• Asian-Australasian Journal of Animal Sciences
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• v.25 no.5
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• pp.613-620
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• 2012

Marbling from intramuscular fat is an important trait of meat quality and has an economic benefit for the beef industry. Quantitative trait loci (QTL) fine mapping was performed to identify the marbling trait in 266 Hanwoo steers using a 10K single nucleotide polymorphism panel with the combined linkage and linkage disequilibrium method. As a result, we found nine putative QTL regions for marbling: three on BTA6, two on BTA17, two on BTA22, and two on BTA29. We detected candidate genes for marbling within 1 cM of either side of the putative QTL regions. Additionally, to understand the functions of these candidate genes at the molecular level, we conducted a functional categorization using gene ontology and pathway analyses for those genes involved in lipid metabolism or fat deposition. In these putative QTL regions, we found 95 candidate genes for marbling. Using these candidate genes, we found five genes that had a direct interaction with the candidate genes. We also found SCARB1 as a putative candidate gene for marbling that involves fat deposition related to cholesterol transport.

• Journal of Microbiology and Biotechnology
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• v.18 no.2
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• pp.234-241
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• 2008

Agrobacterum tumefaciens-mediated transformation (ATMT) is becoming an effective system as an insertional mutagenesis tool in filamentous fungi. We developed and optimized ATMT for two Colletotrichum species, C. falcatum and C. acutatum, which are the causal agents of sugarcane red rot and pepper anthracnose, respectively. A. tumefaciens strain SK1044, carrying a hygromycin phosphotransferase gene (hph) and a green fluorescent protein (GFP) gene, was used to transform the conidia of these two Colletotrichum species. Transformation efficiency was correlated with co-cultivation time and bacterial cell concentration and was higher in C. falcatum than in C. acutatum. Southern blot analysis indicated that about 65% of the transformants had a single copy of the T-DNA in both C. falcatum and C. acutatum and that T-DNA integrated randomly in both fungal genomes. T-DNA insertions were identified in transformants through thermal asymmetrical interlaced PCR (TAIL-PCR) followed by sequencing. Our results suggested that ATMT can be used as a molecular tool to identify and characterize pathogenicity-related genes in these two economically important Colletotrichum species.

• Asian-Australasian Journal of Animal Sciences
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• v.15 no.7
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• pp.938-943
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• 2002

This study was perfonned to detect polymorphisms of the two candidate genes, bovine BTN (Butyrophilin) and ST AT5a (Signal Transducers and Activators of Transcription) gene using 98 Holstein bulls' frozen semen, and to offer the basic information for QTL (Quantitative Trait Loci) analysis. Each BTN PCR product was digested with endonuclease restriction enzyme. The digested fragments of four BTN PCR products were observed as follows: 316,280, and 162 bp in BTN1, 568, 305 and 263 bp in BTN2, 576, 332, and 244 bp in BTN3, and 573, 291, and 282 bp in BTN4, respectively. The gene frequencies of A and B allele in four BTN loci were as follows: 0.8980 and 0.1020 in BTN1, 0.5510 and 0.4490 in BTN2, 0.8163 and 0.1837 in BTN3, and 0.8875 and 0.1122 in BTN4, respectively. And three genotypes (homotypel, heterotype, and homotype2) for STAT5a were observed by SSCP (single stranded conformational polymorphism) method and the genotype frequencies are 78.57%, 19.39%, and 2.04%, respectively. The PlC (Polymorphism Information Content) value and heterozygosity of four BTN loci were as follows: 0.1695 and 0.1870 in BTN1, 0.3713 and 0.4927 in BTN2, 0.2549 and 0.2999 in BTN3, and 0.1794 and 0.1992 in BTN4, respectively. Comparing with the reported data, PlC value of BTN2 might have the possibility to be useful marker. Other BTN loci indicated skewed allele distribution.

• Asian-Australasian Journal of Animal Sciences
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• v.19 no.10
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• pp.1409-1414
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• 2006

The objective of this study was to screen single nucleotide polymorphisms (SNPs) of the chicken lipoprotein lipase gene (LPL), using 545 F1 hybrids developed from $4{\times}4$ diallel crossing of four chicken breeds, and to analyze the associations between polymorphisms of the LPL and chicken fat deposition traits. PCR-SSCP was used to detect SNPs in LPL. Fifteen sets of primers were designed to amplify DNA fragments covering the 5'flanking and coding regions of LPL. It showed that there existed 5 polymorphic loci in the 5'flanking region and coding region, respectively. Association analysis was carried out between 10 polymorphic loci and intermuscular fat width, abdominal fat weight, and thickness of subcutaneous fat using ANCOVA, respectively. The results indicated that, in the 5'flanking region, the loci d and e significantly affected thickness of subcutaneous fat (p<0.05), abdominal fat weight (p<0.01) and subcutaneous fat (p<0.05), while in the coding region, synonymous mutation in exon 8 was significantly associated with intermuscular fat width (p<0.05), however, the non-synonymous mutations in exon 7 and exon 9 did not show statistically significant effects on fat deposition traits in this study.

• Journal of the Korean Academy of Child and Adolescent Psychiatry
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• v.23 no.1
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• pp.8-13
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• 2012

Objectives : Urocanase domain containing 1 (UROC1) has never been studied in prior studies on autism spectrum disorders (ASDs). UROC1 causes urocanic aciduria, one of the symptoms of which is mental retardation. The aim of this study was to investigate the association between the UROC1 gene and ASDs in a Korean population. Methods : A total of 258 control and 214 patients with ASD were used as subjects of this study. SNPs selected from UROC1 were genotyped using Illumina Golden-Gate Genotyping assay with VeraCode$^{(R)}$ technology. Statistical analysis was performed using SAS and Plink software. Results : We found no association of the 12 SNPs in the UROC1 gene with ASDs in a Korean population. Conclusion : Our study suggests that the 12 SNPs (11 SNPs and 1 SNP in the intron and 3'UTR region, respectively) in the UROC1 were not associated with ASDs in a Korean population. Further study on the exon region of UROC1 is needed.

• Journal of Gastric Cancer
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• v.3 no.4
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• pp.206-213
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• 2003

Purpose: The clinical implication of p53 mutation in gastric cancer is still unclear, as shown by the discordant results that continue to be reported in the literature. Materials and Methods: To assess p53 gene mutation, tumor p53 overexpression, and serum anti-p53 antibody, we employed a polymerase chain reaction-single strand conformation polymorphism (PCR-SSCP) analysis, an immunohistochemistry using monoclonal antibody DO-7, and an enzymelinked immunosorbent assay (ELISA), respectively. Results: Of 169 surgical specimens of gastric cancer, mutation at exon $5\∼8$ of the p53 was identified in 33 ($19.5\%$) and was significantly correlated with lymph node metastasis. Overexpression of p53 was found in 62 specimens ($36.7\%$) and had a significant correlation with tumor differentiation. Serum anti-p53 antibody was positive in 18 patients ($10.7\%$). Twenty-three of the mutated tumors ($69.7\%$) and 39 of the non-mutated tumors ($28.7\%$) displayed immunoreactivity. Twelve of the immunopositive tumors ($19.4\%$) and 6 of the immunonegative tumors produced anti-p53 antibody. These differences were statistically significant (P<0.001 and P=0.005, respectively). There was no significant difference in survival according to the mutation of p53. Conclusion: Mutation and overexpression of p53 can be easily detected by immunohistochemistry. However, standardization of the immunohistochemical staining method, as well as guidelines for interpreting the stained result, will produce concordant results and thereby improve clinical application.

• Asian Pacific Journal of Cancer Prevention
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• v.16 no.14
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• pp.5647-5654
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• 2015

Gall bladder cancer (GBC) is a gastro-intestinal cancer with high prevalence among north Indian women. Platelet derived growth factor-B (PDGFB) and human epidermal growth factor receptor-2 (HER2) may play roles in the etiology of GBC through the inflammation-hyperplasia-dysplasia-carcinoma pathway. To study the association of PDGFB and HER2 polymorphisms with risk of GBC, 200 cases and 300 controls were considered. PDGFB +286A>G and +1135A>C polymorphisms were investigated with an amplification refractory mutation system and the HER2 $Ile^{655}Val$ polymorphism by restriction fragment length polymorphism. Significant risk associations for PDGFB +286 GG (OR=5.25) and PDGFB +1135 CC (OR=3.19) genotypes were observed for GBC. Gender wise stratification revealed susceptibility for recessive models of PDGFB +1135A>C (OR=3.00) and HER2 $Ile^{655}Val$ (OR=2.52) polymorphisms among female GBC cases. GBC cases with gall stones were predisposed to homozygous +286 GG and +1135 CC genotypes. Significant risk associations were found for ACIle (OR=1.48), GAVal (OR=1.70), GAIle (OR=2.00) haplotypes with GBC cases and GCIle haplotype with female GBC cases (OR=10.37, P=<0.0001). Pair-wise linkage disequilibrium revealed negative associations among variant alleles. On multi-dimensional reduction analysis, a three factor model revealed significant gene-gene interaction for PDGFB +286A>G, PDGFB +1135A>C and HER2 Ile165Val SNPs with GBC. Protein-protein interaction showed significant association of PDGFB and HER2 with the epidermal growth factor receptor signaling pathway.

• Asian Pacific Journal of Cancer Prevention
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• v.15 no.15
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• pp.6021-6024
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• 2014

Background: The STK15 gene located on chromosome 20q13.2 encodes a centrosome-associated kinase critical for regulated chromosome segregation and cytokinesis. Recent studies have demonstrated STK15 to be significantly associated with many tumors, with aberrant expression obseved in many human malignancies. The purpose of this study was to investigate expression of STK15 in esophageal squamous cell carcinomas (ESCCs) in a Mongolian population. Methods: Two non-synonymous single nucleotide polymorphisms in the coding region of STK15, rs2273535 (Phe31Ile) and rs1047972 (Val57Ile) were assessed in 380 ESCC patients and 380 healthy controls. We also detected STK15 mRNA expression in 39 esophageal squamous cell carcinomas and corresponding adjacent tissues by real time PCR. Results: rs2273535 showed a significant association with ESCC in our Mongolian population (rs227353, P allele = 0.0447, OR (95%CI) = 1.259 (1.005~1.578)). Real time PCR analysis of ESCC tissues showed that expression of STK15 mRNA in cancer tissues was higher than in normal tissues (p = 0.013). Conclusions: Our study showed that functional SNPs in the STK15 gene are associated with ESCC in a Mongolian population and up-regulation of STK15 mRNAoccurs in ESCC tumors compared adjacent normal tissues. STK15 may thus have an important role in the prognosis of ESCC and be a potential therapeutic target.

• BMB Reports
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• v.41 no.5
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• pp.388-393
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• 2008

The Pphsc70 (heat shock cognate 70) gene was isolated from the endoparasitoid Pteromalus puparum and then characterized. The full-length cDNA was 2204 base pair (bp) and contained a single 1968 bp ORF that encoded a polypeptide of 656 amino acids with a predicted molecular mass of 71.28 kDa. Phylogenetic analysis based on Hsc70 amino acid sequences from fifteen insect species agreed with the present phylogeny. In addition, genomic DNA confirmed the presence of three introns located at the coding region as well as the 5'UTR. A significant elevation of Pphsc70 expression was observed following heat treatment, however, continued exposure to heat shock or recovery caused the expression of induced mRNA to gradually decline to levels that were significantly lower than those of control pupae (P < 0.05). In addition, a significant increase was observed in the emergence rate of pupae that were preheated at $40^{\circ}C$ and then exposed to $50^{\circ}C$ for 1 h when compared with the pupae that were not preheated, but instead directly exposed to $50^{\circ}C$. Taken together, these results revealed that exposure to gradually increasing temperatures can enhance an insects thermo-tolerance.

• Journal of Microbiology and Biotechnology
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• v.19 no.11
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• pp.1306-1318
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• 2009

The filamentous ascomycete Sclerotinia sclerotiorum is well known for its ability to produce a large variety of hydrolytic enzymes. Two $\alpha$-amylases ScAmy54 and ScAmy43 predicted to play an important role in starch degradation were showed to produce specific oligosaccharides essentially maltotriose that have a considerable commercial interest. Primary structure of the two enzymes was established by N-terminal sequencing, MALDI-TOF masse spectrometry and cDNA cloning. The two proteins have the same N-terminal catalytic domain and ScAmy43 derived from ScAmy54 by truncation of 96 amino acids at the carboxyl-terminal region. Data of genomic analysis suggested that the two enzymes originated from the same $\alpha$-amylase gene and that truncation of ScAmy54 to ScAmy43 occurred probably during S. sclerotiorum cultivation. The structural gene of Scamy54 consisted of 9 exons and 8 introns, containing a single 1,500-bp open reading frame encoding 499 amino acids including a signal peptide of 21 residues. ScAmy54 exhibited high amino acid homology with other liquefying fungal $\alpha$-amylases essentially in the four conserved regions and in the putative catalytic triad. A 3D structure model of ScAmy54 and ScAmy43 was built using the 3-D structure of 2guy from A. niger as template. ScAmy54 is composed by three domains A, B, and C, including the well-known $(\beta/\alpha)_8$ barrel motif in domain A, have a typical structure of $\alpha$-amylase family, whereas ScAmy43 contained only tow domains A and B is the first fungal $\alpha$-amylase described until now with the smallest catalytic domain.