Ontology highlight
ABSTRACT:
PROVIDER: PRJNA1015169 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR26014069_1.fastq.gz | Fastqsanger.gz | |||
| SRR26014070_1.fastq.gz | Fastqsanger.gz | |||
| SRR26014071_1.fastq.gz | Fastqsanger.gz | |||
| SRR26014072_1.fastq.gz | Fastqsanger.gz | |||
| SRR26014073_1.fastq.gz | Fastqsanger.gz |
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Project description:Laying performance is a key factor affecting production efficiency in poultry farming, but its molecular mechanism is still unclear. In this study, Yaoshan chickens, a local breed in Guizhou, China, and commercial chickens (GYR) with higher egg yield after the three-line cross improvement hybridization of Yaoshan chickens were used as animal samples. To explore the regulatory mechanism of the differences in laying performance, RNA-seq and ultra-performance liquid chromatography-tandem mass spectrometry (UPLC‒MS/MS) were used to portray the transcriptional and metabolic profiles of the ovaries of Yaoshan and GYR chickens. At the transcriptional level, 288 differentially expressed genes were upregulated in Yaoshan chickens and 353 differentially expressed genes were upregulated in GYR chickens. In addition, GSEA revealed that ECM-receptor interactions and the TGF-β signalling pathway were inhibited, resulting in increased egg production in GYR chickens. Furthermore, the upregulation of thiamine and carnitine was identified by metabolomic analysis to promote the laying performance of chickens. Finally, comprehensive analyses of the transcriptome and metabolome found that thiamine and carnitine were negatively correlated with ECM-receptor interactions and the TGF-β signalling pathway, which jointly regulate the laying performance of Yaoshan chickens and GYR chickens. In conclusion, our study delineates differences in the transcriptional and metabolic profiles of the ovaries of Yaoshan and GYR chickens during the peak egg production period and provides new hypotheses and clues for further research on poultry egg production performance and the improvement of economic benefits.
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Project description:Veterinary drug mequindox, 3-methyl-2-acethyl-quindoxaline-N-1,4-dioxide, belongs to a class of antibiotic and growth-prompting drug called quinoxalines that are often used in livestock and poultry industry. Previous researches focused on traditional toxicity. However, the effect of mequindox on endogenous metabolic profile remains unknown. We used microarrays to detail the global programme of gene expression underlying mequindox toxicity.
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Project description:Hatchery fumigation is recognized as a crucial step to control the microbial bloom in the environment and formaldehyde is one of the most widely used disinfectants, to ensure successful hatchability and healthy production. Although in humans its usage is strictly regulated in many developed countries due to its carcinogenic properties, FA remains widely used in poultry hatcheries. Recent studies have shown it also poses significant risks to poultry health and performance. Yet, the impact of formaldehyde fumigation at molecular and cellular levels is not studied in poultry. The current study aimed to capture the in ovo transcriptional response of liver tissue to formaldehyde treatment. Chick embryos were subjected to formaldehyde fumigation treatment for 25 minutes at 24-25°C and 75% relative humidity, keeping a control group as untreated. On the 18th day of incubation at 37.8°C and 58-63% humidity, eggs were broken, and liver tissue were obtained for RNA isolation, cDNA library preparation and RNA sequencing. Bioinformatics analysis revealed 908 significant differentially expressed genes (DEGs), among which 814 were known genes and 94 were novel genes. Key DEGs and transcription factors were involved in oxidative stress, immuno-inflammatory responses, epigenetic modification and cellular adaptation related activities. These molecular and cellular findings might have a broader implication on early chick performance and health, especially in case of predisposition of disease conditions.
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Project description:Veterinary drug mequindox, 3-methyl-2-acethyl-quindoxaline-N-1,4-dioxide, belongs to a class of antibiotic and growth-prompting drug called quinoxalines that are often used in livestock and poultry industry. Previous researches focused on traditional toxicity. However, the effect of mequindox on endogenous metabolic profile remains unknown. We used microarrays to detail the global programme of gene expression underlying mequindox toxicity. Two groups (control and high-dosed mequindox) were selected for GeneChip analysis based on PCA score of liver aqueous extracts and clinical chemistry changes.
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Project description:Hanl Lee & Angelyn Lao. Transmission dynamics and control strategies assessment of avian influenza A (H5N6) in the Philippines. Infectious Disease Modelling 3 (2018).
Due to the outbreaks of Highly Pathogenic Avian Influenza A (HPAI) H5N6 in the Philippines (particularly in Pampanga and Nueva Ecija) in August 2017, there has been an increase in the need to cull the domestic birds to control the spread of the infection. However, this control method poses a negative impact on the poultry industry. In addition, the pathogenicity and transmissibility of the H5N6 in both the birds and the humans remain largely unknown which call for the necessity to develop more strategic control methods for the virus. In this study, we constructed a mathematical model for the bilinear and half-saturated incidence to compare their corresponding effect on transmission dynamics of H5N6. The simulations of half-saturated incidence model were similar to what occurred during the H5N6 outbreak (2017) in the Philippines. Instead of culling the birds, we implemented other control strategies such as non-medicinal (personal protection and poultry isolation) and medicinal (poultry vaccination) ways to prevent, reduce, and control the rate of the H5N6 virus transmission. Among the proposed control strategies, we have shown that the poultry isolation strategy is still the most effective in reducing the infected birds.
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