Finding Single Copy Genes Out of Sequenced Genomes for Multilocus Phylogenetics in Non-Model Fungi

Historically, fungal multigene phylogenies have been reconstructed based on a small number of commonly used genes. The availability of complete fungal genomes has given rise to a new wave of model organisms that provide large number of genes potentially useful for building robust gene genealogies. Unfortunately, cross-utilization of these resources to study phylogenetic relationships in the vast majority of non-model fungi (i.e. “orphan” species) remains an unexamined question. To address this problem, we developed a method coupled with a program named “PHYLORPH” (PHYLogenetic markers for ORPHans). The method screens fungal genomic databases (107 fungal genomes fully sequenced) for single copy genes that might be easily transferable and well suited for studies at low taxonomic levels (for example, in species complexes) in non-model fungal species. To maximize the chance to target genes with informative regions, PHYLORPH displays a graphical evaluation system based on the estimation of nucleotide divergence relative to substitution type. The usefulness of this approach was tested by developing markers in four non-model groups of fungal pathogens. For each pathogen considered, 7 to 40% of the 10–15 best candidate genes proposed by PHYLORPH yielded sequencing success. Levels of polymorphism of these genes were compared with those obtained for some genes traditionally used to build fungal phylogenies (e.g. nuclear rDNA, β-tubulin, γ-actin, Elongation factor EF-1α). These genes were ranked among the best-performing ones and resolved accurately taxa relationships in each of the four non-model groups of fungi considered. We envision that PHYLORPH will constitute a useful tool for obtaining new and accurate phylogenetic markers to resolve relationships between closely related non-model fungal species

QUBIC: A Fizeau Interferometer Targeting Primordial B-Modes

Q and U Bolometric Interferometer for Cosmology (QUBIC) is a Fizeau interferometer sensitive to linear polarisation, to be deployed at the Antarctic station of Dome C. This experiment in its final configuration will be operated at 97, 150 and 220 GHz and is intended to target CMB primordial B-modes in a multipole window 20<ℓ<150. A sensitivity of r=0.05 (95 % CL) can be reached by the first module alone, after 2 years of operation. Here we review in particular its working principles, and we show how the QUBIC interferometric configuration can be considered equivalent to a pupil-plane filtered imaging system. In this context, we show how our instrument can be self-calibrated. Finally, we conclude by showing an overview of the first dual-band module (150/220 GHz), which will serve also as a demonstrator for the subsequent units, and review the technological choices we made for each subsystem, with particular emphasis on the detection system

Influence of aroma compounds on the mechanical properties of pectin gels

International audienc

Flavor release and rheology behavior of straberry fatfree stirred yogurt during storage

International audienc

Flavor release and rheology behavior of straberry fatfree stirred yogurt during storage

International audienc

Effets des constituants d'une émulsion modèle sur la germination et la croissance de spores bactériennes

International audienceIn foodstuffs, interactions between spores, inhibitors and food components may occur (i.e. physicochemical interactions and/or physical constraints). Then, the objective of this study was to understand such phenomena using a model emulsion as a microbial medium to improve, in the long term, bacterial spores control. Emulsions were prepared with mineral oil mixed with distilled water using sonication and were stabilized by Tween 80 and Span 80. Oil content was either 35 % (v/v) or 50 % (v/v) and each emulsion was studied in the presence of organic acid (acetic, lactic or hexanoic) at two pH levels (5.5 and 6). Bacillus weihenstephanensis (strain KBAB4) was used as a model of a high prevalence food spoiler. It was enumerated by a most probable number assay in microplate. Growth in a Bioscreen® and flow cytometry were used to quantify antimicrobial effect on spores and cells. Self-diffusion coefficients of emulsion components were measured by Pulsed Field Gradient-Nuclear Magnetic Resonance (PFG-NMR). Main results are that the antimicrobial activity depends on oil volume ratio. In the same conditions, spores germinated/grew by more than 25% more in the 50/50 O/W emulsion than in the 35/65. This could be explained by a Tween 80 antimicrobial effect, dependant on pH, and by the distribution of organic acids between oil and water phases. Tween 80 effect has been hardly described in the literature and this study will be continued on spores of different species

Analyses par PFG-RMN de la diffusion d'acides organiques dans des emulsions huile/eau

International audienceOrganic acids are widely used as hurdles to inactivate foodborne pathogens or spoilage microorganisms in food industry. Their inhibitory effect on bacterial spores is based on their lipophilic character by affecting membrane integrity of spores (van Melis et al., 2012). Yet, the composition and the structure of foodstuffs have also an effect on the microorganism growth. Thus, with the aim of increasing product shelf-life and improve their safety, it is also important to understand the relationships between food structure/composition and inhibitors. Our objective was to evaluate the mobility and the partition of organic acids in model emulsions by measuring their self-diffusion coefficients using Pulsed Field Gradient-Nuclear Magnetic Resonance (PFG-NMR) spectroscopy. Emulsions were prepared with mineral oil mixed with distilled water using sonication, and were stabilized by Tween80 and Span80. Oil content was either 35 % (v/v) or 50 % (v/v) and each emulsion was studied in the presence of organic acid (acetic, lactic and hexanoic) at two pH levels (pH 5.5 and pH 6, reached by organic acid addition). Quality and stability of emulsions were characterized by multiple light scattering. Results showed that whatever the pH of the emulsions, the diffusion coefficient of the organic acids decreased when the oil/water ratio increased : rise of pH increased amount of undissociated forms (-COOH) which may be trapped in oil phase, and/or it may also occur a structure effect on diffusion coefficient. Furthermore, in 35 % (v/v) oil emulsion at pH 5.5 hexanoic acid showed lower values of D/D0 with pH decrease in comparison to AA and LA. Thus, specificity in the diffusion among organic acids was observed due to their different solubility in oil phase which depends on both pka and logP. Finally, in this latter emulsion, fraction of HA showed a completely restricted mean displacement and therefore may be trapped in oil droplets

Fraction volumique de la phase dispersée, acides organiques et Tween80 dans une émulsion modèle: effet sur la germination et la croissance de spores de bactéries weihenstephanensis KBAB4

International audienceIn foodstuffs, physico-chemical interactions and/or physical constraints between spores, inhibitors and food components may exist. Thus, the objective of this study was to investigate such interactions using a model emulsion as a microbial medium in order to improve bacterial spore control with better knowledge of the interactions in the formulation.Emulsions were prepared with hexadecane mixed with nutrient broth using sonication and were stabilized by Tween 80 and Span 80. The hexadecane ratio was either 35% (v/v) or 50% (v/v) and each emulsion was studied in the presence of organic acid (acetic, lactic or hexanoic) at two pH levels (5.5 and 6). Self-diffusion coefficients of emulsion components and the organic acids were measured by Pulsed Field Gradient-Nuclear Magnetic Resonance (PFG-NMR). The inhibition effect on the spore germination and cell growth of Bacillus weihenstephanensis KBAB4 was characterized by the measure of the probability of growth using the most probable number methodology, and the measure of the time taken for the cells to germinate and grow using a single cell Bioscreen® method and using flow cytometry. The inhibition of spore germination and growth in the model emulsion depended on the dispersed phase volume fraction and the pH value. The effect of the dispersed phase volume fraction was due to a combination of (i) the lipophilicity of the biocide, hexanoic acid, that may have had an impact on the distribution of organic acid between hexadecane and the aqueous phases and (ii) the antimicrobial activity of the emulsifier Tween 80 detected at the acidic pH value. The interface phenomena seemed to have a major influence. Future work will focus on the exploration of these phenomena at the interface