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RNAi-suppression of barley caffeic acid O-methyltransferase modifies lignin despite redundancy in the gene family
No full textCaffeic acid O-methyltransferase (COMT), the lignin biosynthesis gene modified in many brown-midrib high-digestibility mutants of maize and sorghum, was targeted for downregulation in the small grain temperate cereal, barley (Hordeum vulgare), to improve straw properties. Phylogenetic and expression analyses identified the barley COMT orthologue(s) expressed in stems, defining a larger gene family than in brachypodium or rice with three COMT genes expressed in lignifying tissues. RNAi significantly reduced stem COMT protein and enzyme activity, and modestly reduced stem lignin content while dramatically changing lignin structure. Lignin syringyl-to-guaiacyl ratio was reduced by similar to 50%, the 5-hydroxyguaiacyl (5-OH-G) unit incorporated into lignin at 10--15-fold higher levels than normal, and the amount of p-coumaric acid ester-linked to cell walls was reduced by similar to 50%. No brown-midrib phenotype was observed in any RNAi line despite significant COMT suppression and altered lignin. The novel COMT gene family structure in barley highlights the dynamic nature of grass genomes. Redundancy in barley COMTs may explain the absence of brown-midrib mutants in barley and wheat. The barley COMT RNAi lines nevertheless have the potential to be exploited for bioenergy applications and as animal feed
A way to model stochastic perturbations in population dynamics models with bounded realizations
No full textIn this paper, we analyze the use of the Ornstein-Uhlenbeck process to model dynamical systems subjected to bounded noisy perturbations. In order to discuss the main characteristics of this new approach we consider some basic models in population dynamics such as the logistic equations and competitive Lotka-Volterra systems. The key is the fact that these perturbations can be ensured to keep inside some interval that can be previously fixed, for instance, by practitioners, even though the resulting model does not generate a random dynamical system. However, one can still analyze the forwards asymptotic behavior of these random differential systems. Moreover, to illustrate the advantages of this type of modeling, we exhibit an example testing the theoretical results with real data, and consequently one can see this method as a realistic one, which can be very useful and helpful for scientists
Reduced density is an environmental friendly and cost effective solution to increase resilence to drought in vineyards in a contexte of climate change
No full textAims: Climate change imposes increasingly warm and dry conditions in most winegrowing regions. Mediterranean vineyards are particularly vulnerable and have registered, in most situations, declining yields over the past years. Although a majority of Mediterranean vineyards are still dry-farmed, yields can be increased by the implementation of irrigation. However, irrigation has an impact on increasingly affected water resources. An alternative solution to irrigation can be the adaptation of training systems. As can be shown by water balance modeling, low density non-irrigated vineyards are much less vulnerable to climatic drought compared to medium or high density vineyards. And while yields tend to be lower in low density vineyards, so are production costs. The aim of this study is to investigate to what extent low density vineyards can be a sustainable and cost effective adaptation for grape growing in dry climates.
Methods and results: A water balance model was applied to conceptual vineyards with different soil water holding capacities and different planting densities over recent past (1981-2010) and near future (2041-2070) climatic conditions for two winegrowing scenarios (Cabernet-Sauvignon in Bordeaux and Grenache in Avignon, Côtes du Rhône). Row spacings of 2.0, 3.0 and 4.0 m were investigated for vineyards with 100, 200 and 300 mm total transpirable soil water (TTSW), while inter-vine spacing, vine architecture, and canopy height were kept similar. Projected yields were estimated to vary according to vine density and water deficit based on a meta-analysis of data published in the literature. Production costs were calculated according to an operation-based costing methodology and compared among the different scenarios on a cost per hectare basis. Gross profit per hectare, defined as grape sales revenue minus production costs, was then computed for two grape sale revenue scenarios (1 €/kg and 3 €/kg). The modeled average fraction of transpirable soil water (FTSW) varied across the different winegrowing scenarios, climate periods (recent past or near future), and TTSW and row spacing assumptions. In soils with 200 or 300 mm TTSW, the 30-day average FTSW prior to modeled grape harvest roughly doubled when 4.0 m versus 2.0 m spacing was assumed in both the recent past and near future climate scenarios. In soils with 100 mm TTSW, water deficit was more severe overall and the effect of row spacing on average FTSW was less pronounced. Changes in projected yields were estimated as a function of vine density and FTSW based on relationships published in the literature. Yields decreased with decreasing vine density and increasing water deficits, while production costs decreased with decreasing vine density. When the assumed revenue from grape sales was lower (1 €/kg), the effect of reduced production cost savings outweighed the loss in revenue caused by reduced yields, leading to increased gross profit per hectare. On the other hand, when higher grape revenue was assumed (3 €/kg), the effect of reduced yield on revenue outweighed the associated reduction in production costs, leading to reduced gross profit per hectare.
Conclusions: Lower density, dry-farmed vineyards will experience less water deficit under warmer and drier climate conditions, although this difference is less pronounced in soils with less water holding capacity. When considering differences in yields, revenues, and production costs, lower density vineyards producing lower value grapes (1 €/kg) may also experience an associated increase in gross profit, while such vineyards producing higher value grapes (3 €/kg) might experience a decrease in gross profit.
Significance and impact of the study: The implementation of dry-farmed, low density vineyards provides a sustainable solution for grape growing by reducing the need for irrigation water. It allows maintaining vineyards in very dry areas where water is not readily available for irrigation and where other crops (except possibly olive trees) cannot be grown. Modeling of yield, revenue, and production costs shows that this solution is also economically viable, particularly for vineyards producing lower value (€/kg) grapes. Unlike goblet trained bush vine, low density trellised vineyards are perfectly adapted for mechanization
Multilocus sequence analysis reveals three distinct populations of ‘Candidatus Phytoplasma palmicola’ with a specific geographical distribution on the African continent
No full textPhytoplasma palmicola' with low intrapopulation diversity. The reasons for the observed genetic bottlenecks resulting in strong geographic patterns remain to be established but could result from the lethality of CLYD and dominance of short distance insect-mediated transmission in its spread
Cell wall hydrolases in bacteria: Insight on the diversity of cell wall amidases, glycosidases and peptidases toward peptidoglycan
No full textThe cell wall (CW) of bacteria is an intricate arrangement of macromolecules, at least constituted of peptidoglycan (PG) but also of (lipo)teichoic acids, various polysaccharides, polyglutamate and/or proteins. During bacterial growth and division, there is a constant balance between CW degradation and biosynthesis. The CW is remodeled by bacterial hydrolases, whose activities are carefully regulated to maintain cell integrity or lead to bacterial death. Each cell wall hydrolase (CWH) has a specific role regarding the PG: (i) cell wall amidase (CWA) cleaves the amide bond between N-acetylmuramic acid and L-alanine residue at the N-terminal of the stem peptide, (ii) cell wall glycosidase (CWG) catalyses the hydrolysis of the glycosidic linkages, whereas (iii) cell wall peptidase (CWP) cleaves amide bonds between amino acids within the PG chain. After an exhaustive overview of all known conserved catalytic domains responsible for CWA, CWG, and CWP activities, this review stresses that the CWHs frequently display a modular architecture combining multiple and/or different catalytic domains, including some lytic transglycosylases as well as CW binding domains. From there, direct physiological and collateral roles of CWHs in bacterial cells are further discussed
Tetracycline gene transfer in staphylococcus xylosus in situ during sausage fermentation
No full textThe presence of determinants of resistance to antibiotics can constitute a possible safety hazard in coagulase-negative staphylococci (CNS), which are widely present in food of animal origin. Among CNS, S. xylosus is a species frequently isolated from fermented meat products. Resistance to tetracycline was found to be one of the most distributed resistances occurring in S. xylosus strains isolated from fermented sausages. We evaluated the transfer of tetracycline resistance in vitro and in situ between S. xylosus strains. We selected three strains isolated from dry fermented sausages, resistant to tetracycline but not to minocycline, their resistance occurring by a mechanism of active efflux encoded by the tetK gene. Only one strain was able to transfer its tetracycline resistance to a recipient strain initially susceptible and plasmid-free using a filter mating procedure. Transfer of tetracycline resistance was observed at very low frequencies of 3.4 x 10(-9) per recipient. To further investigate the transferability of this tetracycline resistance, the donor and recipient strains were tested in pilot-scale fermented sausage production. This transfer was possible but at a low rate, 1.4 x 10(-7), and only under conditions of a high inoculation level of 10(8) CFU/g of meat. The tetK gene is located on a small mobilizable plasmid close to Staphylococcus aureus pT181 plasmid. In conclusion, the transfer of tetracycline resistance between strains of S. xylosus is possible, but at a really low frequency in vitro and in situ in fermented sausages. Even if this represents a very moderate risk, it should be taken into account as required by the European approach of Qualified Presumption of Safety (QPS) and AFSSA safety recommendations, advising that strains used as starter cultures should not carry any transferable antibiotic resistance
Apple whole genome sequences: recent advances and new prospects
No full textIn 2010, a major scientific milestone was achieved for tree fruit crops: publication of the first draft whole genome sequence (WGS) for apple (Malus domestica). This WGS, v1.0, was valuable as the initial reference for sequence information, fine mapping, gene discovery, variant discovery, and tool development. A new, high quality apple WGS, GDDH13 v1.1, was released in 2017 and now serves as the reference genome for apple. Over the past decade, these apple WGSs have had an enormous impact on our understanding of apple biological functioning, trait physiology and inheritance, leading to practical applications for improving this highly valued crop. Causal gene identities for phenotypes of fundamental and practical interest can today be discovered much more rapidly. Genome-wide polymorphisms at high genetic resolution are screened efficiently over hundreds to thousands of individuals with new insights into genetic relationships and pedigrees. High-density genetic maps are constructed efficiently and quantitative trait loci for valuable traits are readily associated with positional candidate genes and/or converted into diagnostic tests for breeders. We understand the species, geographical, and genomic origins of domesticated apple more precisely, as well as its relationship to wild relatives. The WGS has turbo-charged application of these classical research steps to crop improvement and drives innovative methods to achieve more durable, environmentally sound, productive, and consumer-desirable apple production. This review includes examples of basic and practical breakthroughs and challenges in using the apple WGSs. Recommendations for “what’s next” focus on necessary upgrades to the genome sequence data pool, as well as for use of the data, to reach new frontiers in genomics-based scientific understanding of apple
Challenges and Limitations of Karst Aquifer Vulnerability Mapping Based on the PaPRIKa Method-Application to a Large European Karst Aquifer (Fontaine de Vaucluse, France)
No full textAquifer vulnerability maps can improve groundwater management for sustainable anthropogenic development. The latest update of karst aquifer vulnerability mapping is named: the Protection of Aquifers base on Protection, Rock type, Infiltration and KArstification (PaPRIKa). This multi-criteria assessment method is based on a weighting system whose criteria are selected according to the aquifer under study. In this study, the PaPRIKa method has been applied in the Fontaine de Vaucluse karst aquifer using the novel plugin for Quantum Geographic Information System (QGIS) software. The Fontaine de Vaucluse karst aquifer is the largest European karst hydrosystem with a catchment area that measures approximately 1162 km2. Four thematic maps were produced according to the criteria of protection, rock type, infiltration, and karst development. The plugin expedites the weighting system test and generates the final vulnerability map. At a large scale the vulnerability map is globally linked with primary geomorphological units and at the local scale is mostly affected by karst features that drive hydrodynamics. In conclusion, the novel QGIS plugin standardizes the application of the PaPRIKa method, saves time and prevents user omissions. The final vulnerability map provides useful contributions that are most relevant to groundwater managers and decision-makers. We highlight the sensibility of the vulnerability map to the weighting system and validation issues of the vulnerability map are raised
ASICS : identifier et quantifier des métabolites à partir d'un spectre RMN 1H
No full textLa résonance magnétique nucléaire du proton (1H-RMN) est une technologie haut-débit permettant d'obtenir des profils métaboliques, sous forme de spectres, à un coût relativement faible. C'est un outil prometteur pour détecter des biomarqueurs facilement mesurables. Cependant, les métabolites présents dans un mélange complexe ne sont pas identifiables et quantifiables directement, ce qui limite l'interprétabilité de ces approches. Pour faciliter l'utilisation de ces données, nous avons développé une méthode d'analyse automatique, encapsulée dans un nouveau package R/Bioconductor, ASICS, qui permet l'identification et la quantification globale et automatique des métabolites dans un spectre RMN. Le package permet d'enchaîner facilement toutes les étapes de l'analyse (pré-traitements, quantification, outils de diagnostic pour juger de la qualité des quantifications, analyses statistiques post-quantification)