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Farm performance and investment decisions: evidence from the French (Brittany) dairy sector
No full textThe objective of this paper is to investigate the role of farm performance in farmers’ investment
decisions with a theoretical model accounting for adjustment costs and performance. The model
is estimated on a balanced sample of specialised dairy farms in Brittany (western France)
between 2005 and 2014. Two types of farms are considered: with high and with low capital
intensity. The results show that spreading investment over time is, on average, an optimal
strategy for maintaining performance in the presence of adjustment costs. In addition, the effect
of performance on investment behaviour differs between the two farm types.L’objectif de ce travail est d’analyser le rôle de la performance des exploitations agricoles dans
les décisions d’investissement des exploitants, grâce à un modèle théorique prenant en compte
les coûts d’ajustement et la performance. Le modèle est estimé sur un échantillon cylindré
d’exploitations laitières spécialisées en Bretagne entre 2005 et 2014. Deux types d’exploitations
sont considérées : celles avec une forte intensité en capital, et celles avec une faible intensité en
capital. Les résultats montrent que répartir l’investissement sur plusieurs années est en moyenne
une stratégie optimale pour maintenir la performance lorsqu’il y a des coûts d’ajustement. De
plus, l’effet de la performance sur le comportement d’investissement diffère entre les deux types
d’exploitations
NOD2 Expression in Intestinal Epithelial Cells Protects Toward the Development of Inflammation and Associated Carcinogenesis
No full textAlthough the association between Crohn's disease susceptibility and nucleotide-binding oligomerization domain 2 polymorphisms was shown in 2001, the mechanisms involved remain largely unknown. In this review, we report the role of nucleotide-binding oligomerization domain 2 in epithelial cells in the development of colitis and associated carcinogenesis.
Nucleotide-binding oligomerization domain 2 (NOD2) is an intracellular pattern recognition receptor that senses bacterial peptidoglycan-conserved motifs in cytosol and stimulates host immune response including epithelial and immune cells. The association of NOD2 mutations with a number of inflammatory pathologies including Crohn's disease (CD), graft-versus-host diseases, or Blau syndrome, highlights its pivotal role in inflammatory response and the associated-carcinogenesis development. Since its identification in 2001 and its association with CD, the role of NOD2 in epithelial cells and immune cells has been investigated extensively but the precise mechanism by which NOD2 mutations lead to CD and the associated carcinogenesis development is largely unknown. In this review, we present and discuss recent developments about the role of NOD2 inside epithelial cells on the control of the inflammatory process and its linked carcinogenesis development
Restriction-site associated DNA markers provide new insights into the evolutionary history of the bark beetle genus Dendroctonus
No full textThe bark beetle genus Dendroctonus contains some of the most economically important pests of conifers worldwide. Despite many attempts, there is no agreement today on the phylogenetic relationships within the genus, which limits our understanding of its evolutionary history. Here, using restriction-site associated DNA (RAD) markers from 70 specimens representing 17 species (85% of the known diversity) we inferred the phylogeny of the genus, its time of origin and biogeographic history, as well as the evolution of key ecological traits (host plants, larval behavior and adults’ attack strategies). For all combinations of tested parameters (from 6,444 to 23,570 RAD tags analysed), the same, fully resolved topology was inferred. Our analyses suggest that the most recent common ancestor (mrca) of all extant Dendroctonus species was widely distributed across eastern Palearctic and western Nearctic during the early Miocene, from where species dispersed to other Holarctic regions. A first main inter-continental vicariance event occurred during early Miocene isolating the ancestors of D. armandi in the Palearctic, which was followed by the radiation of the main Dendroctonus lineages in North America. During the Late Miocene, the ancestor of the ‘rufipennis’ species group colonized north-east Palearctic regions from western North America, which was followed by a second main inter-continental vicariance event isolating Pleistocene populations in Asia (D. micans) and western North America (D. murrayanae and D. punctatus). The present study supports previous hypotheses explaining intercontinental range disjunctions across the Northern Hemisphere by the fragmentation of a continuous distribution due to climatic cooling, host range fragmentation and geological changes during the late Cenozoic. The reconstruction of ancestral ecological traits indicates that the mrca bored individual galleries and mass attacked the boles of pines. The gregarious feeding behavior of the larvae as well as the individual attack of the base of trees have apparently independently evolved twice in North America (in the ‘rufipennis’ and the ’valens’ species groups), which suggests a higher adaptive potential than previously thought and may be of interest for plant protection and biodiversity conservation in a rapidly changing world
Soils drowned in water impoundments: A new frontier
No full textWater impoundments have major impacts on biogeochemical cycles at the local and global scales. However, although reservoirs flood soils, their biogeochemical evolution below water and its ecological consequences are very poorly documented. We took advantage of the complete emptying of the Guerledan Reservoir (Brittany, France) to compare the composition of soils flooded for 84 years with that of adjacent non-flooded soils used as reference, in 3 situations contrasted by their soil type (Cambisol and Podzol) and initial land-use (forest or grassland). In the annual drawdown zone, upper horizons of submerged soils are eroded, especially near the upper shore and on slopes. In the permanently drowned area, silty sediments cover drowned soils. Compared to reference soils, forest soils drowned for 84 years maintain their original morphological differentiation, but colors are dull, and the humus (O horizons) have virtually disappeared. Spodic horizons are depleted in poorly crystallized iron minerals while the accumulation of amorphous aluminum compounds remains unchanged. Soil bulk density increases as well as pH while total phosphorus content is almost unchanged. On the other hand, the pH of drowned grassland soils is lower by almost one unit, and the total phosphorus content was halved compared to reference soils. In this context, in addition to the effects of flooding, differences are attributed to post-1950 changes in agricultural practices i.e., liming and fertilization. Organic matter stocks decrease by almost 40%. This rate is similar in Cambisols and Podzols. Assuming that carbon was lost as CO2 and CH4, the corresponding flux averaged over the reservoir's life is close to global areal estimates of CO2 emissions in temperate reservoirs and offsets a significant proportion of the carbon burial in reservoir sediments. Hence, flooded soils contribute significantly to the GHG budget of reservoirs, provide original long-term experimental sites to measure the effects of anoxia on soils and contain archives of past soil properties
Destabilization of chromosome structure by histone H3 lysine 27 methylation
No full textChromosome and genome stability are important for normal cell function as instability often correlates with disease and dysfunction of DNA repair mechanisms. Many organisms maintain supernumerary or accessory chromosomes that deviate from standard chromosomes. The pathogenic fungus Zymoseptoria tritici has as many as eight accessory chromosomes, which are highly unstable during meiosis and mitosis, transcriptionally repressed, show enrichment of repetitive elements, and enrichment with heterochromatic histone methylation marks, e.g., trimethylation of H3 lysine 9 or lysine 27 (H3K9me3, H3K27me3). To elucidate the role of heterochromatin on genome stability in Z. tritici, we deleted the genes encoding the methyltransferases responsible for H3K9me3 and H3K27me3, kmt1 and kmt6, respectively, and generated a double mutant. We combined experimental evolution and genomic analyses to determine the impact of these deletions on chromosome and genome stability, both in vitro and in planta. We used whole genome sequencing, ChIP-seq, and RNA-seq to compare changes in genome and chromatin structure, and differences in gene expression between mutant and wildtype strains. Analyses of genome and ChIP-seq data in H3K9me3-deficient strains revealed dramatic chromatin reorganization, where H3K27me3 is mostly relocalized into regions that are enriched with H3K9me3 in wild type. Many genome rearrangements and formation of new chromosomes were found in the absence of H3K9me3, accompanied by activation of transposable elements. In stark contrast, loss of H3K27me3 actually increased the stability of accessory chromosomes under normal growth conditions in vitro, even without large scale changes in gene activity. We conclude that H3K9me3 is important for the maintenance of genome stability because it disallows H3K27me3 in regions considered constitutive heterochromatin. In this system, H3K27me3 reduces the overall stability of accessory chromosomes, generating a metastable state for these quasi-essential regions of the genome. Author summary Genome and chromosome stability are essential to maintain normal cell function and viability. However, differences in genome and chromosome structure are frequently found in organisms that undergo rapid adaptation to changing environmental conditions, and in humans are often found in cancer cells. We study genome instability in a fungal pathogen that exhibits a high degree of genetic diversity. Regions that show extraordinary diversity in this pathogen are the transposon-rich accessory chromosomes, which contain few genes that are of unknown benefit to the organism but maintained in the population and thus considered quasi-essential. Accessory chromosomes in all fungi studied so far are enriched with markers for heterochromatin, namely trimethylation of H3 lysine 9 and 27 (H3K9me3, H3K27me3). We show that loss of these heterochromatin marks has strong but opposing effects on genome stability. While loss of the transposon-associated mark H3K9me3 destabilizes the entire genome, presence of H3K27me3 favors instability of accessory chromosomes. Our study provides insight into the relationship between chromatin and genome stability and why some regions are more susceptible to genetic diversity than others
Comprehensive sensory and chemical data on the flavor of 16 red wines from two varieties: Sensory descriptive analysis, HS-SPME-GC-MS volatile compounds quantitative analysis, and odor-active compounds identification by HS-SPME-GC-MS-O
No full textThis paper describes data collected on 2 sets of 8 French red wines from two grape varieties: Pinot Noir (PN) and Cabernet Franc (CF). It provides, for the 16 wines, (i) sensory descriptive data obtained with a trained panel, (ii) volatile organic compounds (VOC) quantification data obtained by Headspace Solid Phase Micro-Extraction - Gas Chromatography - Mass Spectrometry (HS-SPME-GC-MS) and (iii) odor-active compounds identification by Headspace Solid Phase Micro-Extraction - Gas Chromatography - Mass Spectrometry - Olfactometry (HS-SPME-GC-MS-O). The raw data are hosted on an open-access research data repository [1]
Characterization of the putative polysaccharide synthase CpsA and its effects on the virulence of the human pathogen Aspergillus fumigatus
No full textThe fungus Aspergillus fumigatus is a ubiquitous opportunistic human pathogen capable of causing a life-threatening disease called invasive aspergillosis, or IA, with an associated 40-90% mortality rate in immunocompromised patients. Of the approximately 250 species known in the genus Aspergillus, A. fumigatus is responsible for up to 90% of IA infections. This study focuses on examining the role of the putative polysaccharide synthase cpsA gene in A. fumigatus virulence. Additionally, we evaluated its role in cellular processes that influence invasion and colonization of host tissue. Importantly, our results support that cpsA is indispensable for virulence in A. fumigatus infection of non-neutropenic hosts. Our study revealed that cpsA affects growth and sporulation in this fungus. Absence of cpsA resulted in a drastic reduction in conidiation, and forced overexpression of cpsA produced partially fluffy colonies with low sporulation levels, suggesting that wild-type cpsA expression levels are required for proper conidiation in this fungus. This study also showed that cpsA is necessary for normal cell wall integrity and composition. Furthermore, both deletion and overexpression of cpsA resulted in a reduction in the ability of A. fumigatus to adhere to surfaces, and caused increased sensitivity to oxidative stress. Interestingly, metabolomics analysis indicated that cpsA affects A. fumigatus secondary metabolism. Forced overexpression of cpsA resulted in a statistically significant difference in the production of fumigaclavine A, fumigaclavine B, fumigaclavine C, verruculogen TR-2, and tryprostatin A
Effect of oral physiology parameters on in-mouth aroma compound release using lipoprotein matrices: An in vitro approach
No full textTemporal aroma compound release during eating is a function of the physicochemical properties of the food matrix, aroma compounds, and oral physiology of individuals. However, the influence of each parameter on the release of each aroma component should be clarified. Two flavored lipoprotein matrices varying in composition were chewed in a chewing simulator that reproduced most of the physiological functions of the mouth. Aroma compound releases (butanoic acid, 2-heptanone, ethyl butyrate, 3-octanone, and 2-nonanone) were followed in real time by direct connection of the device to APCI-MS (atmospheric pressure chemical ionization mass spectrometry). Each oral parameter was controlled and decoupled using the in vitro device. The food matrix composition had only a low impact on aroma compound release, but the controlled oral parameters had significantly different influences on the release of aroma compounds according to their physicochemical characteristics. The release of certain compounds seemed more sensitive to bite force, while others seemed more sensitive to the shearing angle. The salivary flow rate primarily influenced the more hydrophobic compounds. Significant interactions were also observed between shear angle, salivary flow rate, and lipoprotein matrix composition, mainly for the release of the more hydrophobic volatile compounds; this needs further investigations to be clarified