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Identification of hanks-type kinase PknB-specific targets in the Streptococcus thermophilus phosphoproteome
No full textProtein phosphorylation especially on serine/threonine/tyrosine residues are frequent in many bacteria. This post-translational modification has been associated with pathogenicity and virulence in various species. However, only few data have been produced so far on generally recognized as safe bacteria used in food fermentations. A family of kinases known as Hanks-type kinases is suspected to be responsible for, at least, a part of these phosphorylations in eukaryotes as in bacteria. The objective of our work was to establish the first phosphoproteome of Streptococcus thermophilus, a lactic acid bacterium widely used in dairy fermentations in order to identified the proteins and pathways tagged by Ser/Thr/Tyr phosphorylations. In addition, we have evaluated the role in this process of the only Hanks-type kinase encoded in the S. thermophilus genome. We have constructed a mutant defective for the Hanks type kinase in S. thermophilus and established the proteomes and phosphoproteomes of the wild type and the mutant strains. To do that, we have enriched our samples in phosphopeptides with titane beads and used dimethyl tags to compare phosphopeptide abundances. Peptides and phosphopeptides were analyzed on a last generation LC-MS/MS system. We have identified and quantified 891 proteins representing half of the theoretical proteome. Among these proteins, 106 contained phosphorylated peptides. Various functional groups of proteins (amino acid, carbon and nucleotide metabolism, translation, cell cycle, stress response, …) were found phosphorylated. The phosphoproteome was only weakly reduced in the Hanks-type kinase mutant indicating that this enzyme is only one of the players in the phosphorylation process. The proteins that are modified by the Hanks-type kinase mainly belong to the divisome
The stepping stone model in a random environment and the effect of local heterogneities on isolation by distance patterns
No full textWe study a one-dimensional spatial population model where the population sizes of the subpopulations are chosen according to a translation invariant and ergodic distribution and are uniformly bounded away from 0 and infinity. We suppose that the frequencies of a particular genetic type in the colonies evolve according to a system of interacting diffusions, following the stepping stone model of Kimura. We show that, over large spatial and temporal scales, this model behaves like the solution to a stochastic heat equation with Wright-Fisher noise with constant coefficients. These coefficients are the effective diffusion rate of genes within the population and the effective local population density. We find that, in our model, the local heterogeneity leads to a slower effective diffusion rate and a larger effective population density than in a uniform population. Our proof relies on duality techniques, an invariance principle for reversible random walks in a random environment and a convergence result for a system of coalescing random walks in a random environment
Contributions de l'offre et de la demande à l'évolution de la qualité de l'alimentation
No full textCette étude s’intéresse à l’évolution de la qualité nutritionnelle de l’alimentation et vise à quantifier les contributions respectives des reformulations des produits alimentaires réalisées par les industriels, du renouvellement de l’offre de produits sur le marché (et des transferts de volumes de ventes associés) et des substitutions opérées par les consommateurs parmi les produits déjà existants sur le marché. [br/]
Dans cette étude, la qualité nutritionnelle de l’alimentation est appréciée par secteur. Celle-ci est mesurée par les teneurs moyennes en nutriments d’intérêt des produits commercialisés, pondérées par les parts de marché en volumes de ventes. Quatre secteurs alimentaires ont été analysés : les pizzas fraiches, les pizzas surgelées, les plats cuisinés appertisés et les plats cuisinés surgelés. Selon le secteur, les données servant à établir le bilan initial (t0) ont été collectées entre 2009 et 2012 et les deuxièmes séries de collecte (t1) ont été effectuées entre 2015 et 2016. [br/]
Cette étude montre que les industriels améliorent les produits existants pour certains couples secteur-nutriment ciblés, et qu’en ce sens, ils contribuent aux efforts à réaliser pour atteindre les objectifs de santé publique en matière de nutrition. Les résultats de l’étude indiquent cependant que les nouveaux produits introduits sur le marché (et les produits retirés du marché) ne participent pas nécessairement à cette dynamique d’amélioration de la qualité nutritionnelle de l’offre. Enfin, on note que du côté des consommateurs, les substitutions, qui s’opèrent au cours de la période observée pour les secteurs considérés, ne vont pas toujours dans le sens d’une amélioration de la qualité nutritionnelle des consommations
Assessing inbreeding networks from partial correlations and information theory in rabbits
No full textAccurate estimates of inbreeding (F) are crucial for the management of populations inselection schemes. Traditionally, inbreeding has been estimated from pedigree-basedinformation. Currently, genome-based estimates of inbreeding can be obtained fromSNP chip data. The correlation between pedigree and different genome-based estimatesof inbreeding is usually discussed in the literature. However, some of these correlationscould be spurious. Using partial correlations and information theory (PCIT) it ispossible to distinguish a significant association between two variables which isindependent from associations with a third variable. The objective of this study is toimplement PCIT to assess the relationship between different estimates of inbreeding andphenotypes using a selected population of rabbits. Pedigree data and genomicinformation from a 200K chip were available. After applying filtering criteria, the dataset constituted 490 animals genotyped for 114,604 autosomal SNPs. Phenotypic recordsfor average dairy gain (ADG) were also accessible for full (f) and restricted (r) feeding.Pedigree-based inbreeding estimates (ped) were decomposed in ancient (A),intermediate (I) and recent (R) inbreeding. Accordingly, genomic estimates ofinbreeding based on runs of homozygosity (roh) were also decomposed in A, I and R.Other genomic estimates of inbreeding were also evaluated: VanRaden (van),proportion of homozygous SNPs (snp), proportion of homozygous SNPs for the minorallele frequency (PHoMA) and the compression efficiency (CE). The results indicatethat FrohR is an essential node with 6 edges, one of which is negative with FrohA (-0.31). CE is a balanced node with 2 positive (Fsnp and FrohR) and 2 negative (FrohAand FpedI) edges. Fvan is the less related node with only one positive edge withPHoMA (0.70). When including phenotypic information, FpedI is correlated negativelywith ADGf (-0.11) and positively with ADGr (0.10). In addition, ADGr has a negativeedge with FrohA (-0.11). These results indicate that PCIT approach allows inferringmeaningful associations between estimates of inbreeding
Consistency of impact assessment protocols for non-native species
No full textStandardized tools are needed to identify and prioritize the most harmful non-native species (NNS). A plethora of assessment protocols have been developed to evaluate the current and potential impacts of non-native species, but consistency among them has received limited attention. To estimate the consistency across impact assessment protocols, 89 specialists in biological invasions used 11 protocols to screen 57 NNS (2614 assessments). We tested if the consistency in the impact scoring across assessors, quantified as the coefficient of variation (CV), was dependent on the characteristics of the protocol, the taxonomic group and the expertise of the assessor. Mean CV across assessors was 40%, with a maximum of 223%. CV was lower for protocols with a low number of score levels, which demanded high levels of expertise, and when the assessors had greater expertise on the assessed species. The similarity among protocols with respect to the final scores was higher when the protocols considered the same impact types. We conclude that all protocols led to considerable inconsistency among assessors. In order to improve consistency, we highlight the importance of selecting assessors with high expertise, providing clear guidelines and adequate training but also deriving final decisions collaboratively by consensus
Arnica montana : évaluation des ressources génétiques françaises en vue du développement de la culture en plaine et en montagne
No full textL’arnica des montagnes est une espèce médicinale importante dont la production est principalement
issue de la cueillette à l’état sauvage, notamment sur le territoire métropolitain. La ressource étant en
régression, le maintien, voire le développement de la production française passe donc par la mise en
culture, actuellement anecdotique car difficile. Certains freins pourraient être levés par la mise en
évidence de matériel végétal adapté à la production. L’objectif de ce projet était de mettre en culture 24
populations d’origines sauvages (prospectées en France métropolitaine) et de les comparer à deux
variétés commerciales témoins ‘Arbo’ et ‘Arnimed’, sur 4 sites d’expérimentation aux contextes
pédoclimatiques variés mais a priori adaptés à la culture de l’espèce. Durant les 3 années d’essai, un
suivi morphologique et agronomique des populations a été réalisé. Des analyses des sesquiterpènes
lactones et flavonoïdes ont été effectuées, et une nouvelle méthodologie de dosage de ces composés a
été développée. Les résultats mettent en exergue la forte variabilité de l’expression phénotypique et
chimique des différentes souches testées. Une forte mortalité globale a pu être constatée sur
l’ensemble des populations sauvages étudiées sans que les causes aient pu en être identifiées. Sur
l’ensemble des variables suivies, les variétés commerciales ‘Arbo’ et ‘Arnimed’ sont particulièrement
performantes, et deux populations sauvages se démarquent par leurs résultats intéressants : l’une
parait pertinente pour démarrer des travaux de sélection d’une variété adaptée à la basse altitude,
tandis que l’autre, originaire du Massif central, pourrait se proposer comme une alternative d’origine
locale (française) à la culture de variétés commerciales sélectionnées (suisse et allemande).Arnica montana is a major medicinal specie, which is now mainly produced from wild harvesting,
especially in mainland France. As the wild resource is decreasing, and in order to maintain or even
Gourlin L. et al. 68 Innovations Agronomiques 71 (2019), 67-80 develop the French production, cultivation is a good option, that is still very limited, because of its difficulty. Finding the right plant material could help to enhance cultivation programs. This project aimed at growing 24 wild populations, which were collected in mainland France, and to compare them with 2 commercial varieties, ‘Arbo’ and ‘Arnimed’. This was set on 4 experimentation spots, chosen for their potential match for Arnica cultivation. The experiment lasted 3 years, and morphological and
agronomical subjects were studied on the populations. Sesquiterpene lactones and flavonoids
analyzed, and a new methodology of evaluation was developed. The results showed extreme variability
of phenotypic and chemical expression of the different populations. An important death rate has been
noticed on wild populations, but the causes are still unknown. On the set of variables chosen,
commercial varieties ‘Arbo’ and ‘Arnimed’ were particularly competitive, and two wild populations stand
out with promising results. One seems appropriate for starting selection works on a variety that would be
suitable for loaw altitude, and the other one could be a local (French) alternative to the cultivation of
selected varieties (‘Arbo’ and ‘Arnimed’ are from Swiss and German selection work)
The functional trait spectrum of European temperate grasslands
No full textQuestions What is the functional trait variation of European temperate grasslands and how does this reflect global patterns of plant form and function? Do habitat specialists show trait differentiation across habitat types? Location Europe. Methods We compiled 18 regeneration and non-regeneration traits for a continental species pool consisting of 645 species frequent in five grassland types. These grassland types are widely distributed in Europe but differentiated by altitude, soil bedrock and traditional long-term management and disturbance regimes. We evaluated the multivariate trait space of this entire species pool and compared multi-trait variation and mean trait values of habitat specialists grouped by grassland type. Results The first dimension of the trait space accounted for 23% of variation and reflected a gradient between fast-growing and slow-growing plants. Plant height and SLA contributed to both the first and second ordination axes. Regeneration traits mainly contributed to the second and following dimensions to explain 56% of variation across the first five axes. Habitat specialists showed functional differences between grassland types mainly through non-regeneration traits. Conclusions The trait spectrum of plants dominating European temperate grasslands is primarily explained by growth strategies which are analogous to the trait variation observed at the global scale, and secondly by regeneration strategies. Functional differentiation of habitat specialists across grassland types is mainly related to environmental filtering linked with altitude and disturbance. This filtering pattern is mainly observed in non-regeneration traits, while most regeneration traits demonstrate multiple strategies within the same habitat type
Novel and known signals of selection for fat deposition in domestic sheep breeds from Africa and Eurasia
No full textGenomic regions subjected to selection frequently show signatures such as within-population reduced nucleotide diversity and outlier values of differentiation among differentially selected populations. In this study, we analyzed 50K SNP genotype data of 373 animals belonging to 23 sheep breeds of different geographic origins using the Rsb (extended haplotype homozygosity) and FST statistical approaches, to identify loci associated with the fat-tail phenotype. We also checked if these putative selection signatures overlapped with regions of high-homozygosity (ROH). The analyses identified novel signals and confirmed the presence of selection signature in genomic regions that harbor candidate genes known to affect fat deposition. Several genomic regions that frequently appeared in ROH were also identified within each breed, but only two ROH islands overlapped with the putative selection signatures. The results reported herein provide the most complete genome-wide study of selection signatures for fat-tail in African and Eurasian sheep breeds; they also contribute insights into the genetic basis for the fat tail phenotype in sheep, and confirm the great complexity of the mechanisms that underlie quantitative traits, such as the fat-tail
Co-expression network analysis identifies gonad- and embryo- associated protein modules in the sentinel species Gammarus fossarum
No full textNext generation sequencing and mass spectrometry technologies have recently expanded the availability of whole transcriptomes and proteomes beyond classical model organisms in molecular biology, even in absence of an annotated genome. However, the fragmented nature of transcriptomic and proteomic data reduces the ability to interpret the data, notably in non-model organisms. Network-based approaches may help extracting important biological information from -omics datasets. The reproductive cycle of the freshwater crustacean Gammarus fossarum. provides an excellent case study to test the relevance of a network analysis in non-model organisms. Here, we illustrated how the use of a co-expression network analysis (based on Weighted Gene Co-expression Network Analysis algorithm, WGCNA) allowed identifying protein modules whose expression profiles described germ cell maturation and embryonic development in the freshwater crustacean Gammarus fossarum. Proteome datasets included testes, ovaries or embryos samples at different maturation or developmental stages, respectively. We identified an embryonic module correlated with mid-developmental stages corresponding to the organogenesis and it was characterized by enrichment in proteins involved in RNA editing and splicing. An ovarian module was enriched in vitellogenin-like proteins and clottable proteins, confirming the diversity of proteins belonging to the large lipid transfer family involved in oocytes maturations in this freshwater amphipod. Moreover, our results found evidence of a fine-tuned regulation between energy production by glycolysis and actin-myosin-dependent events in G. fossarum spermatogenesis. This study illustrates the importance of applying systems biology approaches to emergent animal models to improve the understanding of the molecular mechanisms regulating important physiological events with ecological relevance
Pycnoporus cinnabarinus glyoxal oxidases display differential catalytic efficiencies on 5‑hydroxymethylfurfural and its oxidized derivatives
No full textBackground: 5-Hydroxymethylfurfural (HMF), a major residual component of a lignocellulosic bio-refinery process, can be transformed into fundamental building blocks for green chemistry via oxidation. While chemical methods are well established, interest is also being directed into the enzymatic oxidation of HMF into the bio-plastic precursor 2,5-furandicarboxylic acid (FDCA). Results: We demonstrate that three glyoxal oxidases (PciGLOX) isoenzymes from the Basidiomycete fungus Pycnoporus cinnabarinus were able to oxidize HMF, with PciGLOX2 and PciGLOX3 being the most efficient. The major reaction product obtained with the three isoenzymes was 5-hydroxymethyl-2-furancarboxylic (HMFCA), a precursor in polyesters and pharmaceuticals production, and very little subsequent conversion of this compound was observed. However, small concentrations of FDCA, a substitute for terephthalic acid in the production of polyesters, were also obtained. The oxidation of HMF was significantly boosted in the presence of catalase for PciGLOX2, leading to 70% HMFCA yield. The highest conversion percentages were observed on 2,5-furandicarboxaldehyde (DFF), a minor product from the reaction of PciGLOX on HMF. To bypass HMFCA accumulation and exploit the efficiency of PciGLOX in oxidizing DFF and 5-formyl-2-furan carboxylic acid (FFCA) towards FDCA production, HMF was oxidized in a cascade reaction with an aryl alcohol oxidase (UmaAAO). After 2 h of reaction, UmaAAO completely oxidized HMF to DFF and further to FFCA, with FDCA only being detected when PciGLOX3 was added to the reaction. The maximum yield of 16% FDCA was obtained 24 h after the addition of PciGLOX3 in the presence of catalase. Conclusions: At least two conversion pathways for HMF oxidation can be considered for PciGLOX; however, the highest selectivity was seen towards the production of the valuable polyester precursor HMFCA. The three isoenzymes showed differences in their catalytic efficiencies and substrate specificities when reacted with HMF derivatives