Layers response to a suboptimal diet through phenotype and transcriptome changes in four tissues

Poultry meat and eggs are major sources of nutrients in the human diet. The long production career of laying hens expose them to biotic or abiotic stressors, lowering their production. Understanding the mechanisms of adaptation to stress is crucial for selecting robust animals and meeting the needs of a growing human population. In this study, financed by the French ChickStress and the European Feed-a-Gene (grant agreement no. 633531) programs, we compared the effects of a 15%-energy-reduced diet (feed stress, FS) vs a commercial diet (control, CT) on phenotypic traits and adipose, blood, hypothalamus and liver transcriptomes in two feed-efficiency-diverging lines. Phenotypic traits showed differences between lines or diets, but no line × diet interaction. In the FS group, feed intake (FI) increased and hens had lower body- and abdominal adipose weight, compared to CT group. We found no differences in egg production or quality. At the transcriptomic level, 16,461 genes were expressed in one or more tissues, 41% of which were shared among tissues. We found differentially expressed genes between lines or diet in all tissues, and almost no line × diet interactions. Focusing on diet, adipose and liver transcriptomes were unaffected. In blood, pathways linked to amino acids, monosaccharides, and steroid metabolism were affected, while in the hypothalamus, changes were observed in fatty acid metabolism and endocannabinoid signalling. Given the similarities in egg production, the FS animals seem to have adapted to the stress by increasing FI and by mobilizing adipose reserves. Increase in FI did not appear to affect liver metabolism, and the mobilization of adipose reserves was apparently not driven at the transcriptomic level. In blood, the pathways linked to metabolic processes suggest a metabolic role for this tissue in chicken, whose erythrocytes are nucleated and contain mitochondria. FI increase might be linked to the hypothalamic pathway of endocannabinoid signalling, which are lipid-based neurotransmitters, notably involved in the regulation of appetite

Étude de la composante génétique de l’efficience alimentaire (EA) chez des lignées de poules pondeuses divergentes pour l’EA en utilisant la technologie RNA-seq

Feed efficiency (FE) is an important trait of agronomical interest. The variation of FE in a population is mainly due to the variation of gene expression, itself due to variants that regulate them in cis. This thesis had three interconnected objectives.The 1st was to study the tissues and genes involved in the difference in FE between two different strains of layers divergent for this trait. To this end, we studied transcriptomes from four tissues (adipose tissue, blood, hypothalamus and liver) using the possibilities offered by RNA-seq, an RNA sequencing technology.The 2nd objective was to contribute to the functional annotation of the chicken genome by enriching its annotation with long non-coding RNA genes, important expression regulators. We also detected SNPs by RNA-seq, a necessary step in the establishment of a pipeline for the study of allele-specific expression, a marker of cis-regulation.The 3rd objective combined the results of previous work to identify candidate genes that cause FE variation due to a variant impacting the structure of the RNA or associated protein, or a cis-regulatory variant.L’efficience alimentaire (EA) est un important caractère d’intérêt agronomique. La variation de l’EA dans une population est principalement due à la variation d’expression de gènes, elle-même due à des variants qui les régulent en cis. Cette thèse avait trois objectifs interconnectés.Le 1er était d’étudier les tissus et gènes impliqués dans la différence d’EA entre deux lignées de pondeuses divergentes pour ce caractère. Nous avons étudié pour cela les transcriptomes de quatre tissus (tissu adipeux, sang, hypothalamus et foie) à l’aide des possibilités offertes par le RNA-seq, technologie de séquençage des ARN.Le 2e objectif était de contribuer à l’annotation fonctionnelle du génome de la poule, en enrichissant son annotation en gènes d’ARN longs non-codants, d’importants régulateurs de l’expression. Nous avons également détecté les SNP par RNA-seq, étape nécessaire à la mise en place d’un pipeline permettant l’étude de l’expression allèle-spécifique, un marqueur des cis-régulation.Le 3e objectif combinait les résultats des travaux précédents afin d’identifier des gènes candidats causaux de la variation d’EA, en raison d’un variant impactant la structure de l’ARN ou protéine associée, ou bien d’un variant cis-régulateur

Study of the genetic component of feed efficiency (FE) in layer lines divergent for FE using the RNA-seq technology

L’efficience alimentaire (EA) est un important caractère d’intérêt agronomique. La variation de l’EA dans une population est principalement due à la variation d’expression de gènes, elle-même due à des variants qui les régulent en cis. Cette thèse avait trois objectifs interconnectés.Le 1er était d’étudier les tissus et gènes impliqués dans la différence d’EA entre deux lignées de pondeuses divergentes pour ce caractère. Nous avons étudié pour cela les transcriptomes de quatre tissus (tissu adipeux, sang, hypothalamus et foie) à l’aide des possibilités offertes par le RNA-seq, technologie de séquençage des ARN.Le 2e objectif était de contribuer à l’annotation fonctionnelle du génome de la poule, en enrichissant son annotation en gènes d’ARN longs non-codants, d’importants régulateurs de l’expression. Nous avons également détecté les SNP par RNA-seq, étape nécessaire à la mise en place d’un pipeline permettant l’étude de l’expression allèle-spécifique, un marqueur des cis-régulation.Le 3e objectif combinait les résultats des travaux précédents afin d’identifier des gènes candidats causaux de la variation d’EA, en raison d’un variant impactant la structure de l’ARN ou protéine associée, ou bien d’un variant cis-régulateur.Feed efficiency (FE) is an important trait of agronomical interest. The variation of FE in a population is mainly due to the variation of gene expression, itself due to variants that regulate them in cis. This thesis had three interconnected objectives.The 1st was to study the tissues and genes involved in the difference in FE between two different strains of layers divergent for this trait. To this end, we studied transcriptomes from four tissues (adipose tissue, blood, hypothalamus and liver) using the possibilities offered by RNA-seq, an RNA sequencing technology.The 2nd objective was to contribute to the functional annotation of the chicken genome by enriching its annotation with long non-coding RNA genes, important expression regulators. We also detected SNPs by RNA-seq, a necessary step in the establishment of a pipeline for the study of allele-specific expression, a marker of cis-regulation.The 3rd objective combined the results of previous work to identify candidate genes that cause FE variation due to a variant impacting the structure of the RNA or associated protein, or a cis-regulatory variant

Comparative Activity of Ciprofloxacin, Levofloxacin and Moxifloxacin against Klebsiella pneumoniae, Pseudomonas aeruginosa and Stenotrophomonas maltophilia Assessed by Minimum Inhibitory Concentrations and Time-Kill Studies.

The aim of this study was to compare the in vitro susceptibility of Klebsiella pneumoniae, Pseudomonas aeruginosa and Stenotrophomonas maltophilia to three fluoroquinolones. The minimum inhibitory concentrations (MICs) to ciprofloxacin, levofloxacin and moxifloxacin were examined by E-test® for a total of 40 K. pneumoniae strains, 40 S. maltophilia strains and 40 P. aeruginosa strains. Then, the bactericidal activity of these fluoroquinolones was investigated on five strains of each bacterial species by means of time-kill curves. For K. pneumoniae and P. aeruginosa, the distance of the measured MIC from the clinical break-point is a good indicator of the bactericidal activity for ciprofloxacin and levofloxacin as obtained in our experiments. The lower the MIC, the better the bactericidal activity in term of CFU Log decreases. If MIC of ciprofloxacin and levofloxacin against the considered bacteria are far from clinical breakpoint, these two antibiotics are equivalent. According to our MIC50 and modal MIC, the breakpoints of both ciprofloxacin and levofloxacin seem to be somewhat high and data suggest reducing them. On S. maltophilia, none of the tested antibiotics showed a satisfactory activity

Selective sweep mapping in the R+ R-chicken lines divergently selected for RFI (residual feed intake)

International audienceIntense artificial selection of populations leads to the acceleration of evolutionary processes and often results in extreme phenotypes with associated changes across the genome. Selective-sweep mapping makes it possible to identify the genomic regions where allele-frequencies have moved after selection. In this project we performed a selective-sweep mapping in two experimental chicken lines, developed from a common Rhode Island Red base population, by long term divergent selection (40 years) for high (R+) and low (R-) residual food intake, an indicator of feed efficiency

MIC₅₀ MIC₉₀ and modal MICs for each bacteria and antibiotics.

<p>MIC₅₀ MIC₉₀ and modal MICs for each bacteria and antibiotics.</p

Time-kill studies with 5 strains of <i>K</i>. <i>pneumoniae</i>, <i>P</i>. <i>aeruginosa</i>, <i>S</i>. <i>maltophilia</i> with concentration equal to the theoretical plasma peak (ciprofloxacin = 4 μg/mL; levofloxacin = 10 μg/mL; moxifloxacin = 3 μg/mL).

<p>Time-kill studies with 5 strains of <i>K</i>. <i>pneumoniae</i>, <i>P</i>. <i>aeruginosa</i>, <i>S</i>. <i>maltophilia</i> with concentration equal to the theoretical plasma peak (ciprofloxacin = 4 μg/mL; levofloxacin = 10 μg/mL; moxifloxacin = 3 μg/mL).</p

Time-kill studies with 5 strains of <i>K</i>. <i>pneumoniae</i>, <i>P</i>. <i>aeruginosa</i>, <i>S</i>. <i>maltophilia</i> with concentration equal to one fold (A) or two fold (B) the MIC of the strain against the considered antibiotic.

<p>Time-kill studies with 5 strains of <i>K</i>. <i>pneumoniae</i>, <i>P</i>. <i>aeruginosa</i>, <i>S</i>. <i>maltophilia</i> with concentration equal to one fold (A) or two fold (B) the MIC of the strain against the considered antibiotic.</p

MICs (μg/mL) of the bacteria strains tested by time-kill studies.

<p>MICs (μg/mL) of the bacteria strains tested by time-kill studies.</p

Mitochondrial Function in Peripheral Blood Mononuclear Cells (PBMC) Is Enhanced, Together with Increased Reactive Oxygen Species, in Severe Asthmatic Patients in Exacerbation

Asthma is a chronic inflammatory lung syndrome with an increasing prevalence and a rare but significant risk of death. Its pathophysiology is complex, and therefore we investigated at the systemic level a potential implication of oxidative stress and of peripheral blood mononuclear cells&rsquo; (PBMC) mitochondrial function. Twenty severe asthmatic patients with severe exacerbation (GINA 4&ndash;5) and 20 healthy volunteers participated at the study. Mitochondrial respiratory chain complexes activities using different substrates and reactive oxygen species (ROS) production were determined in both groups by high-resolution respirometry and electronic paramagnetic resonance, respectively. Healthy PBMC were also incubated with a pool of plasma of severe asthmatics or healthy controls. Mitochondrial respiratory chain complexes activity (+52.45%, p = 0.015 for VADP) and ROS production (+34.3%, p = 0.02) were increased in asthmatic patients. Increased ROS did not originate mainly from mitochondria. Plasma of severe asthmatics significantly increased healthy PBMC mitochondrial dioxygen consumption (+56.8%, p = 0.031). In conclusion, such asthma endotype, characterized by increased PMBCs mitochondrial oxidative capacity and ROS production likely related to a plasma constituent, may reflect activation of the immune system. Further studies are needed to determine whether increased PBMC mitochondrial respiration might have protective effects, opening thus new therapeutic approaches