• Journal of Animal Science and Technology
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• v.51 no.4
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• pp.283-288
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• 2009

This study was carried out to compare Msp I polymorphisms in the 3rd intron of porcine gene encoding the pituitary-1 transcription factor (POU1F1) from 286 pigs (Landrace $\times$ Yorkshire $\times$ Duroc, LYD) and to determine the associations between its genotypes and carcass traits by using the PCR-RFLP technique. The frequency of the single nucleotide polymorphism (SNP) genotype DD (84.33%) was very higher than that of CC genotype (0.75%). Allelic frequencies for C and D were 0.082 and 0.918, respectively. Each population followed the Hardy-Weinberg equilibrium. Meat colours of Hunter $L^*$ values and visual colour according to two genotypes were all significantly different. However, no significant difference in crossbred (LYD) was found between CD and DD genotypes for other traits. Therefore, this suggests that POU1F1 may be a major gene or marker for carcass traits.

• 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.

• 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.

• The Korean Journal of Physiology and Pharmacology
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• v.12 no.4
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• pp.205-209
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• 2008

Recently, Sun et al (2008) reported that the IL6R polymorphism is associated with schizophrenia. Therefore, to detect the association between polymorphisms of interleukin 31 receptor A (IL31RA) and schizophrenia, we genotyped 9 SNPs [rs9292101 (intron 1), rs1009639 (exon 2, Pr043Pro), rs2161582 (intron 2), rs68761890 (intron 5), rs16884629 (intron 6), rs11956465 (intron 12), rs12153724 (intron 12), and rs16884641 (intron 14)] using the Golden Gate assay on Illumina BeadStation 500 GX. Two hundred eighteen patients with schizophrenia and 379 normal subjects were recruited. Patients with schizophrenia were diagnosed according to DSM-IV, and control subjects without history of psychiatric disorders were selected. We used SNPStats, Haploview, HapAnalyzer, SNPAnalyzer, and Helixtree programs for the evaluation of genetic data. Of nine polymorphisms, three SNPs (rs9292101, rs1009639, and rs11956465) were associated with schizophrenia. The rs9292101 and rs11956465 showed significant associations with the risk of schizophrenia in the codominant [rs9292101, odds ratio (OR)=0.74, 95% confidence interval (CI)=0.58${\sim}$0.95, p=0.017] and recessive (rs11956465, OR=0.64, 95% CI=0.42${\sim}$0.96, p=0.034) models, respectively. The rs1009639 also was statistically related to schizophrenia in both codominant (OR=0.76, 95% CI=0.60${\sim}$0.97, p=0.025) and dominant (OR=0.66, 95% CI=0.44${\sim}$0.98, p=0.035) models. Two linkage disequilibrium (LD) blocks were made. In the analysis of haplotypes, a haplotype (GCT) in block 1 and a haplotype (CCACAG) in block 2 showed significant associations between schizophrenia and control groups (haplotype GCT, frequency=0.509, chi square=4.199, p=0.040; haplotype CCACAG, frequency=0.289, chi square=5.691, p=0.017). The results suggest that IL31RA may be associated with risk of schizophrenia in Korean population.

• Molecules and Cells
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• v.26 no.5
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• pp.474-480
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• 2008

OsMADS1 is a rice MADS box gene necessary for floral development. To identify the key cis-regulatory regions for its expression, we utilized transgenic rice plants expressing GUS fusion constructs. Histochemical analysis revealed that the 5.7-kb OsMADS1 intragenic sequences, encompassing exon 1, intron 1, and a part of exon 2, together with the 1.9-kb 5' upstream promoter region, are required for the GUS expression pattern that coincides with flower-preferential expression of OsMADS1. In contrast, the 5' upstream promoter sequence lacking this intragenic region caused ectopic expression of the reporter gene in both vegetative and reproductive tissues. Notably, incorporation of the intragenic region into the CaMV35S promoter directed the GUS expression pattern similar to that of the endogenous spatial expression of OsMADS1 in flowers. In addition, our transient gene expression assay revealed that the large first intron following the CaMV35S minimal promoter enhances flower-preferential expression of GUS. These results suggest that the OsMADS1 intragenic sequence, largely intron 1, contains a key regulatory region(s) essential for expression.

• Animal cells and systems
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• v.9 no.3
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• pp.107-111
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• 2005

C. elegans DLK-1 has been reported to play an important role in synaptogenesis by shaping the structure of presynaptic terminal. In this study, we investigated the expression pattern and regulation of the dlk-1 gene in C. elegans. To determine the expression pattern, we made a dlk-1::gfp fusion construct, named pPDdg1, which consisted of -2.2 kb 5' upstream region, the first exon, the first intron, and a part of the second exon of the dlk-1 gene. By microinjecting this construct into the worm, we observed that the DLK-1::GFP was expressed mainly in neurons. We next examined the regulatory elements of gene expression by deletion analysis of pPDdg1. Removal of a large portion of the 5' upstream region (${\Delta}-361$ to -2246) of the gene had little effect on the expression pattern, whereas deletion of the first intron led to elimination of the DLK-1::GFP expression in most of the neurons. Our results suggest that the first intron of the C. elegans dlk-1 gene contains the regulatory element critical for gene expression.

• Interdisciplinary Bio Central
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• v.4 no.4
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• pp.14.1-14.6
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• 2012

Splice site prediction in DNA sequence is a basic search problem for finding exon/intron and intron/exon boundaries. Removing introns and then joining the exons together forms the mRNA sequence. These sequences are the input of the translation process. It is a necessary step in the central dogma of molecular biology. The main task of splice site prediction is to find out the exact GT and AG ended sequences. Then it identifies the true and false GT and AG ended sequences among those candidate sequences. In this paper, we survey research works on splice site prediction based on support vector machine (SVM). The basic difference between these research works is nucleotide encoding technique and SVM kernel selection. Some methods encode the DNA sequence in a sparse way whereas others encode in a probabilistic manner. The encoded sequences serve as input of SVM. The task of SVM is to classify them using its learning model. The accuracy of classification largely depends on the proper kernel selection for sequence data as well as a selection of kernel parameter. We observe each encoding technique and classify them according to their similarity. Then we discuss about kernel and their parameter selection. Our survey paper provides a basic understanding of encoding approaches and proper kernel selection of SVM for splice site prediction.

• Horticultural Science & Technology
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• v.35 no.3
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• pp.323-332
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• 2017

Homology-specific transcriptional and post-transcriptional silencing, an intrinsic mechanism of gene regulation in most eukaryotes, can be induced by anti-sense, co-suppression, or hairpin-based double-stranded RNA. Hairpin-based RNA interference (RNAi) has been applied to analyze gene function and genetically modify crops. However, RNAi vector construction usually requires high-cost cloning steps and large amounts of time, or involves methods that are protected by intellectual property rights. We describe a more effective method for generating intron-spliced RNAi constructs. To produce intron-spliced hairpin RNA, an RNAi cassette was ligated with the first intron and splicing sequences of the Brassica rapa ssp. pekinensis histone deacetylase 1 gene. This method requires a single ligation of the PCR-amplified target gene to SpeI-NcoI and SacI-BglII enzyme sites to create a gene-specific silencing construct. We named the resulting binary vector system pKHi and verified its functionality by constructing a vector to silence DIHYDROFLAVONOL 4-REDUCTASE (DFR), transforming it into tobacco plants, and confirming DFR gene-silencing via PCR, RT-qPCR, and analysis of the accumulation of small interfering RNAs. Reduction of anthocyanin biosynthesis was also confirmed by analyzing flower color of the transgenic tobacco plants. This study demonstrates that small interfering RNAs generated through the pKHi vector system can efficiently silence target genes and could be used in developing genetically modified crops.

• 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.

• 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.