Quantitative real-time polymerase chain reaction (RTqPCR) is a rapid and precise method of analysis to quantify the level of gene expression and is widely used in the diagnosis of diseases and quantitative analysis of genes. In RT-qPCR analysis, a reference gene (or housekeeping gene) is used for normalization of experimental results. Since this method of analysis detects a small quantity of the product, it is highly sensitive and it is important for the accuracy and reproducibility of the experiment to select a reference gene suitable for gene expression studies. As the expression levels of the reference gene are affected under different conditions, in order to determine the suitability of the housekeeping gene used as the reference gene, it is necessary to verify the expression stability. In the current study, the stability of the expression of 11 housekeeping genes (B2M, SDHA, GAPDH, RPL13, VIM, EEF1A1, HPRT1, GUSB, RPL19, ACTB, and ABL1) was investigated in the tissues of long-tailed chickens (heart, thigh, and breast). Expression stability evaluation was analyzed with four software: BestKeeper, NormFinder, geNorm, and RefFinder. In our study, GAPDH in heart tissue, HPRT1 in thigh tissue, and RPL13 in breast tissue were selected as the most stable reference genes. Evaluation of the expression stability of housekeeping genes can provide important data in gene expression studies by selecting an appropriate reference gene according to various conditions.

Selectins are cell membrane glycoproteins that recognize specific glycoconjugates expressed on the surface of cells. Then, selectins adjust cell-cell interactions that are important in inflammation, hemostasis and cancer metastasis. Selectins mediate leukocyte calls to move into the site of inflammation through interactions with activated endothelial cells or endogenous selectin ligands expressed in high endothelial venules. Types of selectins are divided into L-selectin, E-selectin and P-selectin, which are called to CD62L, CD62E, and CD62P, respectively. Each selectin is composed of four regions; the C-type lectin region of N-terminal, the epidermal growth factor (EGF) region, the intracellular C-terminal region, and the hydrophobic transmembrane region. They have similar structures but differ in their binding specificities and tissue distributions. The selectin family commonly recognizes the sialyl Lewis X (sLeX) on carbohydrate structures. Although biological ligands bound to each selectin are different from each other, they commonly bind to P-selectin glycoprotein ligand-1 (PSGL-1) ligand. The PSGL-1 ligand is a glycoprotein promoting cell adhesion in inflammatory responses. If the absence of selectins and their ligands in humans and animals are, should lead to persistent infections and diseases. Selectin family must be considered as a key subject for drug discovery since they have various functions depending on the ligand which they bind to.

Cluster of differentiation (CD) 24 or heat stable antigen 24 (HSA) molecule is a mucin-type glycoprotein attached to the cell surface by glycosylphosphatidylinositol (GPI)-anchor, promoting adhesive interactions between cells or in extracellular matrix. The aim of this study was to determine the not yet fully identified porcine CD24 gene and protein structure using computational analysis and to validate variants reported in exons of CD24 gene using direct sequencing. A total of 59 samples belonging to Yorkshire, Landrace, Berkshire, Jeju black pig and wild boar were used in the study. Human CD24 mRNA sequences were used as a reference and subjected to BLAST searches to retrieve the orthologous expressed sequence tags (ESTs) or cDNA sequences against NCBI and Ensemble databases. Assembled ESTs and retrieved cDNA sequences for the porcine CD24 gene were used for specific BLAST search to determine its genomic structure. We found porcine CD24 gene to consist of two exons and a relatively long intron. Second exon of porcine CD24 gene had a long 3’ untranslated region (UTR) and was very similar to that of human, mouse, rat, and sheep. The sequence homology of porcine CD24 protein was 65.38-84.62%, when analyzed with amino acid sequences of rat, mouse, human, cattle, and sheep CD24 protein. N-terminal signal sequence, O-glycosylation sites and GPI-anchoring signal sites were also predicted in pig, which showed these motifs to be evolutionary conserved across the species. Variant analysis in exonic regions of porcine CD24 among the multiple breeds showed that only second exon contained eight SNPs and three insertions in a 3’ UTR. Taken together, this study reports putative porcine CD24 gene and its protein structure using in silico approaches, which will be helpful for any further functional studies.

Bropirimine, a class of antineoplastic agents, is known as one of the potent immunomodulators and is currently under clinical development for the treatment of cancer. However, the effect of bropirimine on the cow remains unknown as a therapeutics agent. In this experiment, the effect of bropirimine in the peripheral blood mononuclear cells (PBMCs) stimulated by lipopolysaccharide (LPS) or concanavalin-A (Con-A) was examined. Jugular venous blood was collected from Korean Hanwoo calves and PBMCs were isolated. It was used to study the effect of bropirimine upon stimulation with LPS or Con-A for 72 hours. The expression pro-inflammatory cytokines like Tumor Necrosis Factor α (TNF-α) and Interferon γ (IFN-γ) were confirmed. Bropirimine significantly inhibited LPS- or Con-A-induced TNF-α and Con-A-induced IFN-γ in dose-dependent manner. Furthermore, Bropirimine inhibited TNF-α and Con-A mRNA expression at the transcription level. These results clearly indicated that bropirimine inhibited LPS or Con-A stimulated up-regulation of proinflammatory cytokines in a dose-dependent manner without conspicuous cytotoxicity. The bropirimine has potential to protect cow from LPS or Con-A induced endotoxin shock, possibly through inhibition of the production of proinflammatory cytokines. It suggesting that bropirimine may be a novel therapeutic agent for the prevention of inflammatory diseases. This result revealed specific features of the immune responses depending on the bropirimine compound and would help to knowledge of bovine immunity.

It became possible to perform genomic predictions using single nucleotide polymorphism (SNP) with advancements in genomics technology, not only in human but in livestock as well. There are strong interests in improving economical traits in livestock through identifying causative mutation, genes or predicting genomic breeding values. We present the current status of genome prediction studies for phenotype estimation of economic traits in livestock from various perspectives based on the genomic area. First, we introduce theoretical background of genomic prediction methods and newest development on SNP information. Thanks to develop sequencing technology, multi-omics data can be used to predict phenotypes associated with the economic traits. In particular, many studies show that genomic prediction accuracy of genomic partitioning data based on the biological information is higher than that of commercial SNP chip. Therefore, multi-omics data can be useful for genomic prediction studies. It is also important that researchers should consider factors affecting genomic prediction accuracy such as heritability, Quantitative Trait Loci (QTL) and marker density, size and structure of reference population. We also introduce genomic prediction studies based on the integration of multi-omics data that shows improvement of prediction accuracy than typical Genomic Best Linear Unbiased Prediction (GBLUP) models. We concluded that genomic prediction studies can be expanded to apply social issues, new phenotypes, or precision agriculture such as diseases, climate change, and metabolism including economic traits with multi-omics data using high-throughput technologies.

Toll-like receptor 7 (TLR7) is critical for the triggering of innate immune response by recognizing the conserved molecular patterns of single-stranded RNA (ssRNA) viruses and mediated antigenic adaptive immunity. To understand how TLR7 distinguish pathogen-derived molecular patterns from the host self, it is essential to be able to identify TLR7 receptor interaction interfaces, such as active sites or R848-agonist binding sites. The functional interfaces of TLR7 can serve as targets for structure-based drug design in studying the TLR7 receptor’s structure-function relationship. In contrast to mammalian TLR7, chicken TLR7 (chTLR7) is unknown for its important biological function. Therefore, it has been targeted to mediate contrasting evolutionary patterns of positive selection into non-synonymous SNPs across eleven species using TLR7 conservation patterns (evolutionary conserved and class-specific trace residues), where protein sequence differences to the TLR7 receptors of interest record mutation that have passed positive section across the species. In this study, we characterized the Lys609 residue on chTLR7-ECD homodimer interfaces to reflect the current tendency of evolving positive selection to be transfer into a stabilization direction of the R848-agonist/ chTLR7-ECDs complex under the phylogenetically variable position across species and we suggest a potential indicator for contrasting evolutionary patterns of both the species TLR-ECDs.

우리나라 고유 품종인 한우는 표현형 중 외모에 따라 일반적으로 한우라 불리는 황갈색 한우, 칡소, 흑우로 구분되어 있다. 한우 집단 중, 칡소는 한우의 원형으로 여겨지고 있으나, 제주흑우와 비슷하게 국내 희소품종으로 분류되어 있다. 현재 본 연구에서는 황갈색 한우와 칡소의 50K 고밀도 칩을 활용하여 선발신호를 검출할 수 있는 Rsb 분석에 따라 인위적 선발에 의해 진화적으로 선택된 유전체 영역을 탐색하였다. 그 결과, 37개의 후보유전체 영역이 한우와 비교하였을 때 칡소에서 유의적으로 다름을 알수 있었다. 후보 유전체 영역 내에 존재하는 유전자군을 대상으로 유전자 기능에 대한 주석 달기를 진행하였을 때, 불포화지방산 대사 과정, 면역 반응 등의 기능들이 통계적으로 유의함을 알 수 있었다. 이러한 유전체 영역들이 진화적 관점에서 칡소의 적응과정에 있어서 칡소만의 고유한 유전적 특성을 가지는데 기여하였다고 사료된다. 또한, 황갈색 한우의 선발신호와 칡소의 선발신호를 비교한 결과, 염색체 1번 2-2.5Mb 영역이 진화적 관점에서 공통적으로 선발되고 있음을 관찰할 수 있었으며, 해당 영역의 유전자를 살펴본 결과, 각 발달과정에 관여하는 유전자가 포함되어 있음을 알 수 있었다. 이는 한우라는 공통적 특성을 가지며 진화적으로 유지, 보존하고 있다고 예측할 수 있다. 칡소와 황갈색 한우가 가지는 선발신호는 거의 대부분이 다르다는 것을 Rsb 분석에 의해 확인하였다. 추가적으로 집단 내 고정된 단일염기서열변이 및 이형접합율을 비교한 결과 소수 집단에서 가지고 있는 유전적 변이 감소, 유전적 흐름의 급격한 변화 등의 유전적 특성이 칡소 집단에서 나타났으며, 이는 칡소의 선발신호 분석결과와 유사한 결과를 보임을 제시하고 있다. 이러한 결과는 향후 칡소를 비롯한 국내 한우에 대한 연구에 기초자료가 될 것이라 판단되며, 국내 한우 집단 차이의 정확한 원인에 대한 연구는 추가적으로 수행할 필요가 있을 것이라 사료된다.

The swine is one of the most widespread mammalian throughout the whole world. Presently, many studies concer-ning microsatellites in swine, especially domestic pigs, have been carried out in order to investigate general diversity patterns among either populations or breeds. Until now, a lot of time and effort spend into a single PCR method. But simple and more rapid multiplex PCR methods have been developed. The purpose of this study is to develop a robust set of microsatellites markers (MS marker) for traceability and individual identification. Using multiplex-PCR method with 23 MS marker divided 2 set, various alleles occurring to 5 swine breed (Berkshire, Landrace, Yorkshire, Duroc and Korea native pig) used markers to determine allele frequency and heterozygosity. MS marker found 4 alle-les at SW403, S0227, SWR414, SW1041 and SW1377. The most were found 10 alleles at SW1920. Heterozygosity represented the lowest value of 0.102 at SWR414 and highest value of 0.861 at SW1920. So, it was recognized appro-priate allele frequency for individual identification in swine. Using multiplex-PCR method, MS markers used to determine individual identification biomarker and breed-specific marker for faster, more accurate and lower analysis cost. Based on this result, a scientific basis was established to the existing pedigree data by applying genetics additio-nally. Swine traceability is expected to be very useful system and be conducted nationwide in future.

Many countries have implemented genetic evaluation for fertility traits in recent years. In particular, reproductive trait is a complex trait and need to require a system-level approach for identifying candidate genes related to the trait. To find the candidate gene associated with reproductive trait, we applied a weighted gene co-expression network ana-lysis from expression value of bovine genes. We identified three co-expressed modules associated with reproductive trait from bovine microarray data. Hub genes (ZP4, FHL2 and EGR4) were determined in each module; they were topologically centered with statistically significant value in the gene co-expression network. We were able to find the highly co-expressed gene pairs with a correlation coefficient. Finally, the crucial functions of co-expressed modules were reported from functional enrichment analysis. We suggest that the network-based approach in livestock may an important method for analyzing the complex effects of candidate genes associated with economic traits like repro-duction.

우리나라 고유 품종인 한우는 표현형 중 외모에 따라 일반적으로 한우라 불리는 황갈색 한우, 칡소, 흑우로 구분되어 있다. 한우 집단 중, 황갈색 한우만이 육질, 육량 형질을 중심으로 체계적인 개량프로그램에 의해 개량되었다. 본 연구에서는 황갈색 한우와 칡소의 50K 고밀도 칩을 활용하여 선발신호를 검출할 수 있는 세 가지 분석법(Rsb, iHS, FST)에 따라 인위적 선발에 의해 진화적으로 선택된 유전체영역을 탐색하였다. 그 결과, Rsb, iHS, FST 분석법에 따라 각각 41개, 23개, 50개의 후보유전체 영역이 칡소와 비교하였을 때 황갈색 한우에서 유의적으로 다름을 알 수 있었다. 또한, 후보 유전체 영역 내에 존재하는 유전자군을 대상으로 유전자 기능에 대한 주석 달기를 진행하였을 때, 근육 발달, 면역반응 등의 기능들이 통계적으로 유의함을 알 수 있었다. 이러한 유전체 영역들이 진화적 관점에서 황갈색 한우의 적응과정에 있어서 육질 등 생산성을 높이는 데에 기여하였다고 사료된다

This study was conducted to find a useful marker for gene polymorphism analysis using Microsatellite marker (MS marker) in Gyeongju Donggyeong dog. Twenty three MS marker analyzed the genetic features of DNA using 100 Gyeongju Donggyeong dogs in Gyeongju area. It was performed multiplex PCR with 3 set primer divided 9, 10 and 4 by analysis of conditions among MS markers. The results were calculated heterozygosity, polymorphic information content (PIC), allele frequency and number of allele at each locus using Microsatellite Toolkit software and Cervus 3.0 program. Total 148 alleles were genotyped to determine and average 6.43 alleles was detected. FH3381 had the highest of 15 alleles and FH2834 had the lowest of 2 alleles. Expected heterozygosity had a wide range from 0.282 to 0.876 and had average value of 0.6496. Also, Observed heterozygosity had a more wide range from 0.200 to 0.950 and had average value of 0.6404. PIC had range from 0.262 to 0.859 and average PIC was calculated 0.606. Especially, FH2998 represented the highest rate of observed heterozygosity of 0.950 and FH3381 represented the highest rate of expected heterozygosity of 0.876 and PIC of 0.859. The use of these markers was considered to be useful to study genetic traits of Gyeongju Donggyeong dog.