Showing papers by "Agrocampus Ouest published in 2012"

The EMEP MSC-W chemical transport model -- technical description

Abstract: The Meteorological Synthesizing Centre-West (MSC-W) of the European Monitoring and Evaluation Programme (EMEP) has been performing model calculations in support of the Convention on Long Range Transboundary Air Pollution (CLRTAP) for more than 30 years The EMEP MSC-W chemical transport model is still one of the key tools within European air pollution policy assessments Traditionally, the model has covered all of Europe with a resolution of about 50 km x 50 km, and extending vertically from ground level to the tropopause (100 hPa) The model has changed extensively over the last ten years, however, with flexible processing of chemical schemes, meteorological inputs, and with nesting capability: the code is now applied on scales ranging from local (ca 5 km grid size) to global (with 1 degree resolution) The model is used to simulate photo-oxidants and both inorganic and organic aerosols In 2008 the EMEP model was released for the first time as public domain code, along with all required input data for model runs for one year The second release of the EMEP MSC-W model became available in mid 2011, and a new release is targeted for summer 2012 This publication is in-tended to document this third release of the EMEP MSC-W model The model formulations are given, along with details of input data-sets which are used, and a brief background on some of the choices made in the formulation is presented The model code itself is available at wwwemepint, along with the data required to run for a full year over Europe

New insight into the history of domesticated apple: secondary contribution of the European wild apple to the genome of cultivated varieties.

Abstract: The apple is the most common and culturally important fruit crop of temperate areas. The elucidation of its origin and domestication history is therefore of great interest. The wild Central Asian species Malus sieversii has previously been identified as the main contributor to the genome of the cultivated apple (Malus domestica), on the basis of morphological, molecular, and historical evidence. The possible contribution of other wild species present along the Silk Route running from Asia to Western Europe remains a matter of debate, particularly with respect to the contribution of the European wild apple. We used microsatellite markers and an unprecedented large sampling of five Malus species throughout Eurasia (839 accessions from China to Spain) to show that multiple species have contributed to the genetic makeup of domesticated apples. The wild European crabapple M. sylvestris, in particular, was a major secondary contributor. Bidirectional gene flow between the domesticated apple and the European crabapple resulted in the current M. domestica being genetically more closely related to this species than to its Central Asian progenitor, M. sieversii. We found no evidence of a domestication bottleneck or clonal population structure in apples, despite the use of vegetative propagation by grafting. We show that the evolution of domesticated apples occurred over a long time period and involved more than one wild species. Our results support the view that self-incompatibility, a long lifespan, and cultural practices such as selection from open-pollinated seeds have facilitated introgression from wild relatives and the maintenance of genetic variation during domestication. This combination of processes may account for the diversification of several long-lived perennial crops, yielding domestication patterns different from those observed for annual species.

Physicochemical Properties of Starch and Flour from Different Rice Cultivars

Abstract: The starches and flours from four different rice cultivars were evaluated for composition, crystallinity characteristics, blue value, turbidity, swelling power, solubility, pasting properties, and textural and retrogradation properties. The amylose content of starches and flours from different rice cultivars differed significantly. The results showed that the physicochemical properties of rice starch and rice flour were correlated to amylose content. The crystallinity degree of rice starch and flour depended on amylose content. The blue value, turbidity value, and gel hardness were positively correlated to amylose content; however, the swelling power, solubility, and gel adhesiveness were negatively correlated to amylose content. Furthermore, the pasting properties and gel textural and retrogradation properties of rice flours were related to the structure properties of rice starch. And the characteristics of starch, protein, and lipid significantly influenced the turbidity, pasting properties, and gel textural and retrogradation properties of rice flours.

Experimental assessment of nutrient limitation along a 2‐million‐year dune chronosequence in the south‐western Australia biodiversity hotspot

Abstract: Summary 1. The classical model of long-term ecosystem development suggests that primary productivity is limited by nitrogen (N) on young substrates and phosphorus (P) on older substrates. Measurements of foliar and soil nutrients along soil chronosequences support this model, but direct tests through nutrient-addition experiments are rare. 2. We conducted a nutrient-limitation bioassay using phytometer species grown in soils from five stages of a >2-million-year dune chronosequence in south-western Australia. This long-term chronosequence is located within a region of exceptionally high plant species diversity and has not been previously studied in the context of ecosystem development. 3. Growth of unfertilized phytometers, a proxy for primary productivity, peaked on young soils (hundreds to a few thousand years) and then declined steadily on older soils. This decline was linked to P limitation, and its rapid appearance (<7000 years) compared to other sequences reflects the low P concentration in the parent material. As predicted, growth of canola was N-limited on the youngest soil (stage 1), co-limited by multiple nutrients in stage 2 and increasingly P-limited thereafter. 4. Growth of wheat was P-limited from stage 2 onwards, yet on the youngest soil it was co-limited by potassium (K) and micronutrients – most likely iron (Fe). Nitrogen addition also decreased the root:shoot ratio of wheat such that shoot growth was higher than in the control. We attribute these responses to a parent material that is very low in K and N and strongly alkaline (pH [H2O] > 9), being of a marine origin (i.e. carbonate dunes). Fe is poorly soluble at high pH and K likely plays a role in the secretion of Fe-mobilizing exudates from wheat roots. 5. Synthesis. Our results provide strong support for the long-term ecosystem-development model, particularly with regard to the appearance of P limitation and associated declines in productivity. However, our study also shows that N cannot be assumed to invariably be the most important limiting nutrient in young soils, and it is unlikely to be the only limiting nutrient in calcareous soils. This south-western Australian long-term chronosequence provides an excellent opportunity to explore edaphic controls over plant species diversity.

Temporal profiling of the heat-stable proteome during late maturation of Medicago truncatula seeds identifies a restricted subset of late embryogenesis abundant proteins associated with longevity

Abstract: Developing seeds accumulate late embryogenesis abundant (LEA) proteins, a family of intrinsically disordered and hydrophilic proteins that confer cellular protection upon stress. Many different LEA proteins exist in seeds, but their relative contribution to seed desiccation tolerance or longevity (duration of survival) is not yet investigated. To address this, a reference map of LEA proteins was established by proteomics on a hydrophilic protein fraction from mature Medicago truncatula seeds and identified 35 polypeptides encoded by 16 LEA genes. Spatial and temporal expression profiles of the LEA polypeptides were obtained during the long maturation phase during which desiccation tolerance and longevity are sequentially acquired until pod abscission and final maturation drying occurs. Five LEA polypeptides, representing 6% of the total LEA intensity, accumulated upon acquisition of desiccation tolerance. The gradual 30-fold increase in longevity correlated with the accumulation of four LEA polypeptides, representing 35% of LEA in mature seeds, and with two chaperone-related polypeptides. The majority of LEA polypeptides increased around pod abscission during final maturation drying. The differential accumulation profiles of the LEA polypeptides suggest different roles in seed physiology, with a small subset of LEA and other proteins with chaperone-like functions correlating with desiccation tolerance and longevity.

Milk Fermented by Propionibacterium freudenreichii Induces Apoptosis of HGT-1 Human Gastric Cancer Cells

Abstract: BACKGROUND: Gastric cancer is one of the most common cancers in the world. The "economically developed countries" life style, including diet, constitutes a risk factor favoring this cancer. Diet modulation may lower digestive cancer incidence. Among promising food components, dairy propionibacteria were shown to trigger apoptosis of human colon cancer cells, via the release of short-chain fatty acids acetate and propionate. METHODOLOGY/PRINCIPAL FINDINGS: A fermented milk, exclusively fermented by P. freudenreichii, was recently designed. In this work, the pro-apoptotic potential of this new fermented milk was demonstrated on HGT-1 human gastric cancer cells. Fermented milk supernatant induced typical features of apoptosis including chromatin condensation, formation of apoptotic bodies, DNA laddering, cell cycle arrest and emergence of a subG1 population, phosphatidylserine exposure at the plasma membrane outer leaflet, reactive oxygen species accumulation, mitochondrial transmembrane potential disruption, caspase activation and cytochrome c release. Remarkably, this new fermented milk containing P. freudenreichii enhanced the cytotoxicity of camptothecin, a drug used in gastric cancer chemotherapy. CONCLUSIONS/SIGNIFICANCE: Such new probiotic fermented milk may thus be useful as part of a preventive diet designed to prevent gastric cancer and/or as a food supplement to potentiate cancer therapeutic treatments.

Insights into Populus XIP aquaporins: evolutionary expansion, protein functionality, and environmental regulation

Abstract: A novel category of major intrinsic proteins which share weak similarities with previously identified aquaporin subfamilies was recently identified in land plants, and named X (for unrecognized) intrinsic proteins (XIPs). Because XIPs are still ranked as uncharacterized proteins, their further molecular characterization is required. Herein, a systematic fine-scale analysis of XIP sequences found in flowering plant databases revealed that XIPs are found in at least five groups. The phylogenetic relationship of these five groups with the phylogenetic organization of angiosperms revealed an original pattern of evolution for the XIP subfamily through distinct angiosperm taxon-specific clades. Of all flowering plant having XIPs, the genus Populus encompasses the broadest panel and the highest polymorphism of XIP isoforms, with nine PtXIP sequences distributed within three XIP groups. Comprehensive PtXIP gene expression patterns showed that only two isoforms (PtXIP2;1 and PtXIP3;2) were transcribed in vegetative tissues. However, their patterns are contrasted, PtXIP2;1 was ubiquitously accumulated whereas PtXIP3;2 was predominantly detected in wood and to a lesser extent in roots. Furthermore, only PtXIP2;1 exhibited a differential expression in leaves and stems of drought-, salicylic acid-, or wounding-challenged plants. Unexpectedly, the PtXIPs displayed different abilities to alter water transport upon expression in Xenopus laevis oocytes. PtXIP2;1 and PtXIP3;3 transported water while other PtXIPs did not.

Using stable isotope analyses to determine the ecological effects of non-native fishes.

Abstract: Freshwater fish ecology has greatly benefited from the use of innovative tools such as stable isotope analysis to determine the ecological effects of non-native fishes. Stable isotope analyses are based on the predictable relationship between the isotope composition of a consumer and its prey, and have become increasingly popular amongst aquatic ecologists. In parallel, they have been implemented as a sensitive, cost-effective and temporally integrative tool to analyse the trophic interactions between native and non-native species, and to detect some subtle ecological effects of human activities, such as the introduction of non-native freshwater fish species. This review aimed to understand how stable isotope analyses have been used and how they have provided new insights into the ecological impacts of non-native freshwater fishes. Specifically, the published literature (45 articles) was reviewed to establish the current state-of-the-art. The use of stable isotope analyses in the field is still an emerging approach. The majority of studies were conducted on lentic ecosystems in North America targeting three main families of non-native fish species. Measurements were most commonly made with carbon and nitrogen stable isotopes using muscle samples. The most recent theoretical and methodological advances were illustrated by selecting some case studies conducted with different non-native species and biotic interactions. Finally, several recommendations for an optimised use of stable isotope analyses for freshwater ecological studies related to trophic interactions of non-native freshwater fish species were established.

The role of organisms in hyporheic processes: gaps in current knowledge, needs for future research and applications

Abstract: Fifty years after the hyporheic zone was first defined (Orghidan, 1959), there are still gaps in the knowledge regarding the role of biodiversity in hyporheic processes. First, some methodological questions remained unanswered regarding the interactions between biodiversity and physical processes, both for the study of habitat characteristics and interactions at different scales. Furthermore, many questions remain to be addressed to help inform our understanding of invertebrate community dynamics, especially regarding the trophic niches of organisms, the functional groups present within sediment, and their temporal changes. Understanding microbial community dynamics would require investigations about their relationship with the physical characteristics of the sediment, their diversity, their relationship with metabolic pathways, their inter- actions with invertebrates, and their response to environmental stress. Another fundamental research question is that of the importance of the hyporheic zone in the global metabolism of the river, which must be explored in relation to organic matter recycling, the effects of disturbances, and the degradation of contaminants. Finally, the application of this knowledge requires the development of methods for the estimation of hydro- logical exchanges, especially for the management of sediment clogging, the optimization of self-purification, and the integration of climate change in environmental policies. The development of descriptors of hyporheic

AFM imaging of milk casein micelles: Evidence for structural rearrangement upon acidification

Abstract: Milk casein micelles are natural association colloids that we all encounter in everyday life, yet we still lack an accurate description of their internal structure and the interactions that stabilize it. In this letter, we provide for the first time detailed images of intact casein micelles as obtained through atomic force microscopy under liquid conditions close to physiological. The micelles appear as heterogeneous raspberry-like particles, which is consistent with a hierarchical/spongelike structure made of connected 10−40 nm dense casein regions. Upon in situ acidification to pH 5, the micelles decrease in size and lose their surface heterogeneities, indicating that this structure is highly sensitive to variations in mineral content and caseins net charge.

Effect of feed restriction on hormones, performance, carcass traits, and meat quality in immunocastrated pigs.

Abstract: The aim of this study was to assess the effect of feed restriction applied to immunocastrated pigs in the period after the second vaccination (V2) against GnRH on hormonal status, performance, car- cass traits, and meat quality. Immunocastrated pigs (IC) were compared with entire males (EM) and surgical castrates fed ad libitum. Pigs (Large White × Landrace) × Pietrain were either left entire or surgically castrated within 1 wk after birth (SC, n = 22). At 83 d of age, the entire males were further allotted to treatment groups (individual housing) of ad libitum fed EM (n = 24), ad libitum fed IC (IC-L, n = 21), or restrictively fed IC (IC-R, n = 21). At that time, the fi rst vaccination (V1) was applied to IC-L and IC-R pigs. One week after V2 (age 130 d), feed restriction (≈80% of the ad libitum feed intake of SC pigs) was applied to IC-R pigs. The experiment ended 5 wk after V2, when pigs were 165 d old. Immunocastration successfully reduced boar taint compounds and size of reproductive organs. At 130 d, serum leptin concentrations were similar in all groups, whereas IGF-I concentration was less in SC (P ≤ 0.002) than in the other groups. Three weeks after V2, leptin concentrations of both IC groups were in between EM (least) and SC (greatest). The reverse was observed for IGF-I. Feed restriction had no effect on leptin or IGF-I concentrations in IC pigs. In the period V1 to V2, per- formance differed mainly between EM and SC, whereas both IC groups had feed intake and feed conversion ratio similar to EM and intermediate daily BW gain, not differing from either EM or SC. After V2, IC-L pigs increased their feed intake to the concentrations of SC, with faster growth compared with the other 3 groups (P < 0.05) and fatter carcasses compared with EM pigs (P = 0.007). Similar performance and carcass leanness were observed for IC-R and EM pigs. During preslaughter handling more carcass lesions were noted in EM and IC-R than in IC-L or SC pigs (P < 0.002). Neither immu- nocastration nor feed restriction had any effect on meat quality, but EM had greater drip loss, less intramuscular fat, and decreased tenderness than SC pigs. In conclu- sion, restricting feed intake can increase production effi ciency but also aggressiveness of IC pigs.

Comparison of muscle transcriptome between pigs with divergent meat quality phenotypes identifies genes related to muscle metabolism and structure.

Abstract: Background Meat quality depends on physiological processes taking place in muscle tissue, which could involve a large pattern of genes associated with both muscle structural and metabolic features. Understanding the biological phenomena underlying muscle phenotype at slaughter is necessary to uncover meat quality development. Therefore, a muscle transcriptome analysis was undertaken to compare gene expression profiles between two highly contrasted pig breeds, Large White (LW) and Basque (B), reared in two different housing systems themselves influencing meat quality. LW is the most predominant breed used in pig industry, which exhibits standard meat quality attributes. B is an indigenous breed with low lean meat and high fat contents, high meat quality characteristics, and is genetically distant from other European pig breeds. Methodology/Principal Findings Transcriptome analysis undertaken using a custom 15 K microarray, highlighted 1233 genes differentially expressed between breeds (multiple-test adjusted P-value<0.05), out of which 635 were highly expressed in the B and 598 highly expressed in the LW pigs. No difference in gene expression was found between housing systems. Besides, expression level of 12 differentially expressed genes quantified by real-time RT-PCR validated microarray data. Functional annotation clustering emphasized four main clusters associated to transcriptome breed differences: metabolic processes, skeletal muscle structure and organization, extracellular matrix, lysosome, and proteolysis, thereby highlighting many genes involved in muscle physiology and meat quality development. Conclusions/Significance Altogether, these results will contribute to a better understanding of muscle physiology and of the biological and molecular processes underlying meat quality. Besides, this study is a first step towards the identification of molecular markers of pork quality and the subsequent development of control tools.

Phylogenetic analysis and polyphasic characterization of Clavibacter michiganensis strains isolated from tomato seeds reveal that nonpathogenic strains are distinct from C. michiganensis subsp. michiganensis.

Abstract: The genus Clavibacter comprises one species and five subspecies of plant-pathogenic bacteria, four of which are classified as quarantine organisms due to the high economic threat they pose. Clavibacter michiganensis subsp. michiganensis is one of the most important pathogens of tomato, but the recommended diagnostic tools are not satisfactory due to false-negative and/or -positive results. To provide a robust analysis of the genetic relatedness among a worldwide collection of C. michiganensis subsp. michiganensis strains, relatives (strains from the four other C. michiganensis subspecies), and nonpathogenic Clavibacter-like strains isolated from tomato, we performed multilocus sequence-based analysis and typing (MLSA and MLST) based on six housekeeping genes (atpD, dnaK, gyrB, ppK, recA, and rpoB). We compared this "framework" with phenotypic and genotypic characteristics such as pathogenicity on tomato, reaction to two antisera by immunofluorescence and to five PCR identification tests, and the presence of four genes encoding the main C. michiganensis subsp. michiganensis pathogenicity determinants. We showed that C. michiganensis subsp. michiganensis is monophyletic and is distinct from its closest taxonomic neighbors. The nonpathogenic Clavibacter-like strains were identified as C. michiganensis using 16S rRNA gene sequencing. These strains, while cross-reacting with C. michiganensis subsp. michiganensis identification tools, are phylogenetically distinct from the pathogenic strains but belong to the C. michiganensis clade. C. michiganensis subsp. michiganensis clonal complexes linked strains from highly diverse geographical origins and also strains isolated over long periods of time in the same location. This illustrates the importance of seed transmission in the worldwide dispersion of this pathogen and its survival and adaptation abilities in a new environment once introduced.

Linking microbial community to soil water-stable aggregation during crop residue decomposition

Abstract: The dynamics of soil water-stable aggregation (WSA) following organic matter (OM) addition are controlled by microbial activity, which in turn is influenced by carbon substrate quality and mineral N availability. However, the role of microbial communities in determining WSA at different stages of OM decomposition remains largely unknown. This study aimed at evaluating the role of microbial communities in WSA during OM decomposition as affected by mineral N. In a 35-day incubation experiment, we studied the decomposition of two high-C/N crop residues (miscanthus, C/N = 311.3; and wheat, C/N = 125.6) applied at 4 g C kg−1 dry soil with or without mineral N addition (120 mg N kg−1 dry soil). Microbial characteristics were measured at day 0, 7, and 35 of the experiment, and related to previous results of WSA. Early increase in WSA (at 7 days) was related to an overall increase of the microbial biomass (MBC) with wheat residues showing higher values in MBC and WSA than miscanthus. In the intermediate stage of decomposition (from day 7 to 35), the dynamics of WSA were more associated with the dynamics of microbial polysaccharides and greatly influenced by mineral N addition. Mineral N addition resulted in a decrease or leveling off of WSA whereas it increased in its absence. We suggest that opportunistic bacterial populations stimulated by N addition may have consumed binding agents which decreased WSA or prevented its increase. To the contrary, microbial polysaccharide production was high when no mineral N was added which led to the higher WSA in the late stage of decomposition in this treatment. The late stage of decomposition was associated with a particular fungal community also influenced by the mineral N treatment. We suggest that WSA dynamics in the late stage of decomposition can be considered as a « narrow process³ where the structure of the microbial community plays a greater role than during the initial stages.

Providing a diet deficient in valine but with excess leucine results in a rapid decrease in feed intake and modifies the postprandial plasma amino acid and α-keto acid concentrations in pigs.

Abstract: Indispensable AA are involved in the control of feed intake. When a diet deficient in Val is offered to pigs, feed intake is typically reduced. This effect is aggravated when dietary Leu is supplied in excess of the requirement. If an unbalanced supply of branched-chain AA (BCAA) is harmful, an anorectic response may serve as a mechanism to prevent this situation. We verified this hypothesis by measuring the voluntary feed intake of a balanced diet offered during the 30-min period 1 h after ingestion of a test meal deficient or not in Val (Val- and Val+) with an excess of Leu. Twelve and four 6-wk-old crossbred female pigs were used in Exp. 1 and 2, respectively. Prior ingestion of the Val- test meal resulted in a 14% reduction in feed intake compared with that observed after ingestion of the Val+ test meal (P = 0.06) in Exp. 1, indicating that the signal to reduce feed intake occurred within 1 h. It is possible that the plasma concentration of the limiting AA serves as a signal for the dietary AA deficiency. We therefore determined the postprandial plasma concentrations of BCAA and their α-keto acids after ingestion of Val- and Val+ in 4 pigs in Exp. 2. After ingestion of the Val- diet, plasma concentrations of Val and its keto acid were reduced compared with values observed after ingestion of the Val+ diet. The peak concentration occurred earlier after ingestion of the Val- diet compared with that of the Val+ diet. Although the plasma concentration increased after the meal, it declined rapidly in pigs offered Val-, and the Val concentration 4 h after ingestion of the meal was even less than that observed in the fasted state. In conclusion, it appears that the pig is able to detect a deficient supply of Val within 1 h after ingestion. The plasma concentration of Val or its concentration relative to the other BCAA during the postprandial period may act as a signal indicating the AA deficiency.

How do agricultural policies influence farm size inequality? The example of France

Abstract: We investigate farm size inequality in France using agricultural censuses and farm structure surveys at the NUTS3 level (‘departements’) during the period 1970–2007. Using calculated Gini coefficients, we show that farm size inequality has not systematically increased in France. An econometric analysis of the determinants of farm size inequality reveals that policy measures significantly affected farm size inequality, with most of the measures considered decreasing it. Empirical results suggest that the main contributor was the activity of the SAFER (Societe d'Amenagement Foncier et d'Etablissement Rural), a specific feature of the French farm structural policy aimed at regulating rural land management. Besides, this research highlights the great complexity of the dynamics underlying the evolution of farm size distribution.

Arginase Induction Represses Gall Development During Clubroot Infection In Arabidopsis

Abstract: Arginase induction can play a defensive role through the reduction of arginine availability for phytophageous insects. Arginase activity is also induced during gall growth caused by Plasmodiophora brassicae infection in roots of Arabidopsis thaliana; however, its possible role in this context has been unclear. We report here that the mutation of the arginase-encoding gene ARGAH2 abrogates clubroot-induced arginase activity and results in enhanced gall size in infected roots, suggesting that arginase plays a defensive role. Induction of arginase activity in infected roots was impaired in the jar1 mutant, highlighting a link between the arginase response to clubroot and jasmonate signaling. Clubroot-induced accumulation of the principal amino acids in galls was not affected by the argah2 mutation. Because ARGAH2 was previously reported to control auxin response, we investigated the role of ARGAH2 in callus induction. ARGAH2 was found to be highly induced in auxin/cytokinin-triggered aseptic plant calli, and callus development was enhanced in argah2 in the absence of the pathogen. We hypothesized that arginase contributes to a negative control over clubroot symptoms, by reducing hormone-triggered cellular proliferation.

The duplicated genes database: identification and functional annotation of co-localised duplicated genes across genomes

Abstract: Background There has been a surge in studies linking genome structure and gene expression, with special focus on duplicated genes. Although initially duplicated from the same sequence, duplicated genes can diverge strongly over evolution and take on different functions or regulated expression. However, information on the function and expression of duplicated genes remains sparse. Identifying groups of duplicated genes in different genomes and characterizing their expression and function would therefore be of great interest to the research community. The ‘Duplicated Genes Database’ (DGD) was developed for this purpose. Methodology Nine species were included in the DGD. For each species, BLAST analyses were conducted on peptide sequences corresponding to the genes mapped on a same chromosome. Groups of duplicated genes were defined based on these pairwise BLAST comparisons and the genomic location of the genes. For each group, Pearson correlations between gene expression data and semantic similarities between functional GO annotations were also computed when the relevant information was available. Conclusions The Duplicated Gene Database provides a list of co-localised and duplicated genes for several species with the available gene co-expression level and semantic similarity value of functional annotation. Adding these data to the groups of duplicated genes provides biological information that can prove useful to gene expression analyses. The Duplicated Gene Database can be freely accessed through the DGD website at http://dgd.genouest.org.