Showing papers by "Institut national de la recherche agronomique published in 2005"

Europe-wide reduction in primary productivity caused by the heat and drought in 2003

Abstract: Future climate warming is expected to enhance plant growth in temperate ecosystems and to increase carbon sequestration. But although severe regional heatwaves may become more frequent in a changing climate their impact on terrestrial carbon cycling is unclear. Here we report measurements of ecosystem carbon dioxide fluxes, remotely sensed radiation absorbed by plants, and country-level crop yields taken during the European heatwave in 2003.We use a terrestrial biosphere simulation model to assess continental-scale changes in primary productivity during 2003, and their consequences for the net carbon balance. We estimate a 30 per cent reduction in gross primary productivity over Europe, which resulted in a strong anomalous net source of carbon dioxide (0.5 Pg Cyr21) to the atmosphere and reversed the effect of four years of net ecosystem carbon sequestration. Our results suggest that productivity reduction in eastern and western Europe can be explained by rainfall deficit and extreme summer heat, respectively. We also find that ecosystem respiration decreased together with gross primary productivity, rather than accelerating with the temperature rise. Model results, corroborated by historical records of crop yields, suggest that such a reduction in Europe's primary productivity is unprecedented during the last century. An increase in future drought events could turn temperate ecosystems into carbon sources, contributing to positive carbon-climate feedbacks already anticipated in the tropics and at high latitudes.

On the Separation of Net Ecosystem Exchange into Assimilation and Ecosystem Respiration: Review and Improved Algorithm

Abstract: This paper discusses the advantages and disadvantages of the different methods that separate net ecosystem exchange (NEE) into its major components, gross ecosystem carbon uptake (GEP) and ecosystem respiration (Reco). In particular, we analyse the effect of the extrapolation of night-time values of ecosystem respiration into the daytime; this is usually done with a temperature response function that is derived from long-term data sets. For this analysis, we used 16 one-year-long data sets of carbon dioxide exchange measurements from European and US-American eddy covariance networks. These sites span from the boreal to Mediterranean climates, and include deciduous and evergreen forest, scrubland and crop ecosystems. We show that the temperature sensitivity of Reco, derived from long-term (annual) data sets, does not reflect the short-term temperature sensitivity that is effective when extrapolating from night- to daytime. Specifically, in summer active ecosystems the long

Dietary polyphenols and the prevention of diseases

Abstract: Polyphenols are the most abundant antioxidants in the diet and are widespread constituents of fruits, vegetables, cereals, dry legumes, chocolate, and beverages, such as tea, coffee, or wine. Experimental studies on animals or cultured human cell lines support a role of polyphenols in the prevention of cardiovascular diseases, cancers, neurodegenerative diseases, diabetes, or osteoporosis. However, it is very difficult to predict from these results the effects of polyphenol intake on disease prevention in humans. One of the reasons is that these studies have often been conducted at doses or concentrations far beyond those documented in humans. The few clinical studies on biomarkers of oxidative stress, cardiovascular disease risk factors, and tumor or bone resorption biomarkers have often led to contradictory results. Epidemiological studies have repeatedly shown an inverse association between the risk of myocardial infarction and the consumption of tea and wine or the intake level of some particular flavonoids, but no clear associations have been found between cancer risk and polyphenol consumption. More human studies are needed to provide clear evidence of their health protective effects and to better evaluate the risks possibly resulting from too high a polyphenol consumption.

Conserving biodiversity under climate change: the rear edge matters.

Abstract: Modern climate change is producing poleward range shifts of numerous taxa, communities and ecosystems worldwide. The response of species to changing environments is likely to be determined largely by population responses at range margins. In contrast to the expanding edge, the low-latitude limit (rear edge) of species ranges remains understudied, and the critical importance of rear edge populations as long-term stores of species' genetic diversity and foci of speciation has been little acknowledged. We review recent findings from the fossil record, phylogeography and ecology to illustrate that rear edge populations are often disproportionately important for the survival and evolution of biota. Their ecological features, dynamics and conservation requirements differ from those of populations in other parts of the range, and some commonly recommended conservation practices might therefore be of little use or even counterproductive for rear edge populations.

Abscisic acid biosynthesis and catabolism

Abstract: The level of abscisic acid (ABAabscisic acid) in any particular tissue in a plant is determined by the rate of biosynthesis and catabolism of the hormone. Therefore, identifying all the genes involved in the metabolism is essential for a complete understanding of how this hormone directs plant growth and development. To date, almost all the biosynthetic genes have been identified through the isolation of auxotrophic mutants. On the other hand, among several ABA catabolic pathways, current genomic approaches revealed that Arabidopsis CYP707A genes encode ABA 8′-hydroxylases, which catalyze the first committed step in the predominant ABA catabolic pathway. Identification of ABA metabolic genes has revealed that multiple metabolic steps are differentially regulated to fine-tune the ABA level at both transcriptional and post-transcriptional levels. Furthermore, recent ongoing studies have given new insights into the regulation and site of ABA metabolism in relation to its physiological roles.

A dynamic global vegetation model for studies of the coupled atmosphere-biosphere system

Abstract: This work presents a new dynamic global vegetation model designed as an extension of an existing surface-vegetation-atmosphere transfer scheme which is included in a coupled ocean-atmosphere general circulation model. The new dynamic global vegetation model simulates the principal processes of the continental biosphere influencing the global carbon cycle (photosynthesis, autotrophic and heterotrophic respiration of plants and in soils, fire, etc.) as well as latent, sensible, and kinetic energy exchanges at the surface of soils and plants. As a dynamic vegetation model, it explicitly represents competitive processes such as light competition, sapling establishment, etc. It can thus be used in simulations for the study of feedbacks between transient climate and vegetation cover changes, but it can also be used with a prescribed vegetation distribution. The whole seasonal phenological cycle is prognostically calculated without any prescribed dates or use of satellite data. The model is coupled to the IPSL-CM4 coupled atmosphere-ocean-vegetation model. Carbon and surface energy fluxes from the coupled hydrology-vegetation model compare well with observations at FluxNet sites. Simulated vegetation distribution and leaf density in a global simulation are evaluated against observations, and carbon stocks and fluxes are compared to available estimates, with satisfying results.

Is soil carbon mostly root carbon? Mechanisms for a specific stabilisation

Abstract: Understanding the origin of the carbon (C) stabilised in soils is crucial in order to device management practices that will foster Caccumulation in soils. The relative contributions to soilC pools of roots vs. shoots is one aspect that has been mostly overlooked, although it appears a key factor that drives the fate of plant tissueC either as mineralized CO2 or as stabilized soil organic matter (SOM). Available studies on the subject consistently indicate that rootC has a longer residence time in soil than shootC. From the few studies with complete datasets, we estimated that the mean residence time in soils of root-derived C is 2.4times that of shoot-derived C. Our analyses indicate that this value is biased neither by an underestimation of root contributions, as exudation was considered in the analysis, nor by a priming effect of shoot litter on SOM. Here, we discuss the main SOM stabilisation mechanisms with respect to their ability to specifically protect root-derived SOM. Comparing in situ and incubation experiments suggests that the higher chemical recalcitrance of root tissues as compared to that of shoots is responsible for only a small portion, i.e. about one fourth, of the difference in mean residence time in soils of root-derived vs. shoot-derivedC. This suggests that SOM protection mechanisms other than chemical recalcitrance are also enhanced by root activities: (1)physico-chemical protection, especially in deeper horizons, (2)micrometer-scale physical protection through myccorhiza and root-hair activities, and (3)chemical interactions with metal ions. The impact of environmental conditions within deeper soil layers on rootC stabilisation appear difficult to assess, but is likely, if anything, to further increase the ratio between the mean residence time of root vs. shootC in soils. Future advances are expected from isotopic studies conducted at the molecular level, which will help unravel the fate of individual shoot and root compounds, such as cutins and suberins, throughout soil profiles.

Clustered regularly interspaced short palindrome repeats (CRISPRs) have spacers of extrachromosomal origin.

Abstract: Numerous prokaryote genomes contain structures known as clustered regularly interspaced short palindromic repeats (CRISPRs), composed of 25-50 bp repeats separated by unique sequence spacers of similar length. CRISPR structures are found in the vicinity of four genes named cas1 to cas4. In silico analysis revealed another cluster of three genes associated with CRISPR structures in many bacterial species, named here as cas1B, cas5 and cas6, and also revealed a certain number of spacers that have homology with extant genes, most frequently derived from phages, but also derived from other extrachromosomal elements. Sequence analysis of CRISPR structures from 24 strains of Streptococcus thermophilus and Streptococcus vestibularis confirmed the homology of spacers with extrachromosomal elements. Phage sensitivity of S. thermophilus strains appears to be correlated with the number of spacers in the CRISPR locus the strain carries. The authors suggest that the spacer elements are the traces of past invasions by extrachromosomal elements, and hypothesize that they provide the cell immunity against phage infection, and more generally foreign DNA expression, by coding an anti-sense RNA. The presence of gene fragments in CRISPR structures and the nuclease motifs in cas genes of both cluster types suggests that CRISPR formation involves a DNA degradation step.

Geneland: a computer package for landscape genetics

Abstract: Geneland is a computer package that allows to make use of georeferenced individual multilocus genotypes for the inference of the number of populations and of the spatial location of genetic discontinuities between those populations. Main assumptions of the method are: (i) the number of populations is unknown and all values are considered a priori equally likely, (ii) populations are spread over areas given by a union of some polygons of unknown location in the spatial domain, (iii) Hardy-Weinberg equilibrium is assumed within each population and (iv) allele frequencies in each population are unknown and treated as random variable either following the so-called Dirichlet model or Falush model. Different algorithms implemented in Geneland to perform inferences are first briefly presented. Then major running steps and outputs (i.e. histogram of number of populations and map of posterior probabilities of population membership) are illustrated from the analysis of a simulated data set, which was also produced by Geneland. (Resume d'auteur)

Electrical resistivity survey in soil science: a review .

Abstract: Electrical resistivity of the soil can be considered as a proxy for the spatial and temporal variability of many other soil physical properties (i.e. structure, water content, or fluid composition). Because the method is non-destructive and very sensitive, it offers a very attractive tool for describing the subsurface properties without digging. It has been already applied in various contexts like: groundwater exploration, landfill and solute transfer delineation, agronomical management by identifying areas of excessive compaction or soil horizon thickness and bedrock depth, and at least assessing the soil hydrological properties. The surveys, depending on the areas heterogeneities can be performed in one-, two- or three-dimensions and also at different scales resolution from the centimetric scale to the regional scale. In this review, based on many electrical resistivity surveys, we expose the theory and the basic principles of the method, we overview the variation of electrical resistivity as a function of soil properties, we listed the main electrical device to performed one-, two- or three-dimensional surveys, and explain the basic principles of the data interpretation. At least, we discuss the main advantages and limits of the method.

Nuclear processing and export of microRNAs in Arabidopsis

Abstract: In mammalian cells, the nuclear export receptor, Exportin 5 (Exp5), exports pre-microRNAs (pre-miRNAs) as well as tRNAs into the cytoplasm. In this study, we examined the function of HASTY (HST), the Arabidopsis ortholog of Exp5, in the biogenesis of miRNAs and tRNAs. In contrast to mammals, we found that miRNAs exist as single-stranded 20- to 21-nt molecules in the nucleus in Arabidopsis. This observation is consistent with previous studies indicating that proteins involved in miRNA biogenesis are located in the nucleus in Arabidopsis. Although miRNAs exist in the nucleus, a majority accumulate in the cytoplasm. Interestingly, loss-of-function mutations in HST reduced the accumulation of most miRNAs but had no effect on the accumulation of tRNAs and endogenous small interfering RNAs, or on transgene silencing. In contrast, a mutation in PAUSED (PSD), the Arabidopsis ortholog of the tRNA export receptor, Exportin-t, interfered with the processing of tRNA-Tyr but did not affect the accumulation or nuclear export of miRNAs. These results demonstrate that HST and PSD do not share RNA cargos in nuclear export and strongly suggest that there are multiple nuclear export pathways for these small RNAs in Arabidopsis.

Polyphenols and prevention of cardiovascular diseases.

Abstract: Purpose of reviewPolyphenols are the most abundant dietary antioxidants and research on their role in the prevention of degenerative diseases has developed quickly over these last few years. This paper reviews the recent studies on the prevention of cardiovascular diseases by polyphenols, focusing o

A spatial statistical model for landscape genetics

Abstract: Landscape genetics is a new discipline that aims to provide information on how landscape and environmental features influence population genetic structure. The first key step of landscape genetics is the spatial detection and location of genetic discontinuities between populations. However, efficient methods for achieving this task are lacking. In this article, we first clarify what is conceptually involved in the spatial modeling of genetic data. Then we describe a Bayesian model implemented in a Markov chain Monte Carlo scheme that allows inference of the location of such genetic discontinuities from individual geo-referenced multilocus genotypes, without a priori knowledge on populational units and limits. In this method, the global set of sampled individuals is modeled as a spatial mixture of panmictic populations, and the spatial organization of populations is modeled through the colored Voronoi tessellation. In addition to spatially locating genetic discontinuities, the method quantifies the amount of spatial dependence in the data set, estimates the number of populations in the studied area, assigns individuals to their population of origin, and detects individual migrants between populations, while taking into account uncertainty on the location of sampled individuals. The performance of the method is evaluated through the analysis of simulated data sets. Results show good performances for standard data sets ( e.g ., 100 individuals genotyped at 10 loci with 10 alleles per locus), with high but also low levels of population differentiation ( e.g ., F ST Gulo gulo ) sampled in the northwestern United States and genotyped at 10 microsatellites.

Modeling Response of Soil Erosion and Runoff to Changes in Precipitation and Cover

Abstract: Global climate has changed over the past century. Precipitation amounts and intensities are increasing. In this study we investigated the response of seven soil erosion models to a few basic precipitation and vegetation related parameters using common data from one humid and one semi-arid watershed. Perturbations were made to inputs for rainfall intensities and amounts, and to ground surface cover and canopy cover. Principal results were that: soil erosion is likely to be more affected than runoff by changes in rainfall and cover, though both are likely to be significantly impacted; percent erosion and runoff will likely change more for each percent change in rainfall intensity and amount than to each percent change in either canopy or ground cover; changes in rainfall amount associated with changes in storm rainfall intensity will likely have a greater impact on runoff and erosion than simply changes in rainfall amount alone; changes in ground cover have a much greater impact on both runoff and erosion than changes in canopy cover alone. The results do not imply that future changes in rainfall will dominate over changes in land use, since land use changes can often be drastic. Given the types of precipitation changes that have occurred over the last century, and the expectations regarding changes over the next century, the results of this study suggest that there is a significant potential for climate change to increase global soil erosion rates unless offsetting conservation measures are taken.

From the discovery of the Malta fever's agent to the discovery of a marine mammal reservoir, brucellosis has continuously been a re-emerging zoonosis

Abstract: Brucellosis is not a sustainable disease in humans. The source of human infection always resides in domestic or wild animal reservoirs. The routes of infection are multiple: food-borne, occupational or recreational, linked to travel and even to bioterrorism. New Brucella strains or species may emerge and existing Brucella species adapt to changing social, cultural, travel and agricultural environment. Brucella melitensis is the most important zoonotic agent, followed by Brucella abortus and Brucella suis. This correlates with the fact that worldwide, the control of bovine brucellosis (due to B. abortus) has been achieved to a greater extent than the control of sheep and goat brucellosis (due to B. melitensis), these latter species being the most important domestic animals in many developing countries. The long duration and high cost of treatment of human brucellosis reduces the efficacy of the therapy. There is no human vaccine for brucellosis and the occurrence of brucellosis is directly linked to the status of animal brucellosis in a region. In this context, the Word Health Organization has defined the development of a human vaccine, besides the implementation of control and eradication programs in animals, as a high priority. The pathogenicity for humans of B. suis biovars 1, 3 and 4 is well established, whereas B. suis biovar 2 seems to be less pathogenic. Indeed, although hunters and pig farmers have repeatably experienced infectious contact with B. suis biovar 2 (found in wild boar and outdoor-rearing pigs in Europe), isolation of B. suis biovar 2 from human samples have only been seldom reported. Marine mammal brucellosis, due to two new proposed Brucella species i.e. B. cetaceae and B. pinnipediae, represents a new zoonotic threat but the pathogenicity for humans of the different Brucella species found in cetaceans and pinnipeds still has to be clearly established.

Review article: bifidobacteria as probiotic agents – physiological effects and clinical benefits

Abstract: Bifidobacteria, naturally present in the dominant colonic microbiota, represent up to 25% of the cultivable faecal bacteria in adults and 80% in infants. As probiotic agents, bifidobacteria have been studied for their efficacy in the prevention and treatment of a broad spectrum of animal and/or human gastrointestinal disorders, such as colonic transit disorders, intestinal infections, and colonic adenomas and cancer. The aim of this review is to focus on the gastrointestinal effects of bifidobacteria as probiotic agents in animal models and man. The traditional use of bifidobacteria in fermented dairy products and the GRAS ('Generally Recognised As Safe') status of certain strains attest to their safety. Some strains, especially Bifidobacterium animalis strain DN-173 010 which has long been used in fermented dairy products, show high gastrointestinal survival capacity and exhibit probiotic properties in the colon. Bifidobacteria are able to prevent or alleviate infectious diarrhoea through their effects on the immune system and resistance to colonization by pathogens. There is some experimental evidence that certain bifidobacteria may actually protect the host from carcinogenic activity of intestinal flora. Bifidobacteria may exert protective intestinal actions through various mechanisms, and represent promising advances in the fields of prophylaxis and therapy.

Expansion of geographic range in the pine processionary moth caused by increased winter temperatures

Abstract: Global warming is predicted to cause distributional changes in organisms whose geographic ranges are controlled by temperature. We report a recent latitudinal and altitudinal expansion of the pine processionary moth, Thaumetopoea pityocampa, whose larvae build silk nests and feed on pine foliage in the winter. In north-central France (Paris Basin), its range boundary has shifted by 87 km northwards between 1972 and 2004; in northern Italy (Alps), an altitudinal shift of 110–230 m upwards occurred between 1975 and 2004. By experimentally linking winter temperature, feeding activity, and survival of T. pityocampa larvae, we attribute the expansions to increased winter survival due to a warming trend over the past three decades. In the laboratory we determined the minimum nest and night air temperatures required for larval feeding and developed a mechanistic model based on these temperature thresholds. We tested the model in a translocation experiment that employed natural temperature gradients as spatial an...

The minerals of milk.

Abstract: The salt of milk constitutes a small part of milk (8-9 g.L(-1)); this fraction contains calcium, magnesium, sodium and potassium for the main cations and inorganic phosphate, citrate and chloride for the main anions. In milk, these ions are more or less associated between themselves and with proteins. Depending on the type of ion, they are diffusible (cases of sodium, potassium and chloride) or partially associated with casein molecules (cases of calcium, magnesium, phosphate and citrate), to form large colloidal particles called casein micelles. Today, our knowledge and understanding concerning this fraction is relatively complete. In this review, the different models explaining (i) the nature and distribution of these minerals (especially calcium phosphate) in both fractions of milk and (ii) their behaviour in different physico-chemical conditions, are discussed.

The Tomato Aux/IAA Transcription Factor IAA9 Is Involved in Fruit Development and Leaf Morphogenesis

Abstract: Auxin/indole-3-acetic acid (Aux/IAA) proteins are transcriptional regulators that mediate many aspects of plant responses to auxin. While functions of most Aux/IAAs have been defined mainly by gain-of-function mutant alleles in Arabidopsis thaliana, phenotypes associated with loss-of-function mutations have been scarce and subtle. We report here that the downregulation of IAA9, a tomato (Solanum lycopersicum) gene from a distinct subfamily of Aux/IAA genes, results in a pleiotropic phenotype, consistent with its ubiquitous expression pattern. IAA9-inhibited lines have simple leaves instead of wild-type compound leaves, and fruit development is triggered before fertilization, giving rise to parthenocarpy. This indicates that IAA9 is a key mediator of leaf morphogenesis and fruit set. In addition, antisense plants displayed auxin-related growth alterations, including enhanced hypocotyl/stem elongation, increased leaf vascularization, and reduced apical dominance. Auxin dose–response assays revealed that IAA9 downregulated lines were hypersensitive to auxin, although the only early auxin-responsive gene that was found to be upregulated in the antisense lines was IAA3. The activity of the IAA3 promoter was stimulated in the IAA9 antisense genetic background, indicating that IAA9 acts in planta as a transcriptional repressor of auxin signaling. While no mutation in any member of subfamily IV has been reported to date, the phenotypes associated with the downregulation of IAA9 reveal distinct and novel roles for members of the Aux/IAA gene family.

Arbuscular Mycorrhizal Fungi Elicit a Novel Intracellular Apparatus in Medicago truncatula Root Epidermal Cells before Infection

Abstract: The penetration of arbuscular mycorrhizal (AM) fungi through the outermost root tissues of the host plant is a critical step in root colonization, ultimately leading to the establishment of this ecologically important endosymbiotic association. To evaluate the role played by the host plant during AM infection, we have studied in vivo cellular dynamics within Medicago truncatula root epidermal cells using green fluorescent protein labeling of both the plant cytoskeleton and the endoplasmic reticulum. Targeting roots with Gigaspora hyphae has revealed that, before infection, the epidermal cell assembles a transient intracellular structure with a novel cytoskeletal organization. Real-time monitoring suggests that this structure, designated the prepenetration apparatus (PPA), plays a central role in the elaboration of the apoplastic interface compartment through which the fungus grows when it penetrates the cell lumen. The importance of the PPA is underlined by the fact that M. truncatula dmi (for doesn't make infections) mutants fail to assemble this structure. Furthermore, PPA formation in the epidermis can be correlated with DMI-dependent transcriptional activation of the Medicago early nodulin gene ENOD11. These findings demonstrate how the host plant prepares and organizes AM infection of the root, and both the plant-fungal signaling mechanisms involved and the mechanistic parallels with Rhizobium infection in legume root hairs are discussed.

Is Q Fever an emerging or re-emerging zoonosis?

Abstract: Q fever is a zoonotic disease considered as emerging or re-emerging in many countries. It is caused by Coxiella burnetii, a bacterium developing spore-like forms that are highly resistant to the environment. The most common animal reservoirs are livestock and the main source of infection is by inhalation of contaminated aerosols. Although the culture process for Coxiella is laborious, advances on the knowledge of the life cycle of the bacterium have been made. New tools have been developed to (i) improve the diagnosis of Q fever in humans and animals, and especially animal shedders, (ii) perform epidemiological studies, and (iii) prevent the disease through the use of vaccines. This review summarizes the state of the knowledge on the bacteriology and clinical manifestations of Q fever as well as its diagnosis, epidemiology, treatment and prevention in order to understand what factors are responsible for its emergence or re-emergence.