Implementation with FactoMineR CA and Textual Data Processing Example: The Olympic Games Dataset Example: The White Wines Dataset Example: The Causes of Mortality Dataset Multiple Correspondence Analysis (MCA) Data - Notation - Examples Objectives Defining Distances between Individuals and Distances between Categories CA on the Indicator Matrix Interpreting the Data Implementation with FactoMineR Addendum Example: The Survey on the Perception of Genetically Modified Organisms Example: The Sorting Task Dataset Clustering Data - Issues Formalising the Notion of Similarity Constructing an Indexed Hierarchy Ward's Method Direct Search for Partitions: K-means Algorithm Partitioning and Hierarchical Clustering Clustering and Principal Component Methods Example: The Temperature Dataset Example: The Tea Dataset Dividing Quantitative Variables into Classes Appendix Percentage of Inertia Explained by the First Component or by the First Plane R Software Bibliography of Software Packages Bibliography Index

Competitiveness, Productivity and Efficiency in the Agricultural and Agri-Food Sectors

Abstract: This report reviews the literature on competitiveness, productivity and efficiency in the agricultural and agri-food sectors. It clarifies concepts and terminology used in this area, and provides a critical assessment of approaches and indicators used in the literature to measure competitiveness, productivity and efficiency at sectoral and farm levels. It also discusses recent findings on productivity growth, changes in relative competitiveness between sub-sectors and countries, and determinants of competitiveness, in addition to identifying the major knowledge gaps. This report suggests that more attention should be paid to the agri-food sector, non-price factors of competitiveness, and the impact of government intervention on competitiveness.

Comparative resistance of food proteins to adult and infant in vitro digestion models

Abstract: IgE-mediated allergy to milk and egg is widespread in industrialised countries and mainly affects infants and young children. It may be connected to an incomplete digestion of dietary proteins causing an inappropriate immune response in the gut. In order to study this, a biochemical model of infant gastroduodenal digestion has been developed, which has reduced levels of protease (eightfold for pepsin and tenfold for trypsin and chymotrypsin), phosphatidylcholine and bile salts, compared with the adult model. This model has been used to study the behaviour of three characterised food-relevant proteins (bovine beta-lactoglobulin (beta-Lg), beta-casein (beta-CN) and hen's egg ovalbumin), all of which are relevant cows' milk and hens' egg allergens. Digestion products were characterised using electrophoresis, immunochemical techniques and MS. These showed that ovalbumin and beta-CN were digested more slowly using the infant model compared with the adult conditions. Resistant fragments of beta-CN were found in the infant model, which correspond to previously identified IgE epitopes. Surprisingly, beta-Lg was more extensively degraded in the infant model compared with the adult one. This difference was attributed to the tenfold reduction in phosphatidylcholine concentration in the infant model limiting the protective effect of this phospholipid on beta-Lg digestion.

The complete genome of Propionibacterium freudenreichii CIRM-BIA1T, a hardy actinobacterium with food and probiotic applications.

Abstract: Background: Propionibacterium freudenreichii is essential as a ripening culture in Swiss-type cheeses and is also considered for its probiotic use [1] This species exhibits slow growth, low nutritional requirements, and hardiness in many habitats It belongs to the taxonomic group of dairy propionibacteria, in contrast to the cutaneous species P acnes The genome of the type strain, P freudenreichii subsp shermanii CIRM-BIA1 (CIP 103027T), was sequenced with an 11-fold coverage Methodology/Principal Findings: The circular chromosome of 27 Mb of the CIRM-BIA1 strain has a GC-content of 67% and contains 22 different insertion sequences (35% of the genome in base pairs) Using a proteomic approach, 490 of the 2439 predicted proteins were confirmed The annotation revealed the genetic basis for the hardiness of P freudenreichii, as the bacterium possesses a complete enzymatic arsenal for de novo biosynthesis of aminoacids and vitamins (except panthotenate and biotin) as well as sequences involved in metabolism of various carbon sources, immunity against phages, duplicated chaperone genes and, interestingly, genes involved in the management of polyphosphate, glycogen and trehalose storage The complete biosynthesis pathway for a bifidogenic compound is described, as well as a high number of surface proteins involved in interactions with the host and present in other probiotic bacteria By comparative genomics, no pathogenicity factors found in P acnes or in other pathogenic microbial species were identified in P freudenreichii, which is consistent with the Generally Recognized As Safe and Qualified Presumption of Safety status of P freudenreichii Various pathways for formation of cheese flavor compounds were identified: the Wood-Werkman cycle for propionic acid formation, amino acid degradation pathways resulting in the formation of volatile branched chain fatty acids, and esterases involved in the formation of free fatty acids and esters Conclusions/Significance: With the exception of its ability to degrade lactose, P freudenreichii seems poorly adapted to dairy niches This genome annotation opens up new prospects for the understanding of the P freudenreichii probiotic activity

Food processing increases casein resistance to simulated infant digestion

Abstract: The objective of this study was to determine whether processing could modify the resistance of casein (CN) to digestion in infants. A range of different dairy matrices was manufactured from raw milk in a pilot plant and subjected to in vitro digestion using an infant gut model. Digestion products were identified using MS and immunochemical techniques. Results obtained showed that CNs were able to resist digestion, particularly κ- and αs(2)-CN. Resistant areas were identified and corresponded to fragments hydrophobic at pH 3.0 (gastric conditions) and/or carrying post-translational modifications (phosphorylation and glycosylation). Milk processing led to differences in peptide patterns and heat treatment of milk tended to increase the number of peptides found in digested samples. This highlights the likely impact of milk processing on the allergenic potential of CNs.

Relationships between colostrum production by primiparous sows and sow physiology around parturition.

Abstract: Relationships between hormonal and metabolic changes around parturition and colostrum yield and composition were investigated in 16 Landrace x Large White primiparous sows. Blood samples were taken daily from d 105 of pregnancy to d 2 postpartum (with d 0 being the day of parturition). Colostrum samples were taken at the onset of parturition (T0), and then 3, 6, and 24 h later (T3, T6, and T24, respectively). Colostrum yield was calculated from the beginning of parturition until 24 h later by adding colostrum intake of individual piglets, which was estimated from their BW gain. Colostrum yield averaged 3.22 +/- 0.34 kg. Four sows had very low colostrum production (1.10 +/- 0.12 kg; n = 4), whereas the others produced between 2.83 and 4.64 kg of colostrum (3.93 +/- 0.16 kg; n = 12). Compared with the high-colostrum-producing sows, the low-colostrum-producing sows tended (P 0.1) was found between IgG concentrations in colostrum at any time and prolactin, estradiol-17beta, progesterone, or cortisol. In conclusion, sows that produced a low yield of colostrum were characterized by a leaky mammary epithelium and reduced synthesis of lactose, related to delayed hormonal changes before parturition.

Intrauterine Growth Restriction Modifies the Developmental Pattern of Intestinal Structure, Transcriptomic Profile, and Bacterial Colonization in Neonatal Pigs

Abstract: Neonates with intrauterine growth restriction (IUGR) are prone to suffer from digestive diseases. Using neonatal pigs with IUGR, we tested the hypothesis that IUGR may induce alterations in the developmental pattern of intestinal barrier and thereby may be responsible for IUGR-associated increased morbidity. Piglets with a birth weight near the mean birth weight (+/-0.5 SD) were identified as normal birth weight (control) and piglets with a mean -2 SD lower birth weight (-30%) were defined as piglets with IUGR. The developmental pattern of intestinal structure, transcriptomic profile, and bacterial colonization was investigated from birth to d 5 postnatal. At birth, intestinal weight and length, ileal and colonic weight per unit of length, and villous sizes were lower (P < 0.05) in piglets with IUGR than in same-age control piglets. These IUGR-induced intestinal alterations further persisted, although they were less marked at d 5. Counts of adherent bacteria to ileal and colonic mucosa were greater (P < 0.05) in 2-d-old piglets with IUGR than in same-age control piglets. Dynamic analyses of the transcriptomic profile of the intestine revealed molecular evidence of IUGR-induced intestinal growth impairment that may result from a change in the cell proliferation-apoptosis balance during the first days of life, while a protective process would occur later on. In addition, changes in the expression of several genes suggest a pivotal role of both glucocorticoids and microbiota in driving IUGR intestinal development during the neonatal period.

Energy utilization in pigs selected for high and low residual feed intake

Abstract: Genetic selection on residual feed intake (RFI) can be used as an alternative method to G: F to improve feed efficiency in pigs. The objective of this study was to determine the effects of selection for RFI on digestive and metabolic utilization of energy in 2 lines of purebred French Large White castrated male pigs obtained from a divergent selection experiment over 6 generations. The RFI(+) (high RFI) line consumed more feed than predicted from performance compared with the RFI(-) (low RFI) line. Digestibility of energy and nutrients, total heat production (HP), HP related to physical activity, and energy and N balance were measured in respiration chambers for a 6-d period in pigs offered feed ad libitum. Pigs remained in the chamber for an additional day and did not receive any feed to estimate the fasting HP and calculate the thermic effect of feeding. Five pairs of 2 littermates from the same farrowing batch were used in each line. Because 2 respiration chambers were available for the trial, pigs were measured regularly during the 25- to 95-kg growing period. Two pigs per chamber were used until pigs reached 45 kg of BW, and 1 pig per chamber was used thereafter. Individual feed intake and BW gain were measured continuously from weaning to the end of the trial. Pigs were fed 3 diets with decreasing CP contents during the 25 to 45 (period 1), 45 to 65 (period 2), and 65 to 95 (period 3) kg of BW periods. Average daily feed intake was greater in RFI(+) pigs than in RFI(-) pigs between 25 and 65 kg of BW (2,128 vs. 1,891 g/d; P < 0.01) and G: F was 8% greater in RFI(-) pigs compared with RFI(+) pigs (P < 0.01). There was no line effect on digestibility coefficients or N retention, irrespective of the experimental period studied. Nitrogen retention was 31.2, 28.7, and 20.8 g/d at periods 1, 2, and 3, respectively (P < 0.001). The HP was greater in RFI(+) pigs than in RFI(-) pigs (1,497 vs. 1,383 kJ.kg of BW(-0.60).d(-1); P < 0.01), with no subsequent line effect on energy retention. The activity-related HP tended to be greater in RFI(+) pigs than in RFI(-) pigs (250 vs. 218 kJ.kg of BW(-0.60).d(-1); P = 0.09), and the fasting HP was 10% greater (P = 0.04) in RFI(+) pigs than in RFI(-) pigs (846 vs. 771 kJ.kg of BW(-0.60).d(-1)). The thermic effect of feeding, expressed as a percentage of ME intake, was the same for both lines of pigs (average, 14.7%). In conclusion, the RFI(+) pigs are energetically less efficient because of their greater HP related to physical activity and basal metabolic rate.

Consumer Preferences for Fresh Tomato at the European Scale: A Common Segmentation on Taste and Firmness

Abstract: Although tomato flavor has not been a major goal for breeders, nowadays it becomes important as it is a subject of consumer complaint. A better knowledge of tomato consumer preferences, at the European level, should provide the basis for improvement of fruit quality and for market segmentation. In the framework of a large European project, 806 consumers from 3 countries, The Netherlands, France, and Italy, were presented with a set of 16 varieties representing the diversity of fresh tomato offer in order to evaluate their preferences. In parallel, sensory profiles were constructed by expert panels in each country. Preference maps were then constructed in each country revealing the structure of consumer preferences and allowing identification of the most important characteristics. Then a global analysis revealed that preferences were quite homogeneous across countries. This study identified the overall flavor and firmness as the most important traits for improving tomato fruit quality. It showed that consumer preferences from different European countries, with different cultures and food practices, are segmented following similar patterns when projected onto a common referential plan. Moreover, the results clearly showed that diversification of taste and texture is required to satisfy all consumers' expectations as some consumers preferred firm tomatoes, while others preferred melting ones and were more or less demanding in terms of sweetness and flavor intensity. Detailed comparisons also showed the importance of the fruit appearance in consumer preference.

The sucrose transporter HbSUT3 plays an active role in sucrose loading to laticifer and rubber productivity in exploited trees of Hevea brasiliensis (para rubber tree)

Abstract: Efficient sucrose loading in rubber-producing cells (laticifer cells) is essential for retaining rubber productivity in Hevea brasiliensis, but the molecular mechanisms underlying the regulation of this process remain unknown. Here, we functionally characterized a putative Hevea SUT member, HbSUT3, mainly in samples from regularly exploited trees. When expressed in yeast, HbSUT3 encodes a functional sucrose transporter that exhibits high sucrose affinity with a K(m) value of 1.24 mm at pH 4.0, and possesses features typical of sucrose/H(+) symporters. In planta, when compared to the expression of other Hevea SUT genes, HbSUT3 was found to be the predominant member expressed in the rubber-containing cytoplasm (latex) of laticifers. The comparison of HbSUT3 expression among twelve Hevea tissues demonstrates a relatively tissue-specific pattern, i.e. expression primarily in the latex and in female flowers. HbSUT3 expression is induced by the latex stimulator Ethrel (an ethylene generator), and relates to its yield-stimulating effect. Tapping (the act of rubber harvesting) markedly increased the expression of HbSUT3, whereas wounding alone had little effect. Moreover, the expression of HbSUT3 was found to be positively correlated with latex yield. Taken together, our results provide evidence favouring the involvement of HbSUT3 in sucrose loading into laticifers and in rubber productivity.

Fitness costs associated with unnecessary virulence factors and life history traits: evolutionary insights from the potato late blight pathogen Phytophthora infestans

Abstract: In gene-for-gene models of plant-pathogen interactions, the existence of fitness costs associated with unnecessary virulence factors still represents an issue, both in evolutionary biology and agricultural sciences. Measuring such costs experimentally has proven difficult, especially in pathogens not readily amenable to genetic transformation, since the creation of isogenic lines differing only by the presence or absence of avirulence genes cannot be achieved in many organisms. Here, we circumvented this difficulty by comparing fitness traits in groups of Phytophthora infestans isolates sharing the same multilocus fingerprint, but differing by their virulence/avirulence spectrum. Fitness was assessed from calculations derived from the basic reproduction number, combining several life history traits (latent period, spore density and lesion growth rate) evaluated on leaflets of the potato cultivar Bintje, which is free of resistance genes. A statistically significant fitness cost was found in isolates virulent to the R10 resistance gene. That cost was due to a lower spore production in virulent isolates; however, the latent period was shorter in virulent isolates. Similar trends, although not statistically significant, were observed for the other genes tested. The data likely reflect the adaptive response of the pathogen to the cost associated with virulence. They suggest strong trade-offs between life history traits related to pathogenicity and adaptive biology of pathogens.

The (193-209) 17-residues peptide of bovine β-casein is transported through Caco-2 monolayer.

Abstract: Although the bioavailability of large peptides with biological activity is of great interest, the intestinal transport has been described for peptides up to only nine residues. β-casein (β-CN, 193-209) is a long and hydrophobic peptide composed of 17 amino acid residues (molecular mass 1881 Da) with immunomodulatory activity. The present work examined the transport of the β-CN (193-209) peptide across Caco-2 cell monolayer. In addition, we evaluated the possible routes of the β-CN (193-209) peptide transport, using selective inhibitors of the different routes for peptide transfer through the intestinal barrier. The results showed that the β-CN (193-209) peptide resisted the action of brush-border membrane peptidases, and that it was transported through the Caco-2 cell monolayer. The main route involved in transepithelial transport of the β-CN (193-209) peptide was transcytosis via internalized vesicles, although the paracellular transport via tight-junctions could not be excluded. Our results demonstrated the transport of an intact long-chain bioactive peptide in an in vitro model of intestinal epithelium, as an important step to prove the evidence for bioavailability of this peptide.

Crucial knowledge gaps in current understanding of climate change impacts on coral reef fishes

Abstract: Expert opinion was canvassed to identify crucial knowledge gaps in current understanding of climate change impacts on coral reef fishes. Scientists that had published three or more papers on the effects of climate and environmental factors on reef fishes were invited to submit five questions that, if addressed, would improve our understanding of climate change effects on coral reef fishes. Thirty-three scientists provided 155 questions, and 32 scientists scored these questions in terms of: (i) identifying a knowledge gap, (ii) achievability, (iii) applicability to a broad spectrum of species and reef habitats, and (iv) priority. Forty-two per cent of the questions related to habitat associations and community dynamics of fish, reflecting the established effects and immediate concern relating to climate-induced coral loss and habitat degradation. However, there were also questions on fish demographics, physiology, behaviour and management, all of which could be potentially affected by climate change. Irrespective of their individual expertise and background, scientists scored questions from different topics similarly, suggesting limited bias and recognition of a need for greater interdisciplinary and collaborative research. Presented here are the 53 highest-scoring unique questions. These questions should act as a guide for future research, providing a basis for better assessment and management of climate change impacts on coral reefs and associated fish communities.

Carbohydrate uptake from xylem vessels and its distribution among stem tissues and buds in walnut (Juglans regia L.)

Abstract: Bud break pattern is a key determinant of tree architecture. The mechanisms leading to the precedence of certain buds over the others are not yet fully explained, but the availability of soluble sugars may play a significant role, especially those in the xylem sap at the onset of the growing period. Here, we measured carbon availability in the different tissues (bud, xylem and bark). To assess the capacity of buds to use the xylem sap carbohydrates, the fluxes between xylem vessels and parenchyma cells, bark and buds of walnut (Juglans regia cv 'Franquette') were measured during the rest period until bud break. This uptake capacity varies according to the temperature, the sugar and the position on the branch of the fragment studied. Between December and March, in xylem tissues, the active component of sucrose uptake was predominant compared with diffusion (90% of the total uptake), whereas the active component accounted for more moderate amounts in buds (50% of the uptake). The active uptake of hexoses took place belatedly (April) in xylem. The flow rates between xylem vessels and buds increased 1 month before bud break and reached 2000 microg sucrose h(-)(1) g DW(-)(1). Fluxes seemed to depend on bud position on the branch. However, this study strongly suggests that they were mainly dependent on the sink strength of the buds and on the sink competition between bud, xylem parenchyma and bark.

Promising Immunomodulatory Effects of Selected Strains of Dairy Propionibacteria as Evidenced In Vitro and In Vivo

Abstract: Immunomodulatory properties of 10 dairy propionibacteria, analyzed on human peripheral blood mononuclear cells (PBMCs), revealed a highly strain-dependent induction of anti-inflammatory cytokine interleukin 10 (IL-10). Two selected strains of Propionibacterium freudenreichii showed a protective effect against two models of colitis in mice, suggesting a probiotic potential predicted by immune-based selection criteria for these cheese starter bacteria.

Energy value of wheat distillers grains with solubles for growing pigs and adult sows.

Abstract: Two experiments were conducted to determine the total tract digestibility of energy and the DE and ME values of 10 European wheat dried distillers grains with solubles (DDGS) fed to growing pigs and adult sows. The wheat DDGS were obtained from European ethanol plants and selected to get a large variability. One control diet, based on wheat (87.2%), soybean meal (10.0%), and minerals and vitamins, and 10 experimental diets prepared from the control diet and 25% each of the 10 sources of DDGS, were fed to 66 crossbred barrows (6 per diet) according to a factorial arrangement or 6 adult sows according to a pseudo Latin square design. Animals were placed in metabolism cages that allowed for the total, but separate, collection of feces and urine for 8 to 10 d after a 7- to 11-d adaptation period. By subtracting the contribution from the control diet in the DDGS-containing diets (i.e., difference method), N and GE digestibilities and DE and ME values for each source of DDGS were calculated. The energy digestibility in wheat DDGS averaged 66.5% (56.3 to 76.0%) and 71.2% (59.7 to 78.2%) in growing pigs and adult sows, respectively. Consequently, average (range) DE values of DDGS were 14.0 (11.8 to 16.2) and 14.9 (12.5 to 16.4) MJ/kg of DM for growing pigs and adult sows, respectively. Our data show that DE content of wheat DDGS can be predicted from their ADF content or from the lightness score (L). By excluding the dark and overheated samples (L <50) with the least energy digestibility and DE values, the average energy digestibility values were 69.5 and 74.4% in growing pigs and adult sows, respectively, with corresponding DE values of 14.6 and 15.6 MJ/kg DM, which are more representative of a well-controlled process for DDGS preparation. The negative effect of L on energy value and energy digestibility indicates that the occurrence of Maillard reactions should be reduced to maximize the energy value of wheat DDGS for pigs.