Integrative analysis of the ovarian metabolome and transcriptome of the Yaoshan chicken and its improved hybrids

Introduction: Laying performance is a key factor affecting production efficiency in poultry, but its molecular mechanism is still indistinct. In this study, Yaoshan chickens, a local breed in Guizhou, China, and merchant chickens (GYR) with higher egg yield after the three-line cross improvement hybridization of Yaoshan chickens were used as animal samples. Methods: To explore the regulatory mechanism of the diversities in laying performance, RNA-seq and ultra-performance liquid chromatographytandem mass spectrometry (UPLC-MS/MS) were used to describe the transcriptional and metabolic profiles of the ovaries of Yaoshan and GYR chickens. Results: 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 showed that ECM-receptor interactions and the TGF-β signaling pathway were restrained, resulting in increased egg production in GYR chickens. Furthermore, the upregulation of thiamine and carnitine was identified by metabolomic analysis to facilitate the laying performance of hens. Finally, comprehensive analyses of the transcriptome and metabolome found that thiamine and carnitine were negatively correlated with ECM-receptor interactions and the TGF-β signaling pathway, which jointly regulate the laying performance of Yaoshan chickens and GYR chickens. Discussion: Taken together, our research 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.

Structural characterization and transcript-metabolite correlation network of immunostimulatory effects of sulfated polysaccharides from green alga Ulva pertusa

Three water-soluble polysaccharides (UPPs 1-3) were obtained from edible green alga Ulva pertusa. The chemico-physical analyses indicated that UPPs 1-3 possessed molecular weights of 376.7 kDa, 57.21 kDa, and 131.13 kDa, with sulfate contents of 26.01 ± 8.13%, 9.86 ± 3.24%, and 13.32 ± 6.56%, respectively, and composed of arabinose, galactose, glucose, xylose, galacturonic acid, glucuronic acid, and mannuronic acid, with different ratios. The in vitro studies revealed that UPP-1 showed significant effects on the proliferation and phagocytic activity of macrophage, release of nitric oxide, and secretion of cytokines (TNF-α and IL-6). The transcript-metabolite analysis of UPP-1 treated macrophage revealed 4747 differential genes (2416 up-regulated and 2331 down-regulated) and 94 differential metabolites (77 up-regulated and 17 down-regulated) that significantly co-mapped a transcript-metabolite correlation network of biosynthesis of amino acids, glycerophospholipid metabolism, and carbon metabolism. Thus, these findings provide a valuable foundation for the potential application of U. pertusa polysaccharides.

Integrative analysis of transcriptomics and metabolomics profiling on flesh quality of large yellow croaker Larimichthys crocea fed a diet with hydroxyproline supplementation

A previous study showed that flesh quality of large yellow croaker (LYC) was improved by feeding dietary hydroxyproline (Hyp, 0·69 %). The aim of the present study was to explore the underlying mechanisms using transcriptomics and metabolomics analysis. The metabolomics analysis showed that muscle metabolite profiles could be clearly separated between the basal diet and Hyp supplementation diet. Metabolites including betaine, Hyp, lactate, glucose-6-phosphate, trimethylamine N-oxide, taurine, creatine, inosine monophosphate, histamine and serine made significant contribution to the separation. Compared with the control diet, the transcriptomics analysis identified a total of 334 different expressed genes, of which 298 genes were up-regulated and thirty-six genes were down-regulated in the Hyp supplementation group. The altered genes of the Hyp supplementation group were involved in collagen metabolism, lipid metabolism and energy metabolism. The integrated results revealed that the increased muscle collagen content in the Hyp supplementation diet was partly because of its enhancement of biosynthesis and the reduction of degradation. The improvement of muscle quality by dietary Hyp supplementation could also be related to a good utilisation of glucose through enhancement of glycolysis. It was concluded that dietary Hyp supplementation could improve flesh quality because of comprehensive metabolism changes including elevated collagen content, glycolysis, lipid metabolism and flesh flavour of LYC. The present study provided a novel strategy to understand the underlying molecular mechanism of flesh quality of LYC fed diet with Hyp supplementation.

The comparative analysis of phenotypic and whole transcriptome gene expression data of ascites susceptible versus ascites resistant chickens

Ascites syndrome (AS) is a metabolic disorder that mainly occurs at later ages of meat-type chickens. Despite many research, there is no consensus about the origin of this syndrome. Our main purpose were to investigate the syndrome using both phenotypic and RNA-Seq data to elucidate the most causative factors predisposing the birds to AS. Phenotypic data analysis showed that AS indicator traits (AITs) were moderate to high heritable. Inexistence of consistent direct genetic correlation between AITs and growth related traits, indicated that neither faster growth rate nor heavier body weight is the most causative factor affecting the susceptibility of broilers to AS. However, respiratory capacity was revealed to be the most probable factor predisposing the birds to AS, as both lung weight and lung percentage were negatively correlated with AITs. Transcriptomic data analysis revealed 125 differentially expressed genes (DEGs) between the ascitic and healthy groups. Up-regulated genes in ascitic group enriched mainly in gas transport biological process, while down-regulated genes involved in defense response to bacteria, biological adhesion, cell adhesion, killing of cells of another organism and cell division. Genetic association of the DEGs with human cardiovascular diseases suggested excessive heart problems of the ascitic chicks. Heart is, probably, the first tissue suffering from the incompetence of small respiratory system of the AS-susceptible chickens. In other word, tissue hypoxia, that causes free radicals to concentrate in heart cells, may be the commencement of events that finally result to heart failure, suffocation and death of chicks due to the AS.

Iron oxide nanozyme suppresses intracellular Salmonella Enteritidis growth and alleviates infection in vivo

Rational:Salmonella Enteritidis (S. Enteritidis) is a globally significant zoonotic foodborne pathogen which has led to large numbers of deaths in humans and caused economic losses in animal husbandry. S. Enteritidis invades host cells and survives within the cells, causing resistance to antibiotic treatment. Effective methods of elimination and eradication of intracellular S. Enteritidis are still very limited. Here we evaluated whether a new intracellular antibacterial strategy using iron oxide nanozymes (IONzymes) exerted highly antibacterial efficacy via its intrinsic peroxidase-like activity in vitro and in vivo.Methods: The antibacterial activities of IONzymes against planktonic S. Enteritidis, intracellular S. Enteritidis in Leghorn Male Hepatoma-derived cells (LMH), and liver from specific pathogen free (SPF) chicks were investigated by spread-plate colony count method and cell viability assay. Changes in levels of microtubule-associated protein light chain 3 (LC3), a widely used marker for autophagosomes, were analyzed by immunoblotting, immunofluorescence, and electron microscopy. Reactive oxygen species (ROS) production was also assessed in vitro. High-throughput RNA sequencing was used to investigate the effects of IONzymes on liver transcriptome of S. Enteritidis-infected chicks. Results: We demonstrated that IONzymes had high biocompatibility with cultured LMH cells and chickens, which significantly inhibited intracellular S. Enteritidis survival in vitro and in vivo. In addition, co-localization of IONzymes with S. Enteritidis were observed in autophagic vacuoles of LMH cells and liver of chickens infected by S. Enteritidis, indicating that IONzymes mediated antibacterial reaction of S. Enteritidis with autophagic pathway. We found ROS level was significantly increased in infected LMH cells treated with IONzymes, which might enhance the autophagic elimination of intracellular S. Enteritidis. Moreover, orally administered IONzymes decreased S. Enteritidis organ invasion of the liver and prevented pathological lesions in a chicken-infection model. Non-target transcriptomic profiling also discovered IONzymes could change hepatic oxidation-reduction and autophagy related gene expressions in the S. Enteritidis infected chickens. Conclusion: These data suggest that IONzymes can increase ROS levels to promote the antibacterial effects of acid autophagic vacuoles, and thus suppress the establishment and survival of invading intracellular S. Enteritidis. As a result, IONzymes may be a novel alternative to current antibiotics for the control of intractable S. Enteritidis infections.

UPLC-QTOF MS-Based Serum Metabolomic Profiling Analysis Reveals the Molecular Perturbations Underlying Uremic Pruritus

As one of the most troublesome complications in patients with chronic renal disease, the etiology of uremic pruritus remains unknown, and the current therapeutic approaches are limited and unsatisfactory. To identify potential biomarkers for improving diagnosis and treatment and obtain a better understanding of the pathogenesis of uremic pruritus, we compared serum metabolome profiles of severe uremic pruritus (HUP) patients with mild uremic pruritus (LUP) patients using ultraperformance liquid chromatography-quadruple time-of-flight mass spectrometry (UPLC-QTOF MS). Partial least squares discriminant analysis (PLS-DA) showed that the metabolic profiles of HUP patients are distinguishable from those of LUP patients. Combining multivariate with univariate analysis, 22 significantly different metabolites between HUP and LUP patients were identified. Nine of the 22 metabolites in combination were characterized by a maximum area-under-receiver operating characteristic curve (AUC = 0.899) with a sensitivity of 85.1% and a specificity of 83.0% distinguishing HUP and LUP. Our results indicate that serum metabolome profiling might serve as a promising approach for the diagnosis of uremic pruritus and that the identified biomarkers may improve the understanding of pathophysiology of this disorder. Because the 9 metabolites were phospholipids, uremic toxins, and steroids, further studies may reveal their possible role in the pathogenesis of uremic pruritus.

A Trial Diagnosis of Ascites Syndrome in Broiler Chickens

BACKGROUND

Ascites syndrome is currently a serious disease issue for the global chicken industry. Ascites syndrome is a metabolic disorder frequently found in fast growing broilers including abdominal distention and standing fluid collection in chicken abdomen. It is one of the most common nutrition metabolic disorders.

MATERIALS AND METHODS

In this study, the clinical diagnosis technology of broiler ascites symptoms mainly included the trial inquiry of feeders and administrators, local observation, detection of farm gas and faeces and pathological autopsy.

RESULTS

The study investigated the case of broiler ascites syndrome of local commercial broiler chickens at the age of 4-5 weeks to reduce outburst of ascites syndrome in broiler chickens. Through the trial clinical diagnosis of broiler ascites symptoms and pathological autopsy and observation, it came to the definite diagnosis of broiler ascites. Subsequent investigation found that the rearing houses were closed and sealed with poor ventilation and a high breeding density and much ammonia gas.

CONCLUSION

Under the comprehensive management and drug treatments, there were 800 chickens found ill and later came back to normal from illness after the treatments, except for the death of 38 sick chickens. The appetite and drink of broiler chicken came to normal gradually.

Transcriptome Analysis and Gene Identification in the Pulmonary Artery of Broilers with Ascites Syndrome

BACKGROUND

Pulmonary arterial hypertension, also known as Ascites syndrome (AS), remains a clinically challenging disease with a large impact on both humans and broiler chickens. Pulmonary arterial remodeling presents a key step in the development of AS. The precise molecular mechanism of pulmonary artery remodeling regulating AS progression remains unclear.

METHODOLOGY/PRINCIPAL FINDINGS

We obtained pulmonary arteries from two positive AS and two normal broilers for RNA sequencing (RNA-seq) analysis and pathological observation. RNA-seq analysis revealed a total of 895 significantly differentially expressed genes (DEGs) with 437 up-regulated and 458 down-regulated genes, which were significantly enriched to 12 GO (Gene Ontology) terms and 4 KEGG (Kyoto Encyclopedia of Genes and Genomes) pathways (Padj<0.05) regulating pulmonary artery remodeling and consequently occurrence of AS. These GO terms and pathways include ribosome, Jak-STAT and NOD-like receptor signaling pathways which regulate pulmonary artery remodeling through vascular smooth cell proliferation, inflammation and vascular smooth cell proliferation together. Some notable DEGs within these pathways included downregulation of genes like RPL 5, 7, 8, 9, 14; upregulation of genes such as IL-6, K60, STAT3, STAT5 Pim1 and SOCS3; IKKα, IkB, P38, five cytokines IL-6, IL8, IL-1β, IL-18, and MIP-1β. Six important regulators of pulmonary artery vascular remodeling and construction like CYP1B1, ALDH7A1, MYLK, CAMK4, BMP7 and INOS were upregulated in the pulmonary artery of AS broilers. The pathology results showed that the pulmonary artery had remodeled and become thicker in the disease group.

CONCLUSIONS/SIGNIFICANCE

Our present data suggested some specific components of the complex molecular circuitry regulating pulmonary arterial remodeling underlying AS progression in broilers. We revealed some valuable candidate genes and pathways that involved in pulmonary artery remodeling further contributing to the AS progression.