<i>In-silico</i>investigation of genomic regions related to ascites and identifying their pathways in broilers

Davoodi, P.; Ehsani, Alireza

doi:10.1017/s0043933919000035

Cited by 3 publications

(1 citation statement)

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“…By identifying genes related to avUCP from the literature, a list of genes was extracted according to Davoodi and Ehsani (55) for protein-protein network prediction. The list of most related-genes was provided through the retrospective review of previous studies on avUCP (5,42,(56)(57)(58)(59)(60)(61)(62)(63)(64)(65)(66)(67)(68)(69)(70)(71).…”

Section: Interactive Network Prediction and Gene-based Enrichment Ana...mentioning

confidence: 99%

In silico investigation of uncoupling protein function in avian genomes

et al. 2023

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IntroductionThe uncoupling proteins (UCPs) are involved in lipid metabolism and belong to a family of mitochondrial anionic transporters. In poultry, only one UCP homologue has been identified and experimentally shown to be associated with growth, feed conversion ratio, and abdominal fat according to its predominant expression in bird muscles. In endotherm birds, cell metabolic efficiency can be tuned by the rate of mitochondrial coupling. Thus, avUCP may be a key contributor to controlling metabolic rate during particular environmental changes.MethodsThis study aimed to perform a set of in-silico investigations primarily focused on the structural, biological, and biomimetic functions of avUCP. Thereby, using in silico genome analyses among 8 avian species (chicken, turkey, swallow, manakin, sparrow, wagtail, pigeon, and mallard) and a series of bioinformatic approaches, we provide phylogenetic inference and comparative genomics of avUCPs and investigate whether sequence variation can alter coding sequence characteristics, the protein structure, and its biological features. Complementarily, a combination of literature mining and prediction approaches was also applied to predict the gene networks of avUCP to identify genes, pathways, and biological crosstalk associated with avUCP function.ResultsThe results showed the evolutionary alteration of UCP proteins in different avian species. Uncoupling proteins in avian species are highly conserved trans membrane proteins as seen by sequence alignment, physio-chemical parameters, and predicted protein structures. Taken together, avUCP has the potential to be considered a functional marker for the identification of cell metabolic state, thermogenesis, and oxidative stress caused by cold, heat, fasting, transfer, and other chemical stimuli stresses in birds. It can also be deduced that avUCP, in migrant or domestic birds, may increase heat stress resistance by reducing fatty acid transport/b-oxidation and thermoregulation alongside antioxidant defense mechanisms. The predicted gene network for avUCP highlighted a cluster of 21 genes involved in response to stress and 28 genes related to lipid metabolism and the proton buffering system. Finally, among 11 enriched pathways, crosstalk of 5 signaling pathways including MAPK, adipocytokine, mTOR, insulin, ErbB, and GnRH was predicted, indicating a possible combination of positive or negative feedback among pathways to regulate avUCP functions.DiscussionGenetic selection for fast-growing commercial poultry has unintentionally increased susceptibility to many kinds of oxidative stress, and so avUCP could be considered as a potential candidate gene for balancing energy expenditure and reactive oxygen species production, especially in breeding programs. In conclusion, avUCP can be introduced as a pleiotropic gene that requires the contribution of regulatory genes, hormones, pathways, and genetic crosstalk to allow its finely-tuned function.

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Section: Interactive Network Prediction and Gene-based Enrichment Ana...mentioning

confidence: 99%

In silico investigation of uncoupling protein function in avian genomes

et al. 2023

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A meta-analysis comparing the composition and quality differences between chicken meats produced under the free-range and conventional systems

Davoodi

Ehsani

Torshizi

et al. 2021

World's Poultry Science Journal

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Transcriptomic Study on the Lungs of Broilers with Ascites Syndrome

Guo

Zhang

Han

et al. 2023

Animals

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Although broiler ascites syndrome (AS) has been extensively studied, its pathogenesis remains unclear. The lack of cardiopulmonary function in broilers causes relative hypoxia in the body; hence, the lung is the main target organ of AS. However, the transcriptome of AS lung tissue in broilers has not been studied. In this study, an AS model was successfully constructed, and lung tissues of three AS broilers and three healthy broilers were obtained for RNA sequencing (RNA-seq) and pathological observation. The results showed that 614 genes were up-regulated and 828 genes were down-regulated in the AS group compared with the normal group. Gene Ontology (GO) functional annotation revealed the following up-regulated genes: FABP4, APLN, EIF2AK4, HMOX1, MMP9, THBS1, TLR4, BCL2; and down-regulated genes: APELA, FGF7, WNT5A, CDK6, IL7, IL7R, APLNR. These genes have attracted much attention in cardiovascular diseases such as pulmonary hypertension. Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis showed that multiple metabolic processes were enriched, indicating abnormal lung metabolism of AS in broilers. These findings elucidate the potential genes and signal pathways in the lungs of broilers with AS and provide a potential target for studying the pathogenesis and preventing AS.

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In-silicoinvestigation of genomic regions related to ascites and identifying their pathways in broilers

Cited by 3 publications

References 18 publications

In silico investigation of uncoupling protein function in avian genomes

In silico investigation of uncoupling protein function in avian genomes

A meta-analysis comparing the composition and quality differences between chicken meats produced under the free-range and conventional systems

Transcriptomic Study on the Lungs of Broilers with Ascites Syndrome

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