Fungal Species Diversity in French Bread Sourdoughs Made of Organic Wheat Flour

Microbial communities are essential for the maintenance and functioning of ecosystems, including fermented food ecosystems. The analysis of food microbial communities is mainly focused on lactic acid bacteria (LAB), while yeast diversity is less understood. Here, we describe the fungal diversity of a typical food fermented product, sourdough bread. The species diversity of 14 sourdoughs collected from bakeries located all over France was analyzed. Bakeries were chosen to represent diverse bakery practices and included bakers and farmer-bakers. Both non-culture-based (pyrosequencing of Internal Transcribed Spacer 1 amplicons) and culture-based methods were used. While both identification methods were in agreement regarding the dominant yeast species of each sourdough, the ITS1 metabarcoding analysis identified an increased number of fungal species in sourdough communities. Two third of the identified sequences obtained from sourdoughs were Saccharomycetales, mostly in the Kazachstania genus. No Saccharomycetales species was shared by all the sourdoughs, whereas five other fungal species, mainly known plant pathogens, were found in all sourdoughs. Interestingly, Saccharomyces cerevisiae, known as “baker’s yeast,” was identified as the dominant species in only one sourdough. By contrast, five Kazachstania species were identified as the dominant sourdough species, including one recently described Kazachstania species, Kazachstania saulgeensis and an undescribed Kazachstania sp. Sourdoughs from farmer-bakers harbored Kazachstania bulderi, Kazachstania unispora and two newly described Kazachstania species, while sourdough from bakers mostly carried Kazachstania humilis as the dominant species. Such yeast diversity has not been found in sourdoughs before, highlighting the need to maintain different traditional food practices to conserve microbial diversity

School as a Zero-Sum Game between Boys and Girls: Gender differences in perceptions

Several studies have reported the existence of a gender gap in academic achievement, such as girls have better grades than boys, who are more likely to experience difficulties (Voyer & Voyer, 2014). The present study aims to investigate students’ perceptions of the actual pattern of achievement by assessing their zero-sum beliefs (ZsB)—that is, their tendency to perceive school as a zero-sum game between boys and girls. Based on previous studies showing that a threatening intergroup context influences men’s perception of gender relations, we hypothesized that boys, but not girls, are more likely to endorse gender ZsB regarding school in a threatening academic context compared to less threatening contexts. The academic context was manipulated using short texts emphasizing either boys’ or girls’ academic achievement. As expected, the threatening intergroup comparison context led boys (but not girls) to endorse greater ZsB. Implications for achievement-related outcomes and gender relations are discussed

Caractérisation par microscopie à force atomique des arrangements protéine/sucre impliquant la lectine PA-IL de la bactérie pseudomonas aeruginosa

La bactérie Pseudomonas aeruginosa est un pathogène opportuniste responsable de graves infections chez les personnes affaiblies immunitairement. Présentant des souches résistantes aux antibiotiques, une nouvelle approche thérapeutique est en cours de développement avec pour objectif l inhibition des facteurs de virulence de la bactérie. Lors de son processus d infection, le pathogène utilise les lectines pour reconnaître et se lier de manière spécifique aux glycoconjugués des cellules-hôtes en formant une interaction lectine/glycoconjugué. Plus particulièrement, la lectine PA-IL, spécifique du galactose, a été étudiée. A l aide de glycomimétique, il semble possible de bloquer l action de la lectine en créant une interaction lectine/glycomimétique. Pour développer cette approche, de nombreux glycocluster sont donc été élaborés et leur affinité avec la lectine PA-IL a été évaluée par plusieurs méthodes de caractérisation (SPR, HIA, ELLA, puce à sucre, ).Dans ce projet de thèse, nous avons cherché à visualiser par microscopie à force atomique (AFM) l arrangement des complexes lectine PA-IL/glycocluster formés pour trois glycoclusters différents. Nous avons ainsi pu montrer l influence du cœur du glycocluster et des bras-espaceurs sur l arrangement des complexes. Suivant le glycocluster, l arrangement prend la forme de filaments 1D,de structures dentelées avec des bras sinueux ou encore de larges structures compactes. Dans le cas des filaments, la résolution de nos images AFM nous a permis d identifier les lectines à l intérieur même de la structure filaire. Nous avons aussi démontré, en observant les lectines seules, l existence d une interaction lectine/lectine. De plus, des expériences ont été menées pour déterminer les conditions expérimentales appropriées à leur observation à l air et en milieu liquide.The bacterium P. aeruginosa is an opportunistic pathogen responsible for serious infections in immunocompromised patients. It also develops some strains resistant to antibiotics. A new approach is developed to inhibit virulence factors of the bacterium. During the process of infection, the pathogen uses lectins to recognize and bind specifically to glycoconjugates of the host cells forming alectin/glycoconjugate complex. Particularly, the lectin PA-IL, specific to galactose, was studied. Using glycomimetics, it seems possible to block the action of the lectin by creating lectin/glycomimetic interaction. To develop this approach, many glycoclusters were designed and their affinity with lectin PA-IL was evaluated by various characterization techniques (SPR, HIA, ELLA, microarrays, ).In this thesis project, we have tried to visualize by Atomic Force Microscopy (AFM) the arrangement of lectin PA-IL/glycocluster complexes with three different glycoclusters. Our results show the influence of the glycocluster core and the linker on the arrangement of complexes. Depending on glycocluster, the arrangement takes the form of 1D filaments, 2D "pinked" structures with sinuous branches or large compact structures. In the case of filaments, the resolution of AFM images allows us to identify lectins along the filament. We also demonstrated the existence of lectin/lectin interactions at high concentration of lectin. In addition, some experiments were performed to determine sample preparation techniques to observe lectins in air and in liquid.LYON-Ecole Centrale (690812301) / SudocSudocFranceF

“Ant” and “Grasshopper” Life-History Strategies in Saccharomyces cerevisiae

From the evolutionary and ecological points of view, it is essential to distinguish between the genetic and environmental components of the variability of life-history traits and of their trade-offs. Among the factors affecting this variability, the resource uptake rate deserves particular attention, because it depends on both the environment and the genetic background of the individuals. In order to unravel the bases of the life-history strategies in yeast, we grew a collection of twelve strains of Saccharomyces cerevisiae from different industrial and geographical origins in three culture media differing for their glucose content. Using a population dynamics model to fit the change of population size over time, we estimated the intrinsic growth rate (r), the carrying capacity (K), the mean cell size and the glucose consumption rate per cell. The life-history traits, as well as the glucose consumption rate, displayed large genetic and plastic variability and genetic-by-environment interactions. Within each medium, growth rate and carrying capacity were not correlated, but a marked trade-off between these traits was observed over the media, with high K and low r in the glucose rich medium and low K and high r in the other media. The cell size was tightly negatively correlated to carrying capacity in all conditions. The resource consumption rate appeared to be a clear-cut determinant of both the carrying capacity and the cell size in all media, since it accounted for 37% to 84% of the variation of those traits. In a given medium, the strains that consume glucose at high rate have large cell size and low carrying capacity, while the strains that consume glucose at low rate have small cell size but high carrying capacity. These two contrasted behaviors may be metaphorically defined as “ant” and “grasshopper” strategies of resource utilization. Interestingly, a strain may be “ant” in one medium and “grasshopper” in another. These life-history strategies are discussed with regards to yeast physiology, and in an evolutionary perspective

Niche-driven evolution of metabolic and life-history strategies in natural and domesticated populations of Saccharomyces cerevisiae

<p>Abstract</p> <p>Background</p> <p>Variation of resource supply is one of the key factors that drive the evolution of life-history strategies, and hence the interactions between individuals. In the yeast <it>Saccharomyces cerevisiae</it>, two life-history strategies related to different resource utilization have been previously described in strains from different industrial origins. In this work, we analyzed metabolic traits and life-history strategies in a broader collection of yeast strains sampled in various ecological niches (forest, human body, fruits, laboratory and industrial environments).</p> <p>Results</p> <p>By analysing the genetic and plastic variation of six life-history and three metabolic traits, we showed that <it>S. cerevisiae </it>populations harbour different strategies depending on their ecological niches. On one hand, the forest and laboratory strains, referred to as extreme "ants", reproduce quickly, reach a large carrying capacity and a small cell size in fermentation, but have a low reproduction rate in respiration. On the other hand, the industrial strains, referred to as extreme "grasshoppers", reproduce slowly, reach a small carrying capacity but have a big cell size in fermentation and a high reproduction rate in respiration. "Grasshoppers" have usually higher glucose consumption rate than "ants", while they produce lower quantities of ethanol, suggesting that they store cell resources rather than secreting secondary products to cross-feed or poison competitors. The clinical and fruit strains are intermediate between these two groups.</p> <p>Conclusions</p> <p>Altogether, these results are consistent with a niche-driven evolution of <it>S. cerevisiae</it>, with phenotypic convergence of populations living in similar habitat. They also revealed that competition between strains having contrasted life-history strategies ("ants" and "grasshoppers") seems to occur at low frequency or be unstable since opposite life-history strategies appeared to be maintained in distinct ecological niches.</p

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Idiopathic pulmonary fibrosis (IPF) is a progressive scarring disease of the lung with feweffective therapeutic options. Structural remodelling of the extracellular matrix [i.e. collagen cross-linkingmediated by the lysyl oxidase (LO) family of enzymes (LOX, LOXL1-4)] might contribute to disease pathogenesis and represent a therapeutic target. This study aimed to further our understanding of the mechanisms by which LO inhibitors might improve lung fibrosis. Lung tissues from IPF and non-IPF subjects were examined for collagen structure (second harmonic generation imaging) and LO gene (microarray analysis) and protein (immunohistochemistry and western blotting) levels. Functional effects (collagen structure and tissue stiffness using atomic force microscopy) of LO inhibitors on collagen remodelling were examined in two models, collagen hydrogels and decellularized human lung matrices. LOXL1/LOXL2 gene expression and protein levels were increased in IPF versus non-IPF. Increased collagen fibril thickness in IPF versus non-IPF lung tissues correlated with increased LOXL1/LOXL2, and decreased LOX, protein expression. beta-Aminoproprionitrile (beta-APN; pan-LO inhibitor) but not Compound A (LOXL2-specific inhibitor) interfered with transforming growth factor-beta-induced collagen remodelling in both models. The beta-APN treatment group was tested further, and beta-APN was found to interfere with stiffening in the decellularized matrix model. LOXL1 activity might drive collagen remodelling in IPF lungs. The interrelationship between collagen structural remodelling and LOs is disrupted in IPF lungs. Inhibition of LO activity alleviates fibrosis by limiting fibrillar collagen cross-linking, thereby potentially impeding the formation of a pathological microenvironment in IPF

Artisanal and farmer bread making practices differently shape fungal species community composition in French sourdoughs

Preserving microbial diversity in food systems is one of the many challenges to be met to achieve food security and quality. Although industrialization led to the selection and spread of specific fermenting microbial strains, there are still ongoing artisanal processes that may allow the conservation of a wider species diversity and genetic diversity. We examined whether the diversity of artisanal practices could lead to an increased level in fungal species diversity for bread making. We used an interdisciplinary participatory research approach including bakers, psycho-sociologists and microbiologists to analyze French bread making practices and describe fungal communities in naturally fermented sourdough of 27 bakers and 12 farmer bakers. Bread making practices were classified in two groups: the farmer-like practice group and the artisanal-like practice group. The well-known bakery yeast, Saccharomyces cerevisiae, was dominant (i.e. with a relative abundance over 50%) in only 24% of sourdoughs while other yeast species, belonging to the Kazachstania genus, were dominant in 54% of sourdoughs. Bread making practices were found to drive the distribution of fungal species across sourdoughs. The most striking bread making practice effect was the occurrence of Kazachstania humilis in sourdoughs made with artisanal-like practices and the occurrence of Kazachstania bulderi in sourdoughs made with farmer-like practices. Phenotypic divergences between sourdough and non-sourdough strains were found for K. humilis but not for K. bulderi. Overall, our results showed that preserving bread making practice diversity allows the preservation of a higher species and phenotypic diversity in microbial communities