• Korean Journal of Fisheries and Aquatic Sciences
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• v.35 no.6
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• pp.633-638
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• 2002

Nuclear 18S ribosomal RNA gene (185 rDNA) from the aquaculturable seaweed Porphya yezoensis (Bangiales, Rhodophyta) was amplified using the polymerase chain reaction and its sequence was analysed. Complete 185 rDNA has an 1823 bp exon and a 514 bp intron. The G+ C contents of exon and intron were $48\%$ and $51.4\%$, respectively. The exon sequence showed $99.5\%$ homology to the GenBank accession number AB013177 of the Japanese p. yezoensis. The intron region that was inserted upstream between 568 and 1083 showed $93.4\%$ homology to the AB013177.

• Journal of Plant Biotechnology
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• v.2 no.2
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• pp.101-108
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• 2000

The liverwort Pellia borealis is a diploid, monoecious, allopolypliod species (n=18) that as it was postulated, originated after hybridization and duplication of chromosome sets of two cryptic species: Pellia epiphylta-species N (n=9) and Pellia epiphylla-species 5 (n=9). Our recent results have supported the allopolyploid origin of P.borealis. We have shown that the nuclear genome of P.borealis consists of two nuclear genomes: one derived from P.epiphylla-species N and the other from P.epiphylla-species 5. In this paper we show the origin of chloroplast and mitochondrial genomes in an allopolyploid species P.borealis. To our knowledge there is no information concerning the way of mitochondria and chloroplast inheritance in Brophyta. Using an allopolyploid species of p. borealis as a model species we have decided to look into chloroplast and mitochondrial genomes of P.borealis, P.epiphylla-species N and P.epiphylla-species S for nucleotide sequences that would allow us to differentiate between both cryptic species and to identify the origin of organelle genomes in the alloploid species. We have amplified and sequenced a chloroplast $tRNA^{Leu}$ gene (anticodon UAA) containing an intron that has shown to be highly variable in a nucleotide sequence and used for plant population genetics. Unfortunately these sequences were identical in all three liverwort species tested. The analysis of the nucleotide sequence of chloroplast, an intron containing $tRNA^{Gly}$ (anticodon UCC) genes, gave expected results: the intron nucleotide sequence was identical in the case of both P.borealis and P.epiphyllaspecies N, while the sequence obtained from P.epiphyllasperies S was different in several nucleotide positions. These results were confirmed by the nucleotide sequence of another chloroplast molecular marker the chloroplast, an intron-contaning $tRNA^{Lys}$ gene (anticodon UUU). We have also sequenced mitochondrial, an intron-containing $tRNA^{Ser}$ gene (anticodon GCU) in all three liverwort species. In this case we found that, as in the case of the chloroplast genome, P.borealis mitochondrial genome was inherited from P.epiphylla-species N. On the basis of our results we claim that both organelle genomes of P.borealis derived from P.epiphylla-species N.

• Asian Pacific Journal of Cancer Prevention
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• v.16 no.7
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• pp.3073-3077
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• 2015

Background: TP53 mutations are the most common genetic alterations in human cancers. There are also several polymorphisms in both exons and introns of TP53 that may influence its anti-tumor functions and increase the risk of cancer development. Associations of the TP53 intron 6 G13964C polymorphism with increased risk of development of several cancers have been investigated in numerous studies, but the results were controversial and conflicting. In this study, we aimed to investigate the probable association of this polymorphism with risk of both thyroid and breast cancers among the Iranian-Azeri population. Materials and Methods: We performed two separate case control studies on associations of the intron 6 polymorphism with two different kinds of cancer. In one case-control study, a total of 75 patients with thyroid carcinoma and 180 controls were analyzed and the other study included 170 patients with breast cancer and 135 healthy women. The intron 6 genotype was determined by RFLP-PCR and the SPSS 16 program was applied for data analysis. Results: For thyroid cancer, the frequencies of GG genotype were 96.0% in patients and 93.3% in controls. The GC genotype had a frequency of 4.0 % in patients and 6.7% in controls. In the study on breast cancer, the frequency of GG and GC genotypes in patients were 95.3% and 4.7%, respectively. In breast related control group, the frequency of GG genotype was 93.3 % and the frequency of GC genotype was 6.7%. None of the cases and controls had the CC genotype. Conclusions: There was no significant association between the TP53 intron 6 G13964C polymorphism and risk of development of both thyroid and breast cancer in Iranian-Azeri patients.

• Asian-Australasian Journal of Animal Sciences
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• v.25 no.3
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• pp.421-427
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• 2012

The production of therapeutic proteins from transgenic animals is one of the most important successes of animal biotechnology. Milk is presently the most mature system for production of therapeutic proteins from a transgenic animal. Specifically, ${\beta}$-casein is a major component of cow, goat and sheep milk, and its promoter has been used to regulate the expression of transgenic genes in the mammary gland of transgenic animals. Here, we cloned the porcine ${\beta}$-casein gene and analyzed the transcriptional activity of the promoter and intron 1 region of the porcine ${\beta}$-casein gene. Sequence inspection of the 5'-flanking region revealed potential DNA elements including SRY, CdxA, AML-a, GATA-3, GATA-1 and C/EBP ${\beta}$. In addition, the first intron of the porcine ${\beta}$-casein gene contained the transcriptional enhancers Oct-1, SRY, YY1, C/EBP ${\beta}$, and AP-1, as well as the retroviral TATA box. We estimated the transcriptional activity for the 5'-proximal region with or without intron 1 of the porcine ${\beta}$-casein gene in HC11 cells stimulated with lactogenic hormones. High transcriptional activity was obtained for the 5'-proximal region with intron 1 of the porcine ${\beta}$-casein gene. The ${\beta}$-casein gene containing the mutant TATA box (CATAAAA) was also cloned from another individual pig. Promoter activity of the luciferase vector containing the mutant TATA box was weaker than the same vector containing the normal TATA box. Taken together, these findings suggest that the transcription of porcine ${\beta}$-casein gene is regulated by lactogenic hormone via intron 1 and promoter containing a mutant TATA box (CATAAAA) has poor porcine ${\beta}$-casein gene activity.

• Proceedings of the Korean Statistical Society Conference
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• 2004.11a
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• pp.79-84
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• 2004

We use principal component analysis (PCA) to identify exons of a gene and further analyze their internal structures. The PCA is conducted on the short-time Fourier transform (STFT) based on the 64 codon sequences and the 4 nucleotide sequences. By comparing to independent component analysis (ICA), we can differentiate between the exon and intron regions, and how they are correlated in terms of the square magnitudes of STFTs. The experiment is done on the gene F56F11.4 in the chromosome III of C. elegans. For this data, the nucleotide based PCA identifies the exon and intron regions clearly. The codon based PCA reveals a weak internal structure in some exon regions, but not the others. The result of ICA shows that the nucleotides thymine (T) and guanine (G) have almost all the information of the exon and intron regions for this data. We hypothesize the existence of complex exon structures that deserve more detailed analysis.

• Journal of Microbiology and Biotechnology
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• v.18 no.1
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• pp.23-27
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• 2008

Self-splicing group I introns in tRNA anticodon loops have been found in diverse groups of bacteria. In this work, we identified $tRNA^{fMet}$ group I introns in six strains of marine Synechococcus elongatus. Introns with sizes around 280 bp were consistently obtained in all the strains tested. In a phylogenetic analysis using the nucleotide sequence determined in this study with other cyanobacterial $tRNA^{fMet}$ and $tRNA^{Leu}$ intron sequences, the Synechococcus sequence was grouped together with the sequences from other unicellular cyanobacterial strains. Interestingly, the phylogenetic tree inferred from the intronic sequences clearly separates the different tRNA introns, suggesting that each family has its own evolutionary history.

• Journal of Life Science
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• v.19 no.5
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• pp.664-670
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• 2009

The ${\beta}$3-adrenergic receptor (ADRB3) is expressed mainly in visceral adipose tissue and is thought to contribute to lipolysis and the delivery of free fatty acids to the portal vein. This study was aimed at evaluating the association between high-density lipoprotein cholesterol (HDL-C) and ADRB3 genetic polymophisms. A total of 991 healthy examinees who were examined in a university hospital, located in Busan City, between May and December 2006 were enrolled in this study. Height, weight, body mass index, waist circumference, and systolic and diastolic blood pressures of the subjects were examined. Intravenous concentrations of fasting blood glucose, total cholesterol, HDL-C, low-density lipoprotein cholesterol, and triglyceride were also measured. After extracting DNA from the subjects, mutations of the +188T>C (Trp64Arg) of exon 1 and +3893T>C of intron 2 on the ADRB3 gene were genotyped using the single base extension method. We have identified a novel mutation of ADRB3 that is located in intron 2. The frequency of its minor allele was 0.164. Both the +188T>C mutation of exon 1 and +3893T>C mutation of intron 2 were significantly associated with HDL-C. The mean concentration of serum HDL-C was significantly lower in the presence of their minor allele 'C'. These results suggest that both mutations of +188T>C of exon 1 and +3895T>C of intron 2 have significant associations with HDL-C in the Korean population.

• Korean Journal of Animal Reproduction
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• v.20 no.4
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• pp.371-378
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• 1997

Human lactoferrin (hLF) was expressed in the mammary gland of transgenic mice. Expresion of hLF was achieved by palcing its cDNA under the control of bovine $\beta$-casein gene. To improve the hLF expression level, two artificial introns were introduced into the expression vector. One intron is a hybrid-splice consisting of bovine $\beta$ casein intron 1 and rabbit $\beta$-casem intron II. The other intron is a DNA fragment spanning intron 8 of bovine $\beta$ casein gene. Trans sgenic mice were developed which expressed hLF in their milk. Twenty lines of transgenic mice were produced. hLF was present in the milk at concentrations of 1 ~ 200 ${\mu}\textrm{g}$ / ml. hLF RNA was only detected in the mammary gland of transgenic mice. The expressed RNA was cor r rectly spliced at the exon /intron junctions. To generate transgenic cows secreting active hLF in their milk, we transferred the DNA-injected bovine embryos to recipient heifers by surgical a and non-surgical methods out of 68 embryos transferred to 51 recipients by surgical or non-surgical method, 7 calves were normally born. Effect of embryo quality of DNA-injected blastocysts on pregnancy rate after transfer was investig a ated. Higher pregnancy rate of (38.9%) DNA-injected embryos was shown in excellent embryos. Pregnancy rates in the groups of good a and fair embryos were 15.4 and 14.3%, respectively. Effect of culture period of DNA-injected b bovine embryos on pregnancy rate after transfer was investigated. When Day-6 blastocysts of cuI ture were transferred, there was no pregnancy. Pregnancy rates of Day-7 and -8 blastocysts were 28.6 and 33.3%, respectively. There was no difference on pregnancy rate between Day-7 a and -8 bovine blastocysts after DNA injection. Thus, we established the techniques for transfer a and culture of DNA-injected bovine embryos. In a addition, factors affecting the pregnancy rate of DNA-injected embryos after transfer were investigated .

• Asian Pacific Journal of Cancer Prevention
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• v.15 no.6
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• pp.2631-2634
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• 2014

Background: p53 gene is a well-known tumor suppressor gene that has several polymorphisms in both its exons and introns. It has been suggested that intron 3 16 bp duplication polymorphism may affect the gene function resulting in reduction or suppression of p53 anti tumor activity. In most case control studies a duplicated allele has been noticeably more frequent in cases rather than controls but there are also conflicting results. The aim of this study was to assess the association of intron 3 16 bp duplication polymorphism of p53 with breast cancer risk among Iranian-Azeri population. We also analyzed the clinicopathological information of patients as an epidemiological description of breast cancer in the north-west of Iran. Materials and Methods: This case-control study was performed on 221 breast cancer patients and 170 controls. Genomic DNA was extracted from peripheral blood samples and tumor tissues. p53 PIN3 genotype was determined using electrophoresis of PCR products on 8% non-denaturing polyacrylamide gels and silver staining. Results: In the control and case groups, respectively, 62.9% and 61.1% had no 16 bp insertion (A1A1 genotype), 7.1% and 7.7% had insertion in both p53 alleles (A2A2) and 30% and 31.2% were heterozygous (A1A2). There was no significant difference between genotype frequencies as well as allelic frequencies in two case and control groups. Conclusions: According to the result of the present study, the intron 3 16 bp duplication polymorphism of p53 could not be assessed as a marker of risk factor for predisposition to breast cancer in Azeri population. However, a high frequency of A2 allele (22.1%) in our population suggested that intron 3 16 bp duplication polymorphism may be a valuable marker for study in other cancers with well designed large groups.

• Korean Journal of Plant Tissue Culture
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• v.26 no.1
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• pp.41-47
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• 1999

Phenylalanine ammonia-lyase (PAL; EC 4, 3, 1, 5) genomic clones were isolated from tomato(Lycopersicon esculentum L.) genomic DNA libraries using tomato PAL5 cDNA sequences as probes. The nucleotide sequences of tPAL1, tPAL4 and tPAL5 were compared. tPAL5 contains an open reading frame encoding a polypeptide of 722 amino acids, interrupted by a 710 bp intron in the codon for the amino acid 139. tPAL1 encodes a polypeptide of 249 amino acids which is much shorter than tPAL5 gene due to a premature stop codon and does not contain an intron. tPAL4 encodes a polypeptide of 357 amino acids, interrupted by a 305 bp intron in the codon for the amino acid 138. Premature stop codons observed in tPAL1 and tPAL4 gene produce a short polypeptide rather than a normal polypeptide (722 aa). tPALl shows 87.2% homology with tPAL4 and 85.3% homology with tPAL5 gene whereas tPAL4 showes 91.4% homology with tPAL5 at nucleotide level. In general, phylogenetic analysis showed that genes isolated from tomato, potato, and sweet potato were belong to the same group and another dicot plants such as parsley, bean, soybean, pea and alfalfa formed another group. PAL genes isolated from rice and yeast showed very low homology with other PAL genes and formed the other group.