• Molecules and Cells
• /
• v.27 no.6
• /
• pp.657-665
• /
• 2009

The ovomucoid pre-mRNA has been folded into mini-hairpins adaptable for the RNA recognition motif (RRM) protein binding. The number of mini-hairpins were 372 for pre-mRNA and 83-86 for mature mRNA. The spatial arrangements are, in average, 16 nucleotides per mini-hairpin which includes 7 nt in the stem, 5.6 nt in the loop and 3.7 nt in the inter-hairpin spacer. The constitutive splicing system of ovomucoid-pre-mRNA is characterized by preferred order of intron removal of 5/6 > 7/4 > 2/1 > 3. The 5' splice sites (5'SS), branch point sequences (BPS) and 3' splice sites (3'SS) were identified and free energies involved have been estimated in 7 splice sites. Thermodynamic barriers for splice sites from the least (|lowest| -Kcal) were 5, 4, 7, 6, 2, 1, and 3; i.e., -18.7 Kcal, -20.2 Kcal, -21.0 Kcal, -24.0 Kcal, - 25.4 Kcal, -26.4 Kcal and -28.2 Kcal respectively. These are parallel to the kinetic data of splicing order reported in the literature. As a result, the preferred order of intron removals can be described by a consideration of free energy changes involved in the spliceosomal assembly pathway. This finding is consistent with the validity of hnRNP formation mechanisms in previous reports.

• Tuberculosis and Respiratory Diseases
• /
• v.44 no.3
• /
• pp.534-546
• /
• 1997

Background : The p53 and retinoblastoma(Rb) tumor suppressor genes are associated with the pathogenesis of several types of human cancer. Substantial proportion of the primary lung cancers or cell lines have been reported to have the p53 and/or the Rb gene mutations. But, so far there is no report on the analysis of the Rb gene polymorphism as one of the genetic susceptibility marker. This study was undertaken to establish the gene frequencies of the polymorphic genotypes of the p53 and Rb genes in Koreans to evaluate the possible involvement of these genotypes as a risk factor of lung cancer. Methods : In this study 145 controls without previous and present tumor history and 128 lung cancer patients were subjected to analysis. The two intragenic polymorphisms of the p53 gene(exon 4/ AccII, intron 6/MspI) and one intron 17/XbaI polymorphism of the Rb gene were analysed by the method of polymersae chain reaction- restriction fragment length polymorphisms(PCR-RFLPs). The genotype of the intron 3/16 bp repeat polymorphism of p53 was determined by PCR and direct gel electrophoresis. Results : There were no significant differences in the genotype distributions of the p53 gene between lung cancer patients and controls. But heterozygotes(Arg/Pro) of the exon 4/AccII polymorphisms were slightly over-represented than controls, especially in the Kreyberg type I cancer, which was known to be associated with smoking. The intron 3/16 bp duplication and the intron 6/MspI polymorphisms were in complete linkage disequilibrium. About 95% of the individuals were homozygotes of the common alleles both in the 16 duplication and MspI polymorphisms, and no differences were deteced in the genotype distributions between lung cancer patients and controls. Overall genotype distributions of the Rb gene polymorphisms between lung cancer patients and controls were not significantly different However, the genotype distributions in the Kreyberg type I cancer were significantly different from those of controls(p = 0.0297) or adenocarcinomas(p = 0.0008). It was noticeable that 73.4% of the patients with adenocarcinomas were heterozygotes(r1/r2) whereas 39.2% of the Kreyberg type I cancer were heterozygous at this polymorphisms. In the lung cancer patients, significant differences were also noted between the high dose smokers and low dose smokers including non-smokers(p = 0.0258). The relative risk to Kreyberg type I cancer was significantly reduced in the individuals with the genotype of r1/r2(odds ratio = 0.46, 95% C.I. = 0.25-0.86, p = 0.0124). The combined genotype distribution of the exon 4 AccII of the p53 and the intron 17 Rb gene polymorphisms in Kreyberg type I cancers were significantly different from dose of controls or adenocarcinomas. The highest odds ratio were observed in the individuals with the genotypes of Arg/Pro and r2/r2(odds ratio = 1.97,95% C.I. = 0.84-4.59) and lowest one was in the patients with Arg/Arg, r1/r2 genotype(odds ratio = 0.54, 95% C.I. = 0.25-1.14). Conclusion : The p53 and the Rb gene polymorphisms modulate the risk of smoking induced lung cancer development in Koeans. However, the exact mechanism of risk modulation by these polymorphism remains to be determined. For more discrete clarification of associations between specific genotypes and lung cancer risk, the evaluations of these polymorphisms in other ethnics and more number of patients will be needed.

• Tuberculosis and Respiratory Diseases
• /
• v.58 no.4
• /
• pp.367-374
• /
• 2005

Background : The fact that only 10-20% of chronic cigarette smokers develop chronic obstructive pulmonary disease (COPD) reflects the presence of genetic factors associated with the susceptibility to COPD. Recently, it was reported that the surfactant protein A increases the secretion of matrix metalloprotease 9, which degrades extracellular matrices of the lung, through a Toll-like receptor 2 (TLR2). In this context, possible role of TLR2 in the pathogenesis of COPD was postulated, and a functional dinucleotide repeat polymorphism in intron II of TLR2 was evaluated for any association with COPD. Method : Male patients with COPD and male smokers with a normal pulmonary function were enrolled in this study. The number of Guanine-Thymine repeats in intron II of the TLR2 gene were counted. Because the distributions of the repeats were trimodal, the alleles were classified into three subclasses, 12-16 repeats: short (S) alleles; 17-22 repeats: medium length (M) alleles; and 23-27 repeats: long (L) alleles. Result : 125 male patients with COPD and 144 age- and gender-matched blood donors with a normal lung function were enrolled. There were no differences in the distribution of each allele subclass (S, M and L) between the COPD and control group (p=0.75). The frequencies of the genotypes with and without each allele subclass in the COPD and control group were similar. Conclusion : A microsatellite polymorphism in intron II of TLR2 gene was not associated with the development of COPD in Koreans.

• Asian-Australasian Journal of Animal Sciences
• /
• v.15 no.2
• /
• pp.179-183
• /
• 2002

The fragment in intron I of FSH-${\beta}$ gene was amplified by PCR. According to the polymorphism, we analyzed the distribution of FSH-${\beta}$ retroposon in different pig breeds; its inheritance pattern in Large White${\times}$Meishan reference family; and the association of FSH-${\beta}$ retroposon with litter size, female reproductive organs measurement, ultrasonic backfat and other traits. The results showed that almost each Chinese indigenous pig had the retroposon, while foreign pig breeds rarely had; the frequencies of porcine FSH-${\beta}$ retroposon were strongly associated with breeds (p<0.01); the pattern of inheritance was consistent with Mendelian fashion; total number born (TNB) and number born alive (NBA) were increased per FSH-${\beta}$ retroposon (p<0.01) with additive effects of 1.2-1.8 and 1.4-1.8 pigs/litter, respectively; between the FSH-${\beta}$ retroposon carriers and non-carriers, there was an insignificant difference in the measurement of female reproductive organs, body weight at birth, backfat thickness, loin meat height, lean meat percentage, teat number, days to 100 kg, and average daily gain.

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

• Asian-Australasian Journal of Animal Sciences
• /
• v.17 no.2
• /
• pp.179-182
• /
• 2004

The polymorphism of the locus FSHRB in intron6-Exon7 of FSHR gene was investigated by PCR-RFLPs in Erhualian, Large White and Landrace${\times}$Large White; The association of polymorphism and litter size was analyzed by using SAS. The results showed that 1) the polymorphism of the locus FSHRB was significantly associated with litter size; 2) the total born number (TBN) and number born alive (NBA) of the sows with BB genotype were increased (p<0.05) with additive effects of 1.02-1.42 and 1.04-1.27 pigs per litter, respectively; 3) among the sows with genotype AA, AB or BB, there was an insignificant difference in born weight and weaning weight. This gene may be an effective potential tool used in conjunction with traditional selection methods.

• BMB Reports
• /
• v.39 no.3
• /
• pp.240-246
• /
• 2006

The base compositional correlations that hold among various coding and noncoding regions of the canine genome have been analysed. The distribution pattern of genes, on the basis of $GC_3$ composition, shows a wide range similar to that observed in human. However the occurrence of maximum number of genes was observed in the range of 65-75% of $GC_3$ composition. The correlation between the coding DNA sequences of canine with the different noncoding regions (introns and flanking regions) is found to be significant and in many cases the degree of correlation show similarity to human genome. We found that these correlations are not limited to the GC content alone, but is holding at the level of the frequency of individual bases as well. The present study suggests that canines ideally belong to the predicted 'general mammalian pattern' of genome composition along with human beings.

• Journal of Aquaculture
• /
• v.11 no.3
• /
• pp.295-301
• /
• 1998

Since the end of the Pliocene, ancestral strains of Astyanax fasciatus have been accidently washed into different caves at the time of flooding and have lost their eyes and body pigments. Availability of this independently derived cave fish and their ancestral form within a single species provided a unique opportunity for studying the process of molecular evolution of the visual pigment gene. The nucleotide sequence comparisons of an ancestral river fish and two cave fish showed that nucleotide polymorphism of a green-like visual pigment gene between the eyed and blind form of A. fasciatus was much higher than that between the same blind form. Considering the number of nucleotide substitutions per nucleotide site and the direction of the nucleotide substitutions, more nucleotide substituions between the different forms of fish rater than the same one were probably due to more frequent mutations in the eyed river form. Nucleotide substitutions per site at the intron have been ocurred more than three times faster than those at the exon. This result indicates that the functional constraint has affected the green-like visual pigment gene of the blind cave fish although its eye sight is no longer required.

• Journal of Interdisciplinary Genomics
• /
• v.4 no.1
• /
• pp.15-18
• /
• 2022

Hemophilia A is a rare X-linked congenital deficiency of clotting factor VIII (FVIII) that is traditionally diagnosed by measuring FVIII activity. Various mutations of the FVIII gene have been reported and they influence on the FVIII protein structure. A deficiency of or reduction in FVIII protein manifests as spontaneous or induced bleeding depending on the disease severity. Mutations of the FVIII gene provide important information on the severity of disease and inhibitor development. FVIII mutations also affect the discrepant activities found using different FVIII assays. FVIII activity is affected differently depending on the mutation site. Long-range PCR is commonly used to detect intron 22 inversion, the most common mutation in severe hemophilia. However, point mutations are also common in patients with hemophilia, and direct Sanger sequencing and copy number variant analysis are being used to screen for full mutations in the FVIII gene. Advances in molecular genetic methods, such as next-generation sequencing, may enable accurate analysis of mutations in the factor VIII gene, which may be useful in the diagnosis of mild to moderate hemophilia. Genetic analysis is also useful in diagnosing carriers and managing bleeding control. This review discusses the current knowledge about mutations in hemophilia and focuses on the clinical aspects associated with these mutations and the importance of genetic analysis.

• Journal of Plant Biotechnology
• /
• v.29 no.4
• /
• pp.223-228
• /
• 2002

We have developed a homemade particle inflow gun (PIG) system which has simple operation method, low price and high gene introduction efficiency into rice callus. Rice callus were inflowed with gold particles containing DNA of a plasmid, pIG121Hm, harboring intron GUS ($\beta$-glucuronidase) gene, NPTII gene and HPT gene. For optimal GUS transient expression, the effects of parameters on DNA delivery efficiency of the PIG system was investigated by scoring transient GUS expression. The highest number of blue spots was observed at 16 mM of spemidine and 1.5 M of calcium chloride, respectively. And the amount of gold particles required for the best GUD expression was 2 mg. Optimum GUS transient expression was observed at target distance of 12 cm and helium pressure of 3.5 bar (50 psi). Gene introduction efficiency of the PIG system was observed almost similar to that of the Biolistic Gun (Bio-Rad Company). Since PIG system is simple to operate and one doesn't need disposable accessaries, the PIG system can be easily applied to various replication experiments.