• Animal cells and systems
• /
• v.4 no.2
• /
• pp.141-144
• /
• 2000

Effects of deamido-$\textrm{NAD}^{+}$on self-splicing of primary transcripts of the phage T4 thymidylate synthase gene (td) was investigated. The self-splicing was not affected by deamido-$\textrm{NAD}^{+}$- at concentrations up to 2 mM. However, it began to decrease at 5 mM and the formation of splicing products such as the linear intron, intron-exon 2 and exon 1-exon 2, was slightly reduced. At 20 mM the self-splicing activity was almost completely abolished. This analog of the coenzyme $\textrm{NAD}^{+}$- inhibits the self-splicing of td intron RNA although it does not possess a guanidine group in its structure. The analysis of inhibitory concentrations and structural examination suggests that the key structural features of deamido-$\textrm{NAD}^{+}$ responsible for the inhibition of splicing may be the ADP-ribose moiety.

• Journal of Microbiology
• /
• v.37 no.4
• /
• pp.243-247
• /
• 1999

Effects of divalent cations on self-splicing inhibition by the antibiotic spectinomycin of the phage T4 thymidylate synthase intron (td) have been investigated. $Ca^{2+}$ ion at 1mM concentration suppressed splicing inhibition of spectinomycin by 10% and 50 ${\mu}M\;Co^{2+}$ ion also suppressed splicing inhibition of specinomycin by 10%. $Mg^{2+}$ ion at 6 mM concentration decreased splicing inhibition of spectinomycin by 42% while $Mn^{2+}$ ion decreased the splicing inhibition by 10%. $Zn^{2+}$ ion at 10 uM concentration lowered the splicing inhibition by spectinomycin of 15%. Of all divalent cations tested, $Mg^{2+}$ ion was the most effective in suppressing splicing inhibition by specinomycin whereas $Ca^{2+}$ ion was the least effective. The results suggest that spectinomycin may interact with specific and functional $Mg^{2+}$-binding sites within intron RNA that lead to a displacement of $Mg^{2+}$ essential for catalytic activity.

• Journal of Animal Science and Technology
• /
• v.46 no.4
• /
• pp.555-562
• /
• 2004

본 연구는 목저은 다음과 같다: 1) 돼지에서 150-kDa temary insulin-like growth faetor(IGF)complex의 한 구성 요소인 acid-labile subunit(ALS) 유전자 intron의 존재 확인. cloning 및 돼지 ALS(porcine ALS; pALS) complementary DNA(cDNA)의 3' 비해독(untranslated) 부위(3' UT) 증폭. cloning, 2) intron-spanning primer pair를 이용한 reverse transcription-polymerase chain reaction(RT-PCR) 방법에 의한 돼지 조직에서의 ALS 유전자 발현 분포 확인 및 3) 돼지 hepatocyte에서의 ALS 유전자 발현 여부 확인. 돼지 genomic DNA를 template로 하여 PCR 방법으로 예상된는 intron 부위를 증폭하고 plasmid vector에 삽입하여 염기서열을 결정한 결과 타 종의 ALS 유전자에서와 같은 위치에 1,371-base pair(bp)의 pALS intron이 존재함을 확인하였다. 역시 본 연구에서 간에서 추출한 RNA를 주형으로 시작하여 3' rapid amplification of cDNA end(3' RACE) 방법으로 147-bp의 3'UT를 합성하고 그 염기성열을 결정하였다. RT-PCR 결과 간은 물론 조사된 모든 돼지의 내장기관(신장, 폐, 비장)과 자성 생식기관(난소, 난관, 자궁) 및 골격근육에서 ALS 유전자가 발현됨이 밝혀졌다. 또한 돼지 간 조직에 대한 in-situ hybridization 결과 hepatocyte에서 ALS 유전자가 발현됨이 확인되었다. 이상의 결과는 ALS가 혈중 IGF의 저정/조절체로서의 주기능 외에 모세혈관 밖에서도 미지의 기능이 있을 기능성을 시사한다.

• Journal of Plant Biotechnology
• /
• v.37 no.4
• /
• pp.511-516
• /
• 2010

The process to acquire intron-GUS gene-expressed transformants from somatic embryos (including embryogenic calli) of Rosa hybrida cv. 'Sweet Yellow' using Agrobacterium-meditated transformation method was reported in this study. Somatic embryos including embryogenic calluses were infected with Agrobacterium tumefaciens AGL1 strain (O.D = 0.7~1.6) including intron-GUS gene for 30 min, and were co-cultured for 3 days. After co-cultivation, they were cultured on embryo germination medium (EGM) supplemented with $250\;mg{\cdot}L^{-1}$ cefotaxim at $4^{\circ}C$ for 7 days. Then, transient GUS gene expression was observed. Shoots were regenerated from the shoot primodia induced from the intron-GUS gene-transferred either somatic embryos or embryogenic calli cultured on EGM supplemented with both cefotaxim $250\;mg{\cdot}L^{-1}$ and ppt $2\;mg{\cdot}L^{-1}$. Before induction of rooting from shoots cultured on shoot growing medium supplemented with both cefotaxim $250\;mg{\cdot}L^{-1}$ and ppt $2\;mg{\cdot}L^{-1}$, the shoots were cultured on multi-shoot induction medium supplemented with both cefotaxim $250\;mg{\cdot}L^{-1}$ and ppt $2\;mg{\cdot}L^{-1}$ to induce multi-shoots. When expression of the gene from a part of the multi-shoots was identified by GUS transient assay, the putative transgenic multishoots were transferred to rooting medium supplemented with cefotaxim $250\;mg{\cdot}L^{-1}$. After the formation of healthy roots, transgenic plantlets were transferred to the greenhouse after acclimatization. The expression rate of the intron-GUS gene in the multi-shoots was 100%.

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

• Korean Journal of Microbiology
• /
• v.38 no.1
• /
• pp.13-18
• /
• 2002

Effects of divalent cations such as $Mg^{2+}$, $Mn^{2+}$ and $Zn^{2+}$ on the self-splicing inhibition of the T4 phage thymidylate synthase (td) intron by the coenzyme thiamine pyrophosphate have been investigated. The splicing activity increased in proportion to the concentration of $Mg^{2+}$ up to 30 mM. Without $Mg^{2+}$in the splicing reaction the $Zn^{2+}$ ion tested in the range of 0.1-6 mM concentration only produced the splicing activity about 20% that of the normal splicing rate. A majority of the splicing products were I-E2 and E2 but El-E2 ligation product, Cl and Ll were not detected. Similar patterns of splicing products were also observed with $Mn^{2+}$. At 6 mM $Zn^{2+}$the intron RNA was hydrolyzed. $Mn^{2+}$produced a little higher splicing activity than that of $Zn^{2+}$over the range of concentrations used and at 8 mM about 28% splicing activity was observed. In contrast, $Mn^{2+}\;and\;Zn^{2+}$ ions promoted the splicing activity about 35-40% on an average in the presence of 10 mM $Mg^{2+}$. Of all divalent cations tested, $Mg^{2+}$exhibited the maximum activation effect to counteract the splicing inhibition by thiamine pyrophosphate. This appears to be due to the stabilizing effect of td intron ribozyme structure essential for the catalytic function by $Mg^{2+}$.

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

• Proceedings of the Plant Resources Society of Korea Conference
• /
• 2010.05a
• /
• pp.15-15
• /
• 2010

Koran ginseng(Pnax ginseng) is one of the most important medicinal plants in Orient. Among the nine cultivars of Korea ginseng, Chunpoong commands a much greater market value and has been planted widely. A rapid and reliable method for discriminating the Chunpoong cultivar was developed by exploiting a single nucleotide polymorphism (SNP) in the mitochondrial nad7 intron 4 region of nine Korea ginseng cultivars using universal primers. A SNP was detected between Chunpoong and other cultivars and modified allele-specific primers were designed from this SNP site to effective method for the geneic identification of the Chunpoong cultivar of ginseng.

• Korean Journal of Fisheries and Aquatic Sciences
• /
• v.36 no.1
• /
• pp.35-38
• /
• 2003

Nuclear 18S ribosomal RNA gene (185 rDNA) from the aquaculturable seaweed Porphya tenera (Bangiales, Rhodophyta) was amplified using the polymerase chain reaction and its sequence was analysed. Complete 185 rDNA has an 1,822 bp exon and a 510 bp intron. The G+C contents of exon and intron were $48.68\%\;and\;54,90\%,$ respectively. The exon sequence showed $99.6\%$ homology to the GebBank accession number AB029880 of the Japanese P. tenera. The intron region that is inserted upstream between 568 and 1,079 showed $43.6\%$ homology to the AB029880.

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