• Genomics & Informatics
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• v.6 no.2
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• pp.72-76
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• 2008

Hypoxia-inducible factor $1{\alpha}\;(HIF1{\alpha})$ is a transcription factor that plays a key role in the adaptation of cells to low oxygen stress and oxygen homeostasis. The oxygen-dependent degradation (ODD) domain of $HIF1{\alpha}$ is responsible for the negative regulation of $HIF1{\alpha}$ in normoxia. The interactions of the $HIF1{\alpha}$ ODD domain with partner proteins such as von Hippel-Lindau tumor suppressor (pVHL) and p53 are mediated by two sequence motifs, the N- and C-terminal ODD(NODD and CODD). Multiple sequence alignment with $HIF1{\alpha}$ homologs from human, monkey, pig, rat, mouse, chicken, frog, and zebrafish has demonstrated that the NODD and CODD motifs have noticeably high conservation of the primary sequence across different species and isoforms. In this study, we carried out molecular dynamics simulation of the structure of the $HIF1{\alpha}$ CODD motif in complex with the p53 DNA-binding domain (DBD). The structure reveals specific functional roles of highly conserved residues in the CODD sequence motif of $HIF1{\alpha}$ for the recognition of p53.

• Asian-Australasian Journal of Animal Sciences
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• v.31 no.6
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• pp.791-797
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• 2018

Objective: Trimethylation of histone 3 (H3) at 4th lysine N-termini (H3K4me3) in gene promoter region was the universal marker of active genes specific to cell lineage. On the contrary, coexistence of trimethylation at 27th lysine (H3K27me3) in the same loci-the bivalent H3K4m3/H3K27me3 was known to suspend the gene transcription in germ cells, and could also be inherited to the developed stem cell. In galline species, throughout example of H3K4m3 and H3K27me3 ChIP-seq analysis was still not provided. We therefore designed and demonstrated such procedures using ChIP-seq and mRNA-seq data of chicken follicular mesenchymal cells and male germ cells. Methods: Analytical workflow was designed and provided in this study. ChIP-seq and RNA-seq datasets of follicular mesenchymal cells and male germ cells were acquired and properly preprocessed. Peak calling by Model-based analysis of ChIP-seq 2 was performed to identify H3K4m3 or H3K27me3 enriched regions ($Fold-change{\geq}2$, $FDR{\leq}0.01$) in gene promoter regions. Integrative genomics viewer was utilized for cellular retinoic acid binding protein 1 (CRABP1), growth differentiation factor 10 (GDF10), and gremlin 1 (GREM1) gene explorations. Results: The acquired results indicated that follicular mesenchymal cells and germ cells shared several unique gene promoter regions enriched with H3K4me3 (5,704 peaks) and also unique regions of bivalent H3K4m3/H3K27me3 shared between all cell types and germ cells (1,909 peaks). Subsequent observation of follicular mesenchyme-specific genes-CRABP1, GDF10, and GREM1 correctly revealed vigorous transcriptions of these genes in follicular mesenchymal cells. As expected, bivalent H3K4m3/H3K27me3 pattern was manifested in gene promoter regions of germ cells, and thus suspended their transcriptions. Conclusion: According the results, an example of chicken H3K4m3/H3K27me3 ChIP-seq data analysis was successfully demonstrated in this study. Hopefully, the provided methodology should hereby be useful for galline ChIP-seq data analysis in the future.

• Korean Journal of Poultry Science
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• v.40 no.3
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• pp.223-234
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• 2013

Poultry industry is abounding day by day as it engrosses less cost of investment per bird as compared to large animals. Poultry have the most copious genomic tool box amongst domestic animals for the detection of quantitative trait loci (QTL) and marker assisted selection (MAS). Use of multiple markers and least square techniques for mapping of QTL affecting quality and production traits in poultry is in vogue. Examples of genetic tests that are available to or used in industry programs are documented and classified into causative mutations (direct markers), linked markers in population-wide linkage disequilibrium (LD) with the QTL (LD markers), and linked markers in population wide equilibrium with the QTL (LE markers). Development of genome-wide SNP assays, role of 42 K, 60 K (Illumina) and 600 K (Affymetrix$^{(R)}$ Axim$^{(R)}$) SNP chip with next generation sequencing for identification of single nucleotide polymorphism (SNP) has been documented. Hybridization based, PCR based, DNA chip and sequencing based are the major segments of DNA markers which help in conducting of MAS in poultry. Economic index-marker assisted selection (EI-MAS) provides platform for simultaneous selection for production traits while giving due weightage to their marginal economic values by calculating predicted breeding value, using information on DNA markers which are normally associated with relevant QTL. Understanding of linkage equilibrium, linkage dis-equilibrium, relation between the markers and gene of interest are quite important for success of MAS. This kind of selection is the most useful tool in enhancing disease resistance by identifying candidate genes to improve the immune response. The application of marker assisted selection in selection procedures would help in improvement of economic traits in poultry.

• Animal Bioscience
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• v.35 no.3
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• pp.367-376
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• 2022

Objective: The highly pathogenic avian influenza virus (HPAIV) is a threat to the poultry industry as well as the economy and remains a potential source of pandemic infection in humans. Antiviral genes are considered a potential factor for HPAIV resistance. Therefore, in this study, we investigated gene expression related to cytokine-cytokine receptor interactions by comparing resistant and susceptible Ri chicken lines for avian influenza virus infection. Methods: Ri chickens of resistant (Mx/A; BF2/B21) and susceptible (Mx/G; BF2/B13) lines were selected by genotyping the Mx dynamin like GTPase (Mx) and major histocompatibility complex class I antigen BF2 genes. These chickens were then infected with influenza A virus subtype H5N1, and their lung tissues were collected for RNA sequencing. Results: In total, 972 differentially expressed genes (DEGs) were observed between resistant and susceptible Ri chickens, according to the gene ontology and Kyoto encyclopedia of genes and genomes pathways. In particular, DEGs associated with cytokine-cytokine receptor interactions were most abundant. The expression levels of cytokines (interleukin-1β [IL-1β], IL-6, IL-8, and IL-18), chemokines (C-C Motif chemokine ligand 4 [CCL4] and CCL17), interferons (IFN-γ), and IFN-stimulated genes (Mx1, CCL19, 2'-5'-oligoadenylate synthase-like, and protein kinase R) were higher in H5N1-resistant chickens than in H5N1-susceptible chickens. Conclusion: Resistant chickens show stronger immune responses and antiviral activity (cytokines, chemokines, and IFN-stimulated genes) than those of susceptible chickens against HPAIV infection.

• Korean Journal of Poultry Science
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• v.50 no.2
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• pp.101-108
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• 2023

This study was conducted to investigate the appropriate levels of crude protein (CP) and phytase in the diet of broiler chicks in order to reduce nitrogen and phosphorus contents in feces while maintaining performance of broilers. Six hundred forty-eight 1-day-old male broilers (41.9±0.91 g) had a total of 3 × 3 complex factor of 3 levels of CP (22%, 21%, 20%) and 3 levels of phytase (1,000, 800, 500 FTU/kg) in the diet. Divided into 9 treatments, 4 replications per treatment, 18 birds per replication, were completely randomly assigned and reared in a metabolic cage for 7 days. Seven-day-old body weight (BW) and body weight gain (BWG) of broilers were significantly lower at CP 20% treatment (P<0.05), and feed conversion ratio (FCR) was significantly lower at CP 21% and phytase 800 FTU/kg treatment (P<0.05). Nitrogen and phosphorus contents in chicken excreta were significantly lower in CP 20% and phytase 500 FTU/kg treatment, respectively (P<0.05). Interactions between CP and phytase in the feed were shown for nitrogen and phosphorus in feces (P<0.05). In conclusion, considering the broiler performance and excretion contents of nitrogen and phosphorus, it is thought that CP and phytase levels of broiler chicks diet can be reduced by 21% and 800 FTU/kg, respectively.

• Korean Journal of Poultry Science
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• v.38 no.4
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• pp.293-304
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• 2011

The current work was carried out to investigate the effect of crossbred Korean native chickens (KNC) on performance and meat quality. A total of 720 chicks (1d of age) was used in this work and were divided into groups by crossbreds (A, B, C and D) and sex (male and female). Crossbreds were A) (KNC egg-meat type C strains ${\times}$ KNC meat type S strains) ${\times}$ Ross broiler, B) (KNC egg-meat type C strains ${\times}$ KNC meat type H strains) ${\times}$ KNC meat type S strains, C) (KNC native R strains${\times}$KNC meat type S strains)${\times}$KNC meat type H strains and D(White Semibroiler Chickens). Experimental diets consisted of 3 phases such as starter (0~5 weeks; CP 20.0%, ME 3,050 kcal/kg), earlier (5~8 weeks; CP 18.0%, ME 3,100 kcal/kg) and finisher (8~12 weeks; CP 16.0%, ME 3,150 kcal/kg). They were fed the broiler diets for 12 weeks at the flat house and thirty six chickens were slaughtered at week 5 and 10. There was no significant difference on the fertility of crossbred KNCs, and the hatchability of B crossbred was low compared to other crossbreds. On body weight (BW), D crossbred resulted in a higher BW after 5 weeks (P<0.05). Body weight gain (BWG) and feed intake (FI) of A crossbred were also significant higher compared to the other crossbreds for all periods. On carcass ratio (CR), A crossbred showed higher CR at 5 weeks, there was no significant among crossbreds at 10 weeks. The partial meat ratio(ala, breast, neck, leg) of C crossbred was the lowest among other crossbreds (P<0.05), but the back meat ratio was not difference among treatments at 5 and 10 weeks. pH of meats have no difference among crossbreds at 5 week, and A crossbred was high compared to other crossbreds at 10 week (P<0.05). The moisture content of D crossbred meat and the protein content of B crossbred meat were high compared to other crossbreds at 5 week. Chemical compositions of meats have no difference among crossbreds at 10 week. Lightness and redness have not significance among crossbreds at 5 week, and redness of A crossbred was the highest among all crossbreds (P<0.05). Shear force and cooking loss of A crossbred were high at 5 week, and cooking loss of A crossbred was low compared with other crossbreds at 10 week. These results suggested the basic data that needed to develope the new strains.