Efficiency of the traditional practice of traps to stimulate black truffle production, and its ecological mechanisms.

The black truffle Tuber melanosporum was disseminated all over the world, propelled by the development of a wide variety of empirical practices. A widespread practice, called 'truffle trap', consists of placing pieces of truffles into excavations dug under host trees, and of collecting truffle in these traps in the next years. This research aims at (1) evaluating the effect of this practice on fruitbody production based on the analysis of 9924 truffle traps installed in 11 orchards across T. melanosporum native area in France and (2) exploring the mechanisms involved in fruitbody emergence using traps where the genotypes of introduced truffles were compared with those of fruitbodies collected in the same traps. We confirmed that truffle traps provide a major and highly variable part of truffle ground production, representing up to 89% of the collected fruitbodies. We evidenced a genetic link between introduced spores and collected fruitbodies, and then demonstrated that truffle growers provide paternal partners for mating with local maternal mycelia. We also highlighted that soil disturbance stimulate the vegetative development of established maternal mycelia. This research supports that a widely used traditional practice enhances fruitbody production by shaping favorable conditions and providing sexual partners required for fruiting.

Glycation stimulates cutaneous monocyte differentiation in reconstructed skin in vitro.

Glycation reaction is a recognized mechanism related to chronological aging. Previous investigations in cutaneous biology have considered the effect of glycation on the dermal matrix molecules, involved in tissue stiffening during skin aging. However, little is known about a possible direct effect of glycation upon cell differentiation. To address such issue, the effect of glycation has been re-investigated in a reconstructed skin model integrating monocytes that are cells capable of differentiating according to different pathways. The results showed that, in the absence of glycation, a small number of these CD45+ cells could differentiate either into dendritic-like cells (DC-SIGN+, BDC1a+, DC-LAMP+) or macrophage- like cells (CD14+, CD68+, CD163+) whereas, with glycation, the number of monocytes, dendritic cells, macrophage-like cells were found surprisingly increased. In-vivo our results showed also that dendritic and macrophage-like cells were increased and suggest a possible link with the age-dependent glycation level in the skin. In addition, we found that, unlike fibroblasts incorporated in the reconstructed skin, these cells expressed specific receptors for AGEs (RAGE and SRA). Taken altogether, our data show that cells of the monocyte lineage, in the presence of AGEs, can differentiate into dendritic or macrophage-like cells and could lead to a micro inflammatory environment.

Resampling: An improvement of importance sampling in varying population size models.

Sequential importance sampling algorithms have been defined to estimate likelihoods in models of ancestral population processes. However, these algorithms are based on features of the models with constant population size, and become inefficient when the population size varies in time, making likelihood-based inferences difficult in many demographic situations. In this work, we modify a previous sequential importance sampling algorithm to improve the efficiency of the likelihood estimation. Our procedure is still based on features of the model with constant size, but uses a resampling technique with a new resampling probability distribution depending on the pairwise composite likelihood. We tested our algorithm, called sequential importance sampling with resampling (SISR) on simulated data sets under different demographic cases. In most cases, we divided the computational cost by two for the same accuracy of inference, in some cases even by one hundred. This study provides the first assessment of the impact of such resampling techniques on parameter inference using sequential importance sampling, and extends the range of situations where likelihood inferences can be easily performed.

How the truffle got its mate: insights from genetic structure in spontaneous and planted Mediterranean populations of Tuber melanosporum.

The life cycles and dispersal of edible fungi are still poorly known, thus limiting our understanding of their evolution and domestication. The prized Tuber melanosporum produces fruitbodies (fleshy organs where meiospores mature) gathered in natural, spontaneously inoculated forests or harvested in plantations of nursery-inoculated trees. Yet, how fruitbodies are formed remains unclear, thus limiting yields, and how current domestication attempts affect population genetic structure is overlooked. Fruitbodies result from mating between two haploid individuals: the maternal parent forms the flesh and the meiospores, while the paternal parent only contributes to the meiospores. We analyzed the genetic diversity of T. melanosporum comparatively in spontaneous forests vs. plantations, using SSR polymorphism of 950 samples from South-East France. All populations displayed strong genetic isolation by distance at the metric scale, possibly due to animal dispersal, meiospore persistence in soil, and/or exclusion of unrelated individuals by vegetative incompatibility. High inbreeding was consistently found, suggesting that parents often develop from meiospores produced by the same fruitbody. Unlike maternal genotypes, paternal mycelia contributed to few fruitbodies each, did not persist over years, and were undetectable on tree mycorrhizae. Thus, we postulate that germlings from the soil spore bank act as paternal partners. Paternal genetic diversity and outbreeding were higher in plantations than in spontaneous truffle-grounds, perhaps because truffle growers disperse fruitbodies to maintain inoculation in plantations. However, planted and spontaneous populations were not genetically isolated, so that T. melanosporum illustrates an early step of domestication where genetic structure remains little affected.

IL-1beta mediates MMP secretion and IL-1beta neosynthesis via upregulation of p22(phox) and NOX4 activity in human articular chondrocytes.

OBJECTIVES: Osteoarthritis (OA) is characterized by a progressive alteration of the biochemical properties of the articular cartilage. Inflammation plays a major role in OA, particularly through the cytokine Interleukine-1ß, promoting reactive oxygen species (ROS) generation and matrix metalloproteinases (MMP) synthesis by the chondrocytes, orchestrating matrix proteolysis. NADPH oxidases (NOX) are membrane enzymes dedicated to the production of ROS. Role of oxidative stress is well established in OA; however, contribution of NOX in this process is still poorly documented. In this study, we addressed the role of NOX in primary human articular chondrocytes (HAC) upon inflammatory conditions--namely IL-1ß and OA. DESIGN: HAC were collected from patients undergoing hip surgery. Chondrocytes were treated with IL-1ß and NOX inhibitors Diphenylene Iodonium, GKT136901, Tiron and Heme oxygenase-1 before MMP expression and NOX activity assessment. Finally, NOX4 expression was compared between OA and non OA parts of hip cartilage (n = 14). RESULTS: This study establishes for the first time in human that NOX4 is the main NOX isoform expressed in chondrocytes. We found a significant upregulation of NOX4 mRNA in OA chondrocytes. Expression of NOX4/p22(phox) as well as ROS production is enhanced by IL-1ß. On the other hand, the use of NOX4 inhibitors decreased IL-1ß-induced collagenase synthesis by chondrocytes. Moreover, our study support the existence of a redox dependant loop sustaining pro-catabolic pathways induced by IL-1ß. CONCLUSIONS: This study points out NOX4 as a new putative target in OA and suggests that NOX-targeted therapies could be of interest for the causal treatment of the pathology.

Stability of a flow down an incline with respect to two-dimensional and three-dimensional disturbances for Newtonian and non-Newtonian fluids.

Squire's theorem, which states that the two-dimensional instabilities are more dangerous than the three-dimensional instabilities, is revisited here for a flow down an incline, making use of numerical stability analysis and Squire relationships when available. For flows down inclined planes, one of these Squire relationships involves the slopes of the inclines. This means that the Reynolds number associated with a two-dimensional wave can be shown to be smaller than that for an oblique wave, but this oblique wave being obtained for a larger slope. Physically speaking, this prevents the possibility to directly compare the thresholds at a given slope. The goal of the paper is then to reach a conclusion about the predominance or not of two-dimensional instabilities at a given slope, which is of practical interest for industrial or environmental applications. For a Newtonian fluid, it is shown that, for a given slope, oblique wave instabilities are never the dominant instabilities. Both the Squire relationships and the particular variations of the two-dimensional wave critical curve with regard to the inclination angle are involved in the proof of this result. For a generalized Newtonian fluid, a similar result can only be obtained for a reduced stability problem where some term connected to the perturbation of viscosity is neglected. For the general stability problem, however, no Squire relationships can be derived and the numerical stability results show that the thresholds for oblique waves can be smaller than the thresholds for two-dimensional waves at a given slope, particularly for large obliquity angles and strong shear-thinning behaviors. The conclusion is then completely different in that case: the dominant instability for a generalized Newtonian fluid flowing down an inclined plane with a given slope can be three dimensional.

Stability of two-layer shear-thinning film flows.

The stability of a two-layer film flow of non-Newtonian fluids is studied with a linear temporal approach. Shear-thinning fluids are considered, which follow the four-parameter inelastic Carreau model. A modified Orr-Sommerfeld equation system is obtained, which is solved by using a spectral Tau collocation method based on Chebyshev polynomials. The effects of density and viscosity stratification are considered, as well as the influence of the shear-thinning properties of the fluid. It is found that, when the viscosity is stronger in the upper layer, the base flow and the stability properties are almost not influenced by the change of the shear-thinning properties in this upper layer. In the other situations, the shear-thinning properties have an influence on the different instabilities, the long-wave surface instability and the short- and long-wave interface instabilities.

Much ado about nothing: Nowak et al.'s charge against inclusive fitness theory.

In a recent article, Nowak et al. claim that the mathematical basis of inclusive fitness theory does not stand to scrunity and to have found an alternative explanation for eusociality. We show that these claims are based on false premises, many of which have been exposed more than 25 years ago, such as misrepresentations of the basic components of inclusive fitness and fallacious distinctions between individual fitness and inclusive fitness. Moreover, some limitations ascribed to inclusive fitness are actually limitations of current evolutionary theory, for which Nowak et al. propose no new solution. Likewise, their assertedly 'common sense' empirical alternative to estimating inclusive fitness is not applicable in cases of interest. Finally, their eusociality model merely confirms the importance of all the components of inclusive fitness. We conclude by discussing how rhetorical devices and editorial practices can impede scientific endeavours.

Inferences on pathogenic fungus population structures from microsatellite data: new insights from spatial genetics approaches.

Landscape genetics, which combines population genetics, landscape ecology and spatial statistics, has emerged recently as a new discipline that can be used to assess how landscape features or environmental variables can influence gene flow and spatial genetic variation. We applied this approach to the invasive plant pathogenic fungus Mycosphaerella fijiensis, which causes black leaf streak disease of banana. Around 880 isolates were sampled within a 50 × 50 km area located in a fragmented banana production zone in Cameroon that includes several potential physical barriers to gene flow. Two clustering algorithms and a new F(ST) -based procedure were applied to define the number of genetic entities and their spatial domain without a priori assumptions. Two populations were clearly delineated, and the genetic discontinuity appeared sharp but asymmetric. Interestingly, no landscape features matched this genetic discontinuity, and no isolation by distance (IBD) was found within populations. Our results suggest that the genetic structure observed in this production area reflects the recent history of M. fijiensis expansion in Cameroon rather than resulting from contemporary gene flow. Finally, we discuss the influence of the suspected high effective population size for such an organism on (i) the absence of an IBD signal, (ii) the characterization of contemporary gene-flow events through assignation methods of analysis and (iii) the evolution of the genetic discontinuity detected in this study.

Effective size of the hierarchically structured populations of the agent of malaria: a coalescent-based model.

Using the coalescence theory, we derived a simple expression for the asymptotic inbreeding effective population size of Plasmodium falciparum, the most malignant agent of malaria, in relationship to F-statistics at different hierarchical levels. We consider the effective size of malaria parasites, both for the intrinsic interest of the result for the study of this medically important organism and as an example illustrating general arguments that should clarify effective size calculations in a wide range of organisms with complex life cycles and a hierarchical population structure. We consider in this study a model with four hierarchical levels (villages, oocyst infrapopulations, oocysts within infrapopulations and the oocyst). The derived expression is applicable to both island and isolation by distance models and is a function of three F-statistics: the genetic differentiation among villages (F(VT)), the genetic differentiation among oocyst infrapopulations (F(MV)) and, finally, the departure from panmixia (F(IM)) within oocyst infrapopulations. The logic of the derivation of effective size presented in this study is applicable to any organism showing the same levels of subdivision.

Isolation by distance in a continuous population under stochastic demographic fluctuations.

The local density of individuals is seldom uniform in space and time within natural populations. Yet, formal approaches to the process of isolation by distance in continuous populations have encountered analytical difficulties in describing genetic structuring with demographic heterogeneities, usually disregarding local correlations in the movement and reproduction of genes. We formulate exact recursions for probabilities of identity in continuous populations, from which we deduce definitions of effective dispersal () and effective density (D(e)) that generalize results relating spatial genetic structure, dispersal and density in lattice models. The latter claim is checked in simulations where estimates of effective parameters obtained from demographic information are compared with estimates derived from spatial genetic patterns in a plant population evolving in a heterogeneous and dynamic habitat. The simulations further suggest that increasing spatio-temporal correlations in local density reduce and generally decrease the product , with dispersal kurtosis influencing their sensitivity to density fluctuations. As in the lattice model, the expected relationship between the product and the genetic structure statistic a(r) holds under fluctuating density, irrespective of dispersal kurtosis. The product D sigma(2) between observed census density and the observed dispersal rate over one generation will generally be an upwardly biased (up to 400% in simulations) estimator of in populations distributed in spatially aggregated habitats.

Strong effects of heterosis on the evolution of dispersal rates.

When dispersal is limited, crosses between different regions may generate progeny of higher fitness than crosses within regions, due to the fact that individuals from the same region are more likely to share the same recessive deleterious alleles. This phenomenon (termed heterosis) generates a selective force favouring dispersal; however, the importance of heterosis on dispersal evolution has been a subject for debate. In this paper, we use computer simulations representing deleterious mutations occurring over a whole genome (of arbitrary map length R) to explore the magnitude of heterosis, and its effect on the evolution of dispersal. These results show that heterosis may have important effects on dispersal when it is in the upper range of values observed in natural populations, which occurs in our simulations when the genomic deleterious mutation rate U is also in the upper range of observed values. Comparing the results with extrapolations from an analytical two-locus model indicates that the effect of heterosis is mainly driven by pairwise associations between the locus affecting dispersal and selected loci when U is not too high (roughly, U < 0.5), whereas higher order associations become important for higher values of U.

Is the early-onset torsion dystonia (EOTD) linked to TOR1A gene as frequent as expected in France?

Early onset torsion dystonia are rare movement disorders. Molecular defect is known for only a subgroup, consisting of a unique and recurrent mutation in the TOR1A gene. We undertook a nationwide census of French TOR1A-mutation carriers and the assessment of clinical associated signs. Overall, 53 index cases and 104 relatives were studied and haplotypes linked to the mutation constructed. The previously reported Ashkenazi-Jewish haplotype was found in 11 families with the remainder carrying distinct haplotypes suggesting independent mutation events. This study demonstrates the scarcity of this disease in France with estimated disease frequency of 0.13:100,000 and mutation frequency of 0.17:100,000.

Migration load in plants: role of pollen and seed dispersal in heterogeneous landscapes.

Evolution of local adaptation depends critically on the level of gene flow, which, in plants, can be due to either pollen or seed dispersal. Using analytical predictions and individual-centred simulations, we investigate the specific influence of seed and pollen dispersal on local adaptation in plant populations growing in patchy heterogeneous landscapes. We study the evolution of a polygenic trait subject to stabilizing selection within populations, but divergent selection between populations. Deviations from linkage equilibrium and Hardy-Weinberg equilibrium make different contributions to genotypic variance depending on the dispersal mode. Local genotypic variance, differentiation between populations and genetic load vary with the rate of gene flow but are similar for seed and pollen dispersal, unless the landscape is very heterogeneous. In this case, genetic load is higher in the case of pollen dispersal, which appears to be due to differences in the distribution of genotypic values before selection.

"Clonal" population structure of the malaria agent Plasmodium falciparum in high-infection regions.

The population genetic structure of Plasmodium falciparum, the agent of malignant malaria, has been shown to be predominantly "clonal" (i.e., highly inbred) in regions of low infectivity; in high-infectivity regions, it is often thought to be panmictic, or nearly so, although there is little supporting evidence for this. The matter can be settled by investigating the parasite's genetic makeup in the midgut oocysts of the mosquito vector, where the products of meiosis can directly be observed. The developmental stages of P. falciparum are haploid, except in the oocysts of infected mosquito vectors, where two gametes fuse, diploidy occurs, and meiosis ensues. We have investigated genetic polymorphisms at seven microsatellite loci located on five chromosomes by assaying 613 oocysts in 145 mosquitoes sampled from 11 localities of Kenya, where malignant malaria is perennial and intense. There is considerable allelic variation, 16.3 +/- 2.1 alleles per locus, and considerable inbreeding, approximately 50% on the average. The inbreeding is caused by selfing (approximately 25%) and nonrandom genotype distribution of oocysts among mosquito guts (35%). The observed frequency of heterozygotes is 0.43 +/- 0.03; the expected frequency, assuming random mating, is 0.80 +/- 0.05. Linkage disequilibrium is statistically significant for all 21 pairwise comparisons between loci, even though 19 comparisons are between loci in different chromosomes, which is consistent with strong deviation from panmixia and the consequent reproduction of genomes as clones, without recombination between gene loci. This is of considerable evolutionary significance and of epidemiological consequence, concerning the spread of multilocus drug and vaccine resistance.

Genetic isolation between two sympatric host plant races of the European corn borer, Ostrinia nubilalis Hubner. II: assortative mating and host-plant preferences for oviposition.

The European corn borer, Ostrinia nubilalis Hubner, colonized maize (Zea mays L.) after its introduction into Europe about 500 years ago and is now considered one of the main pests of this crop. In northern France, two sympatric host races have been described: one feeding on maize and the other on mugwort (Artemisia vulgaris L.) and hop (Humulus lupulus L.). In a previous study, we showed that mating between the two races may be impeded by differences in the timing of moth emergence and in the composition of the sex pheromone produced by the females. In this study, we further investigated the genetic isolation of these two races using strains from the maize (Z strain) and mugwort (E strain) races selected for diagnostic alleles at two allozyme loci. In a cage containing maize and mugwort plants and located in natural conditions, mating between individuals of the same strain occurred more often than mating between males and females of the E and Z strains. In particular, we obtained no evidence for crosses between Z females and E males. We also found that females of the Z strain laid their eggs almost exclusively on maize, whereas females of the E strain laid their eggs preferentially, but not exclusively, on mugwort. These results suggest that the genetic differentiation between the two host races may also be favored by host-plant preference, one of the first steps toward sympatric speciation.

Modelling the spatial configuration of refuges for a sustainable control of pests: a case study of Bt cotton.

The 'high-dose-refuge' (HDR) strategy is widely recommended by the biotechnology industry and regulatory authorities to delay pest adaptation to transgenic crops that produce Bacillus thuringiensis (Bt) toxins. This involves cultivating nontoxic plants (refuges) in close proximity to crops producing a high dose of Bt toxin. The principal cost associated with this strategy is due to yield losses suffered by farmers growing unprotected, refuge plants. Using a population genetic model of selection in a spatially heterogeneous environment, we show the existence of an optimal spatial configuration of refuges that could prevent the evolution of resistance whilst reducing the use of costly refuges. In particular, the sustainable control of pests is achievable with the use of more aggregated distributions of nontransgenic plants and transgenic plants producing lower doses of toxin. The HDR strategy is thus suboptimal within the context of sustainable agricultural development.

Effective size in simple metapopulation models.

A coalescent argument is used to derive the effective size in simple models with recurrent local extinctions. Several alternative methods of derivation of this result are given and compared to earlier analyses of this problem. The different methods described in this paper all give the same result, which differs from earlier ones. For two published sets of estimates of demographic parameters, metapopulation structure appears to result in a moderate reduction of effective size relative to total adult population size.