• Asian Pacific Journal of Cancer Prevention
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• v.14 no.5
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• pp.3309-3314
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• 2013

Spleen tyrosine kinase (SYK) is a non-receptor type cytoplasmic protein and a known tumor suppressor gene in breast cancer. Polymorphisms in SYK have been reported to be associated with cell invasion/cell morality and an increased risk of cancer development. In this case control study, all exons of the SYK gene and its exon/ intron boundaries were amplified in 200 breast cancer cases and 100 matched controls and then analyzed by single stranded conformational polymorphism. Amplified products showing altered mobility patterns were sequenced and analyzed. Twelve variations were identified in exonic and intronic regions of DNA encoding SH2 domain and kinase domain of the SYK gene. All of these mutations are novel. Among them, 5 missense mutations were observed in exon 15 while one missense mutation was found in exon 8. In addition to these mutations, six mutations were also identified in intronic regions. We found a significant association between SYK mutations and breast cancer and observed that Glu241Arg, a missense mutation is associated with an increase risk of ~7 fold (OR=6.7, 95% CI=1.54-28.8), Thr581Pro (missense mutation) is associated with increased risk of ~16 fold (OR=15.5, 95%CI=2.07-115.45) and 63367 T>G (missense mutation) is associated with increased risk of ~13 fold (OR=12.8, 95%CI=1.71-96.71) for breast cancer. Significant associations were observed for each of these variations with both late menopause (p<0.01) and early menarche (p<0.005) cases when compared to controls. Our findings suggest that the polymorphic gene SYK may contribute to the development of breast cancer in at least the Pakistani population. This study provides an insight view of SYK which may provide a significant finding for the pharmaceutical and biotechnology industry.

• Asian-Australasian Journal of Animal Sciences
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• v.26 no.10
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• pp.1359-1364
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• 2013

The purpose of this study was to find any association of the bovine growth hormone (bGH) gene with growth and carcass quality traits in Korean native cattle, Hanwoo. Genomic DNA was extracted from 21 Hanwoo individuals, and the 47 to 2,528 bp region of the bGH 2,856 bp (GenBank accession number M57764) including the promoter and the five exons was sequenced. A total of ten bGH SNPs were confirmed, including four (253 C>T, 303 C>T, 502 C>T, and 559 G>A) in the promoter, one (679 C>T) in exon 1, one (1,692 T>C) in intron 3, and four (2141 C>G, 2258 C>T, 2277 C>T, and 2291 A>C) in exon 5. The ten bGH SNPs were genotyped for a sample of 242 Hanwoo steers and association tests were performed to find any significant SNP that was correlated with growth and carcass quality. Of the SNPs, the 303 C>T SNP in the promoter region was significantly associated with 6-month-old weight, the 559 G>A SNP with longissimus dorsi muscle area, the 2141 C>G SNP in exon 5 with daily weight gain, and the 2258 C>T SNP with daily weight gain and carcass weight (p<0.05). The significant SNPs need to be verified in other Hanwoo populations before considering implementation of marker-assisted selection for genetic improvement of growth and carcass quality in Hanwoo.

• Korean Journal of Agricultural Science
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• v.40 no.3
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• pp.215-220
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• 2013

Fatty acids (FAs) were considered in activating nuclear hormone receptors that play significant roles in the cellular lipid metabolism by the regulation of several genes. Previously, fatty acid synthase (FASN) and stearoyl-CoA desaturase (SCD) genes have been known to regulating the FA metabolism. In this study, associations of FASN and SCD genes with fatty acid (FA) composition in broilers were investigated. Tissue samples from 95 Cobb 500 broilers were used for DNA extraction. The g.1222 A>G SNP located in intron 42 of FASN gene and 2 SNPs in SCD gene, one in exon 2 (g.3728A>G) and the other in exon 4 (g.12903G>A), were subjected for genotyping using PCR-RFLP method. One of the SNPs in SCD gene, SNP g.3728A>G had significant association with myristoleic acid (C14:1; P<0.05), palmitic acid (C16:0; P<0.05), palmitoleic acid (C16:1; P<0.05) and saturated FA (SFA; P<0.05). However, the SNP g.1222A>G in FASN gene had only suggestive association with arachidic acid (C20:0; P=0.08). The findings in this study suggest that the SNP in exon 2 of SCD gene can be used as a molecular marker for selecting birds having desirable FA composition in broilers.

• Journal of Genetic Medicine
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• v.9 no.1
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• pp.42-46
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• 2012

Short-chain acyl-CoA dehydrogenase deficiency (SCADD; OMIM # 201470) is an autosomal recessive inborn error of mitochondrial fatty acid ${\beta}$-oxidation, presenting with a variety of clinical signs and symptoms. Developmental delay, hypertonia or hypotonia, ketotic hypoglycemia, and epilepsy are most frequently reported. In general, patients diagnosed through newborn screening have shown normal growth and development in contrast to those diagnosed as a result of clinically initiated evaluations. Here, the case of an asymptomatic Korean newborn with SCADD identified by tandem mass spectrometry is reported. The patient showed an elevated concentration of butyrylcarnitine detected on newborn screening. Urinary excretion of ethylmalonic acid was elevated by urine organic acid analysis. To confirm the diagnosis of SCADD, a direct sequencing analysis of 10 coding exons and the exon-intron boundaries of the ACADS gene were performed. Genetic analysis of ACADS showed the following novel compound heterozygous missense mutations: c.277C>A (p.Leu93Ile) on exon3 and c.682G>A (p.Glu288Lys) on exon6. These results will provide further evidence of mutational heterogeneity for SCADD.

• BMB Reports
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• v.31 no.6
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• pp.578-584
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• 1998

In a previous paper (Kim et al., 1996a), the immediate 5' -flanking region and coding region of the human UDP-N -acetylglucosamine:-D-mannoside-1,4-Nacetylglucosaminyltransferase III (N-acetylglucosaminyitransferase- III; GnT-III) gene was reported, isolated and analyzed. Herein, we report on amplification of a new 5' -noncoding region of the GnT-III mRNA by single-strand ligation to single-stranded cDNA-PCR (5' -RACE PCR) using poly(A)+ RNA isolated from human fetal liver cells. A cDNA clone was obtained with 5' sequences (96 bp) that diverged seven nucleotides upstream from the ATG (+1) start codon. A concensus splice junction sequence, TCTCCCGCAG, was found immediately 5' to the position where the sequences of the cDNA diverged. The result suggested the presence of an intron in the 5' -noncoding region and that the cDNA was an incompletely reversetranscribed cDNA product derived from an mRNA containing a new noncoding exon. When mRNA expression of GnT-III in various human tissues and cancer cell lines was examined, Northern blot analysis indicated high expression levels of GnT-III in human fetal kidney and brain tissues, as well as for a number of leukemia and lymphoma cancer cell lines. Promoter activities of the 5' -flanking regions of exon 1 and the new noncoding region were measured in a human hepatoma cell line, HepG2, by luciferase assays. The 5'-flanking region of exon 1 was the most active, whilst that of exon 2 was inactive.

• Proceedings of the Korean Society for Bioinformatics Conference
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• 2003.10a
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• pp.179-182
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• 2003

The Development of promoter recognition systems is a interesting problem in computational biology. In this paper, we introduce a intelligent system fur promoter recognition with multiple decision models using artificial neural networks. We have trained this models with 1871 human promoter sequences and 5230exon and intron sequences. Our system is found to perform better than other promoter finding systems insensitivity and specificity measures. We have tested our system with Chromosome 22 dataset.

• Proceedings of the Botanical Society of Korea Conference
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• 1987.07a
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• pp.349-356
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• 1987

Insertions of transposable elements in or near a structural gene give rise to null phenotypes, reduced levels of gene expression, or alteration on the tissue-specific pattern of gene expression. Null phenotypes often result from insertions in exons. Reduced levels of gene expression results from insertions in various regions such as promoter region, 5' non-translated region, exon and intron. The maize allele of Adh1-3F1124 is an example of alteration in the tissue-specific patetern of gene expression. Adh1-3F1124 contains a Mu element inserted 31 bp 5' to the transcriptional start site of the wild-type Adh1 activity in seeds and anaerobically-treated seedlings but normal levels in the pollen. Upon the insertion of a transposable element a certain number of host DNA sequences at the insertion site is duplcated. When transposable elements excise, all element sequences are deleted. However, the duplicated host sequences may be left intact or deleted to various extents. This results in null phenotypes, restoration of original levels of gene expression, or altered levels of gene expression. On the basis of effects of transposable-element insertions or excisions on gene expression, the usefulness of transposable ellements for studies on gene expression is discussed.

• Horticultural Science & Technology
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• v.29 no.5
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• pp.461-466
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• 2011

In genetic and molecular breeding studies of plants, researchers need to design various kinds of primers based on their research purposes. So far many kinds of web- or script-based non-commercial programs for primer design are available. Because most of them do not include user interface for multipurpose usage including gene structure prediction and direct target selection on sequences, it has been a laborious work to design primers targeting on the exon or intron regions of interesting genes. Here we report a primer designing graphic user interface program, Pickprimer, that includes gene structure prediction and primer design modules by combining source codes of the Spidey and Primer3 programs. This program provides simple graphic user interface to input sequences and design primers. Genomic sequence and mRNA or coding sequence of genes can be copy and pasted or input as fasta or text files. Based on alignment of the input sequences using the Spidey module, a putative gene structure is graphically visualized along with exon-intron sequences of color codes. Primer design can be easily performed by dragging mouse on the displayed sequences or input primer targeting position with desirable values of primers. The output of designed primers with detailed information is provided by the Primer3 module. PCR evaluation of 24 selected primer sets successfully amplified single amplicons from six Brassica rapa cultivars. The Pickprimer will be a convenient tool for genetic and molecular breeding studies of plants.

• Asian Pacific Journal of Cancer Prevention
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• v.15 no.18
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• pp.7589-7595
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• 2014

Apurinic/apyrimidinic endonuclease 1 (APEX1) is a multifunctional protein which plays a central role in the BER pathway. APEX1 gene being highly polymorphic in cancer patients and has been indicated to have a contributive role in Apurinic/apyrimidinic (AP) site accumulation in DNA and consequently an increased risk of cancer development. In this case-control study, all exons of the APEX1 gene and its exon/intron boundaries were amplified in 530 breast cancer patients and 395 matched healthy controls and then analyzed by single-stranded conformational polymorphism followed by sequencing. Sequence analysis revealed fourteen heterozygous mutations, seven 5'UTR, one 3'UTR, two intronic and four missense. Among identified mutations one 5'UTR (rs41561214), one 3'UTR (rs17112002) and one missense mutation (Ser129Arg, Mahjabeen et al., 2013) had already been reported while the remaining eleven mutations. Six novel mutations (g.20923366T>G, g.20923435G>A, g.20923462G>A, g.20923516G>A, 20923539G>A, g.20923529C>T) were observed in 5'UTR region, two (g.20923585T>G, g.20923589T>G) in intron1 and three missense (Glu101Lys, Ala121Pro, Ser123Trp) in exon 4. Frequencues of 5'UTR mutations; g.20923366T>G, g.20923435G>A and 3'UTR (rs17112002) were calculated as 0.13, 0.1 and 0.1 respectively. Whereas, the frequency of missense mutations Glu101Lys, Ser123Trp and Ser129Arg was calculated as 0.05. A significant association was observed between APEX1 mutations and increased breast cancer by ~9 fold (OR=8.68, 95%CI=2.64 to 28.5) with g.20923435G>A (5'UTR), ~13 fold (OR= 12.6, 95%CI=3.01 to 53.0) with g.20923539G>A (5'UTR) and~5 fold increase with three missense mutations [Glu101Lys (OR=4.82, 95%CI=1.97 to 11.80), Ser123Trp (OR=4.62, 95%CI=1.7 to 12.19), Ser129Arg (OR=4.86, 95%CI=1.43 to 16.53)]. The incidence of observed mutations was found higher in patients with family history and with early menopause. In conclusion, our study demonstrates a significant association between germ line APEX1 mutations and breast cancer patients in the Pakistani population.

• Journal of Animal Science and Technology
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• v.54 no.6
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• pp.411-418
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• 2012

KIT gene is the major causative gene for coat color variation in diverse animal species. This gene regulates melanocyte migration from the neural crest to target tissues and the mutation of this gene can affect dominant white phenotypes in animals. Because this gene has a major influence for the coat color variation, single nucleotide polymorphisms (SNPs) in 14 Korean cattle (Hanwoo) and 5 Holstein individuals were investigated. The Hanwoo DNA samples included three different colored (5 Black, 5 Yellow and 4 Stripe) animals. Total 126 polymorphisms have been identified and 23 of them are located in the exon region. Also, 5 bp (TTCTC) and 3 bp (TCT) intronic indels in intron 3 and intron 5, respectively, were identified. Out of 23 exonic polymorphisms, 15 SNPs are the missense mutations and the rest of the SNPs are silence mutations. The neighbor-joining phylogenetic tree was constructed for the different colored animals using the obtained KIT gene sequences. Holstein breed showed a clear breed-specific cluster in the phylogenetic tree which is differed from Hanwoo. Also, three colored Hanwoo animals were not discriminated among the breeds. The KIT gene polymorphisms identified in this study will possibly give some solutions for the color variations in cattle with further verifications.