The main objective of
package is to carry out a data mining of biological functions and establish links between genes involved in the study. We developed
in R to facilitate functional Gene Ontology ...(GO) analysis of complex experimental design with multiple comparisons of interest. It allows to study large-scale datasets together and visualize GO profiles to capture biological knowledge. The acronym stands for three major concepts of the analysis:
sualization,
emantic similarity and
nrichment
nalysis of
ene
ntology. It provides access to the last current GO annotations, which are retrieved from one of NCBI EntrezGene, Ensembl or Uniprot databases for several species. Using available R packages and novel developments,
extends classical functional GO analysis to focus on functional coherence by aggregating closely related biological themes while studying multiple datasets at once. It provides both a synthetic and detailed view using interactive functionalities respecting the GO graph structure and ensuring functional coherence supplied by semantic similarity.
has been successfully applied on several datasets from different species with a variety of biological questions. Results can be easily shared between bioinformaticians and biologists, enhancing reporting capabilities while maintaining reproducibility. ViSEAGO is publicly available on https://bioconductor.org/packages/ViSEAGO .
As uricoletic animals, chickens produce cleidoic eggs, which are self-contained bacteria-resistant biological packages for extra-uterine development of the chick embryo. The eggshell constitutes a ...natural physical barrier against bacterial penetration if it forms correctly and remains intact. The eggshell's remarkable mechanical properties are due to interactions among mineral components and the organic matrix proteins. The purpose of our study was to identify novel eggshell proteins by examining the transcriptome of the uterus during calcification of the eggshell. An extensive bioinformatic analysis on genes over-expressed in the uterus allowed us to identify novel eggshell proteins that contribute to the egg's natural defenses.
Our 14 K Del-Mar Chicken Integrated Systems microarray was used for transcriptional profiling in the hen's uterus during eggshell deposition. A total of 605 transcripts were over-expressed in the uterus compared with the magnum or white isthmus across a wide range of abundance (1.1- to 79.4-fold difference). The 605 highly-expressed uterine transcripts correspond to 469 unique genes, which encode 437 different proteins. Gene Ontology (GO) analysis was used for interpretation of protein function. The most over-represented GO terms are related to genes encoding ion transport proteins, which provide eggshell mineral precursors. Signal peptide sequence was found for 54 putative proteins secreted by the uterus during eggshell formation. Many functional proteins are involved in calcium binding or biomineralization--prerequisites for interacting with the mineral phase during eggshell fabrication. While another large group of proteins could be involved in proper folding of the eggshell matrix. Many secreted uterine proteins possess antibacterial properties, which would protect the egg against microbial invasion. A final group includes proteases and protease inhibitors that regulate protein activity in the acellular uterine fluid where eggshell formation takes place.
Our original study provides the first detailed description of the chicken uterus transcriptome during formation of the eggshell. We have discovered a cache of about 600 functional genes and identified a large number of encoded proteins secreted into uterine fluid for fabrication of the eggshell and chemical protection of the egg. Some of these uterine genes could prove useful as biological markers for genetic improvement of phenotypic traits (i.e., egg and eggshell quality).
Here, molecular pathways and genes involved in the feed efficiency (FE) and thigh-meat quality of slow-growing Korat chickens were investigated. Individual feed intake values and body weights were ...collected weekly to the calculate feed conversion ratios (FCR) and residual feed intake. The biochemical composition and meat quality parameters were also measured. On the basis of extreme FCR values at 10 weeks of age, 9 and 12 birds from the high and the low FCR groups, respectively, were selected, and their transcriptomes were investigated using the 8 × 60 K Agilent chicken microarray. A weighted gene co-expression network analysis was performed to determine the correlations between co-expressed gene modules and FE, thigh-meat quality, or both. Groups of birds with different FE values also had different nucleotide, lipid, and protein contents in their thigh muscles. In total, 38 modules of co-expressed genes were identified, and 12 were correlated with FE and some meat quality traits. A functional analysis highlighted several enriched functions, such as biological processes, metabolic processes, nucleotide metabolism, and immune responses. Several molecular factors were involved in the interactions between FE and meat quality, including the assembly competence domain, baculoviral IAP repeat containing 5, cytochrome c oxidase assembly factor 3, and myosin light chain 9 genes.
In mammalian ovaries, the theca layers of growing follicles are critical for maintaining their structural integrity and supporting androgen synthesis. Through combining the postnatal monitoring of ...ovaries by abdominal magnetic resonance imaging, endocrine profiling, hormonal analysis of the follicular fluid of growing follicles, and transcriptomic analysis of follicular theca cells, we provide evidence that the exposure of ovine fetuses to testosterone excess activates postnatal follicular growth and strongly affects the functions of follicular theca in adulthood. Prenatal exposure to testosterone impaired androgen synthesis in the small antral follicles of adults and affected the expression in their theca cells of a wide array of genes encoding extracellular matrix components, their membrane receptors, and signaling pathways. Most expression changes were uncorrelated with the concentrations of gonadotropins, steroids, and anti-Müllerian hormone in the recent hormonal environment of theca cells, suggesting that these changes rather result from the long-term developmental effects of testosterone on theca cell precursors in fetal ovaries. Disruptions of the extracellular matrix structure and signaling in the follicular theca and ovarian cortex can explain the acceleration of follicle growth through altering the stiffness of ovarian tissue. We propose that these mechanisms participate in the etiology of the polycystic ovarian syndrome, a major reproductive pathology in woman.
The microbial utilization of dietary carbohydrates is closely linked to the pivotal role of the gut microbiome in human health. Inherent to the modulation of complex microbial communities, a ...prebiotic implies the selective utilization of a specific substrate, relying on the metabolic capacities of targeted microbes. In this study, we investigated the metabolic capacities of 17 commensal bacteria of the human gut microbiome toward dietary carbohydrates with prebiotic potential. First,
experiments allowed the classification of bacterial growth and fermentation profiles in response to various carbon sources, including agave inulin, corn fiber, polydextrose, and citrus pectin. The influence of phylogenetic affiliation appeared to statistically outweigh carbon sources in determining the degree of carbohydrate utilization. Second, we narrowed our focus on six commensal bacteria representative of the
and
phyla to perform an untargeted high-resolution liquid chromatography-mass spectrometry metabolomic analysis:
,
,
,
,
and
exhibited distinct metabolomic profiles in response to different carbon sources. The relative abundance of bacterial metabolites was significantly influenced by dietary carbohydrates, with these effects being strain-specific and/or carbohydrate-specific. Particularly, the findings indicated an elevation in short-chain fatty acids and other metabolites, including succinate, gamma-aminobutyric acid, and nicotinic acid. These metabolites were associated with putative health benefits. Finally, an RNA-Seq transcriptomic approach provided deeper insights into the underlying mechanisms of carbohydrate metabolization. Restricting our focus on four commensal bacteria, including
,
and
, carbon sources did significantly modulate the level of bacterial genes related to the enzymatic machinery involved in the metabolization of dietary carbohydrates. This study provides a holistic view of the molecular strategies induced during the dynamic interplay between dietary carbohydrates with prebiotic potential and gut commensal bacteria.
This study explores at a molecular level the interactions between commensal health-relevant bacteria and dietary carbohydrates holding prebiotic potential. We showed that prebiotic breakdown involves the specific activation of gene expression related to carbohydrate metabolism. We also identified metabolites produced by each bacteria that are potentially related to our digestive health. The characterization of the functional activities of health-relevant bacteria toward prebiotic substances can yield a better application of prebiotics in clinical interventions and personalized nutrition. Overall, this study highlights the importance of identifying the impact of prebiotics at a low resolution of the gut microbiota to characterize the activities of targeted bacteria that can play a crucial role in our health.
Variations in muscle glycogen storage are highly correlated with variations in meat ultimate pH (pHu), a key factor for poultry meat quality. A total of two chicken lines were divergently selected on ...breast pHu to understand the biological basis for variations in meat quality (i.e., the pHu– and the pHu+ lines that are characterized by a 17% difference in muscle glycogen content). The effects of this selection on bird metabolism were investigated by quantifying muscle metabolites by high-resolution NMR (1H and 31P) and serum metabolites by 1H NMR. A total of 20 and 26 discriminating metabolites between the two lines were identified by orthogonal partial least-squares discriminant analysis (OPLS-DA) in the serum and muscle, respectively. There was over-representation of carbohydrate metabolites in the serum and muscle of the pHu– line, consistent with its high level of muscle glycogen. However, the pHu+ line was characterized by markers of oxidative stress and muscle catabolism, probably because of its low level of energy substrates. After OPLS-DA multiblock analysis, a metabolic set of 15 high-confidence biomarkers was identified that could be used to predict the quality of poultry meat after validation on an independent population.
White striping (WS) is an emerging muscular defect occurring on breast and thigh muscles of broiler chickens. It is characterized by the presence of white striations parallel to the muscle fibers and ...has significant consequences for meat quality. The etiology of WS remains poorly understood, even if previous studies demonstrated that the defect prevalence is related to broiler growth and muscle development. Moreover, recent studies showed moderate to high heritability values of WS, which emphasized the role of genetics in the expression of the muscle defect. The aim of this study was to identify the first quantitative trait loci (QTLs) for WS as well as breast muscle yield (BMY) and meat quality traits using a genome-wide association study (GWAS). We took advantage of two divergent lines of chickens selected for meat quality through Pectoralis major ultimate pH (pHu) and which exhibit the muscular defect. An expression QTL (eQTL) detection was further performed for some candidate genes, either suggested by GWAS analysis or based on their biological function.
Forty-two single nucleotide polymorphisms (SNPs) associated with WS and other meat quality traits were identified. They defined 18 QTL regions located on 13 chromosomes. These results supported a polygenic inheritance of the studied traits and highlighted a few pleiotropic regions. A set of 16 positional and/or functional candidate genes was designed for further eQTL detection. A total of 132 SNPs were associated with molecular phenotypes and defined 21 eQTL regions located on 16 chromosomes. Interestingly, several co-localizations between QTL and eQTL regions were observed which could suggest causative genes and gene networks involved in the variability of meat quality traits and BMY.
The QTL mapping carried out in the current study for WS did not support the existence of a major gene, but rather suggested a polygenic inheritance of the defect and of other studied meat quality traits. We identified several candidate genes involved in muscle metabolism and structure and in muscular dystrophies. The eQTL analyses showed that they were part of molecular networks associated with WS and meat quality phenotypes and suggested a few putative causative genes.
In vertebrates, the embryonic environment is known to affect the development and the health of individuals. In broiler chickens, the thermal-manipulation (TM) of eggs during the incubation period was ...shown to improve heat tolerance at slaughter age (35 days of age) in association with several modifications at the molecular, metabolic and physiological levels. However, little is known about the Japanese quail (Coturnix japonica), a closely related avian species widely used as a laboratory animal model and farmed for its meat and eggs. Here we developed and characterized a TM procedure (39.5°C and 65% relative humidity, 12 h/d, from days 0 to 13 of incubation) in quails by analyzing its short and long-term effects on zootechnical, physiological and metabolic parameters. Heat-tolerance was tested by a heat challenge (36°C for 7h) at 35 days of age. TM significantly reduced the hatching rate of the animals and increased mortality during the first four weeks of life. At hatching, TM animals were heavier than controls, but lighter at 25 days of age for both sexes. Thirty-five days after hatching, TM decreased the surface temperature of the shank in females, suggesting a modulation of the blood flow to maintain the internal temperature. TM also increased blood partial pressure and oxygen saturation percentage at 35 days of age in females, suggesting a long-term modulation of the respiration physiology. Quails physiologically responded to the heat challenge, with a modification of several hematologic and metabolic parameters, including an increase in plasma corticosterone concentration. Several physiological parameters such as beak surface temperature and blood sodium concentration revealed that TM birds responded differently to the heat challenge compared to controls. Altogether, this first comprehensive characterization of TM in Japanese quail showed durable effects that may affect the response of TM quails to heat.
The thermal-manipulation (TM) during egg incubation is a cyclic exposure to hot or cold temperatures during embryogenesis that is associated to long-lasting effects on growth performance, physiology, ...metabolism and temperature tolerance in birds. An increase of the incubation temperature of Japanese quail eggs affected the embryonic and post-hatch survival, growth, surface temperatures and blood characteristics potentially related to thermoregulation capacities. To gain new insights in the molecular basis of TM in quails, we investigated by RNA-seq the hypothalamus transcriptome of 35 days-old male and female quails that were treated by TM or not (C, control) during embryogenesis and that were exposed (HC) or not (RT) to a 36 degreesC heat challenge for 7 h before sampling. For males, 76, 27, 47 and 0 genes were differentially expressed in the CHC vs. CRT, CRT vs. TMRT, TMHC vs. TMRT and CHC vs. TMHC comparisons, respectively. For females, 17, 0, 342 and 1 genes were differentially expressed within the same respective comparisons. Inter-individual variability of gene expression response was observed particularly when comparing RT and HC female animals. The differential expression of several genes was corroborated by RT-qPCR analysis. Gene Ontology functional analysis of the differentially expressed genes showed a prevalent enrichment of terms related to cellular responses to stimuli and gene expression regulation in both sexes. Gene Ontology terms related to the membrane transport, the endoplasmic reticulum and mitochondrial functions as well as DNA metabolism and repair were also identified in specific comparisons and sexes. TM had little to no effect on the regulation of gene expression in the hypothalamus of 35 days-old Japanese quails. However, the consequences of TM on gene expression were revealed by the HC, with sex-specific and common functions altered. The effects of the HC on gene expression were most prominent in TM females with a ~ 20-fold increase of the number of differentially expressed genes, suggesting that TM may enhance the gene response during challenging conditions in female quail hypothalamus. TM may also promote new cellular strategies in females to help coping to the adverse conditions as illustrated by the identification of differentially expressed genes related to the mitochondrial and heat-response functions.
Sustainability of poultry farming relies on the development of more efficient and autonomous production systems in terms of feed supply. This implies a better integration of adaptive traits in ...breeding programs, including digestive efficiency, to favor the use of a wider variety of feedstuffs. The objective of the study was to better characterize the kinetics of development of the digestive tract in broilers, in relationship with digestive efficiency by measuring various digestive parameters as well as serum color. Absolute and relative growth of gastrointestinal tract organs were compared between 2 divergent chicken lines selected on digestive efficiency (AMEn) during 7 wk of development. We show that as early as 7 d of age, these 2 lines differs for several organs developments and that these differences remain visible later on. In addition, the allometry of the gizzard and intestine segments is different between the 2 lines, with efficient birds putting more effort in the upper part of the digestive tract during postnatal development and less-efficient birds putting more effort in the lower part of the gastrointestinal tract. Interestingly, we also showed that differences in serum pigmentation, which is a good biomarker for digestive capacity, could be a convenient diagnostic tool to discriminate between chickens with high or low digestive efficiency at early stages of development. In conclusion, this study showed that selection of chickens for AMEn had large impacts in gastrointestinal development including at early stages and is a valuable resource for further studies on the genetic and physiological control of the response of the animal to feed variations.
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