• Ocean and Polar Research
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• 제26권4호
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• pp.551-557
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• 2004

Polymorphism of the lipoprotein lipase (LPL) gene which plays an important role in regulation of lipid deposition was analysed in two red seabream (pagrus major) populations (KF4, cultured KORDI line, n=100 : JPN, imported from Japan, n=100). We amplified a DNA fragment (1,091 bp) including the exon 2 region of the LPL gene, and conducted PCR-RFLP analysis using MspI and AluI. The PCR products were also sequenced. Two alleles (A and B) were found in MspI digestion and Sve alleles (A, B, C, D and E) in AluI digestion. The sequenced data revealed four nucleotide substitutions including one transversion at the MspI recognition site (nt 2,235, $C{\rightarrow}10$) and three transitions at the AluI recognition sites (nt 1,721, $A{\rightarrow}G;$ nt 2,319, $C{\rightarrow}T;$ nt 2,319, $T{\rightarrow}C$). Among them, substitutions at the nt 2,235 and 2,319 sites which are located in the exon 2 were proved to be silent point mutations. MspI polymorphism resulted in 3 genotypes, and the allele frequency was significantly different between the two fish populations, KF4 and JPN. In the case of AluI polymorphism, the 5 alleles (A, B, C, D, E) comprised 12 genotypes of the 5 alleles. KF4 population, alleles D and I were specific to the LPL gene Polymorphisms would be useful DNA markers for red seabream population.

• Journal of Microbiology and Biotechnology
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• 제9권1호
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• pp.113-118
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• 1999

The insulin-like growth factor (IGF) is found in all vertebrates and its type-II molecule is regarded as a fundamental embryonic growth factor during development. We have firstly identified, in this study, a cDNA clone corresponding to IGF-II (flIGF-II) from the adult brain of the teleost, Paralichthys olivaceus. We also examined the tissue expression of flIGF-II in several adult tissues by RT-PCR. The flIGF-II cDNA contained a complete ORF consisting of 215 amino acids and one stop codon. Its molecular characteristics appear to be similar to the previously identified IGF-II molecules, in which a common primary structure exhibiting B, C, A, D, and E domains is evidently observed. This cDNA clone seems to be cleaved at $Ala_{52}$ for the $NH_2$-end signal peptide and appears to produce a 98 amino acid-long E-peptide from the $Arg^{118}$. The functional B-D domain regions, therefore, include 65 amino acids and is able to encode a 7.4-kDa protein. The most prominent structural difference between IGF-I and IGF-II was that the D domain of IGF-II exhibits a two-codon-deleted pattern compared to the 8 amino acid-containing IGF-I. The insulin family signature in the A domain and six cysteins forming three disulfide bridges between the B and A domains were evolutionary-conserved from teleosts to mammalian IGF-II. Interestingly, the E-peptide region appears to provide a distinct hallmark between teleosts in amino acid composition. The flIGF-II shows 85.1% of sequence identity to salmon and trout, 90.6% to tilapia, and 98.4% to perch in amino acid level. In tissue expressions of IGF-II, it is very likely that flIGF-II has a significant expression in the adult brain. However, liver seems to be the main source for IGF-II production, and relatively low signals were observed in the adult muscle and kidney. Taken together, it would be concluded that the functional region for IGF-II mRNA is highly similar in phylogeny and is evolutionary, conserved as a mediator for the growth of vertebrates.

• Molecules and Cells
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• 제25권2호
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• pp.205-210
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• 2008

To develop molecular markers linked to the $L^4$ locus conferring resistance to tobamovirus pathotypes in pepper plants, we performed AFLP with 512 primer combinations for susceptible (S pool) and resistant (R pool) DNA bulks against pathotype 1.2 of pepper mild mottle virus. Each bulk was made by pooling the DNA of five homozygous individuals from a T10 population, which was a near-isogenic $BC_4F_2$ generation for the $L^4$ locus. A total of 19 primer pairs produced scorable bands in the R pool. Further screening with these primer pairs was done on DNA bulks from T102, a $BC_{10}F_2$ derived from T10 by back crossing. Three AFLP markers were finally selected and designated L4-a, L4-b and L4-c. L4-a and L4-c each underwent one recombination event, whereas no recombination for L4-b was seen in 20 individuals of each DNA bulk. Linkage analysis of these markers in 112 $F_2$ T102 individuals showed that they were each within 2.5 cM of the $L^4$ locus. L4-b was successfully converted into a simple 340-bp SCAR marker, designated L4SC340, which mapped 1.8 cM from the $L^4$ locus in T102 and 0.9 cM in another $BC_{10}F_2$ population, T101. We believe that this newly characterized marker will improve selection of tobamovirus resistance in pepper plants by reducing breeding cost and time.

• 한국식품영양학회지
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• 제27권5호
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• pp.845-850
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• 2014

In the present study, the effects of extracts from Korean plants on the DNA damage response in HaCaT cells exposed to ultraviolet B (UVB) were investigated. The activity of cells treated for 24 hr with ethanol extracts from Vaccinium spp. (VS), and Vitis vinifera L (VV) alone was similar to that of the non-treated control, but gradually decreased at concentrations above $200{\mu}g/mL$. However, when post-incubation of UVB-exposed cells was carried out for 24 hr in medium containing VS or VV extracts, the cell activity increased in a concentration-dependent manner compared with that in the normal growth medium. The cell viability of UVB-exposed cells also increased when post-incubated in medium containing VS or VV extracts, in a concentration-dependent manner. Nuclear fragmentation analysis showed that post-incubation with VS or VV extracts decreased the UVB-induced apoptosis by about 10 and 13%, respectively, of that in cells post-incubated in growth medium. After 24 hr of post-incubation in medium containing VS or VV extracts, the level of CPD and 8-OHdG decreased in time- and concentration-dependent manners. Overall these results suggest that VS and VV extracts assist the survival of UVB-exposed cells, in accordance with the respective decrease in the levels of UVB-induced DNA damage.

• Journal of Microbiology and Biotechnology
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• 제20권10호
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• pp.1386-1392
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• 2010

A bacterial strain designated GR5$^T$, previously isolated from a freshwater culture pond in Taiwan while screening for bacteria for antimicrobial compounds, was characterized using a polyphasic taxonomic approach. Strain GR5$^T$ was found to be Gram-negative, aerobic, greenish-yellow colored, rod-shaped, and motile by means of a single polar flagellum. Growth occurred at $10-40^{\circ}C$ (optimum, $35^{\circ}C$), pH 7.0-8.0 (optimum pH 8.0), and with 0-2.0% NaCl (optimum, 0.5-1.0%). The major fatty acids were $C_{16:1}{\omega}7c$(36.3%), $C_{16:0}$(16.6%), $C_{12:0}$ 3-OH (12.5%), and $C_{18:1}{\omega}7c$(9.1%). The major respiratory quinone was Q-8, and the DNA G+C content of the genomic DNA was 51.9 mol%. Phylogenetic analyses based on 16S rRNA gene sequences showed that strain GR5$^T$ belongs to the genus Rheinheimera, where its most closely related neighbors are Rheinheimera texasensis A62-14B$^T$ and Rheinheimera tangshanensis JA3-B52$^T$ with sequence similarities of 98.1% and 97.5%, respectively, and the sequence similarities to any other recognized species within Gammaproteobacteria are less than 96.5%. The mean level of DNA-DNA relatedness between strain GR5$^T$ and R. texasensis A62-14B$^T$, the strain most closely related to the isolate, was $26.5{\pm}7.6%$. Therefore, based on the phylogenetic and phenotypic data, strain GR5$^T$ should be classified as a novel species, for which the name Rheinheimera aquatica sp. nov. is proposed. The type strain is GR5$^T$ (=BCRC 80081$^T$=LMG 25379$^T$).

• 원예과학기술지
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• 제33권1호
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• pp.83-92
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• 2015

xBrassicoraphanus line BB#5, a new synthetic intergeneric hybrid between Brassica rapa L. ssp. pekinensis and Raphanus sativus L. var. rafiphera induced by N-methyl-N-nitroso-urethane mutagenesis in microspore culture, shows high seed fertility and morphological uniformity. Dual-color fluorescence in situ hybridization (FISH) using 5S and 45S rDNA probes and genomic in situ hybridization (GISH) using B. rapa genomic DNA probe were carried out to analyze the chromosome composition and the meiosis pairing pattern compared to its parental lines. The somatic chromosome complement is 2n = 38, which consists of 17 metacentric and two submetacentric chromosomes with lengths of 2.18 to $5.01{\mu}m$. FISH karyotype analysis showed five and eight pairs of 5S and 45S rDNA loci. GISH meiosis pairing analysis showed that 19 complete bivalents were most frequent and accounted for 42% of the 100 pollen mother cells examined. Based on chromosome number, size, morphology, rDNA distribution, and meiosis pairing pattern, both parental genomes of B. rapa and R. sativus appear to exist in xBrassicoraphanus line BB#5, demonstrating its genome integrity. Such stable chromosome constitutions and meiotic pairing patterns in somatic and meiotic cells are very rare in natural and synthetic intergeneric hybrids. Chromosomal studies and genetic and phenotypic changes in allopolyploids a re discussed. The results p resented h erein will b e usef ul f or f urther g enomic s tudy o f xBrassicoraphanus lines and their improvement as promising new breeding varieties.

• 대한의생명과학회지
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• 제26권4호
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• pp.288-295
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• 2020

Infection of Helicobacter pylori on gastric mucosa is associated with various gastric diseases. According to the WHO, H. pylori causes gastric cancer and has been classified as a class I carcinogen. Riboflavin is an essential vitamin which presents in a wide variety of foods. Previous studies have shown that riboflavin/UVA was effective against the growth inhibition of Staphylococcus aureus, S. epidermidis and multidrug-resistant Pseudomonas aeruginosa and had the potential for antimicrobial properties. Thus, we hypothesized that riboflavin has a potential role in the growth inhibition of H. pylori. To demonstrate inhibitory concentration of riboflavin against H. pylori, we performed agar and broth dilution methods. As a result, we found that riboflavin inhibited the growth of H. pylori. The MIC was 1 mM in agar and broth dilution test. Furthermore, to explain the inhibitory mechanism, we investigated whether riboflavin has an influence on the replication-associated molecules of the bacteria using RT-PCR to detect mRNA expression level in H. pylori. Riboflavin treatment of H. pylori led to down-regulation of polA and dnaB mRNA expression levels in a dose dependent manner. After then, we also confirmed whether riboflavin has cytotoxicity to human cells. We used AGS, a gastric cancer cell line, and treated with riboflavin did not show statistically significant decrease of cell viability. Thus, these results indicate that riboflavin can suppress the replication machinery of H. pylori. Taken together, these findings demonstrate that riboflavin inhibits growth of H. pylori by inhibiting replication of the bacteria.

• Genomics & Informatics
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• 제19권4호
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• pp.44.1-44.9
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• 2021

Autism is a complex neurodevelopmental disorder, the prevalence of which has increased drastically in India in recent years. Neuroligin is a type I transmembrane protein that plays a crucial role in synaptogenesis. Alterations in synaptic genes are most commonly implicated in autism and other cognitive disorders. The present study investigated the neuroligin 3 gene in the Indian autistic population by sequencing and in silico pathogenicity prediction of molecular changes. In total, 108 clinically described individuals with autism were included from the North Karnataka region of India, along with 150 age-, sex-, and ethnicity-matched healthy controls. Genomic DNA was extracted from peripheral blood, and exonic regions were sequenced. The functional and structural effects of variants of the neuroligin 3 protein were predicted. One coding sequence variant (a missense variant) and four non-coding variants (two 5'-untranslated region [UTR] variants and two 3'-UTR variants) were recorded. The novel missense variant was found in 25% of the autistic population. The C/C genotype of c.551T>C was significantly more common in autistic children than in controls (p = 0.001), and a significantly increased risk of autism (24.7-fold) was associated with this genotype (p = 0.001). The missense variant showed pathogenic effects and high evolutionary conservation over the functions of the neuroligin 3 protein. In the present study, we reported a novel missense variant, V184A, which causes abnormal neuroligin 3 and was found with high frequency in the Indian autistic population. Therefore, neuroligin is a candidate gene for future molecular investigations and functional analysis in the Indian autistic population.

• Pediatric Gastroenterology, Hepatology & Nutrition
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• 제11권2호
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• pp.137-142
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• 2008

목 적: 인터페론은 소아 만성 B형 간염의 치료에 널리 쓰이고 있으나 50% 이상의 환자에서 인터페론 치료에 반응이 없어 추가적인 다른 치료가 필요하다. 라미부딘은 B형 간염 바이러스 복제의 억제제로 B형 간염 치료제로 널리 쓰이고 있으나, 인터페론 치료에 반응이 없었던 B형 간염 환자에 대한 라미부딘의 치료 효과에 대한 연구가 많지 않다. 방 법: 2000년 1월부터 2007년 12월까지 부산대학교병원 소아청소년과에서 만성 B형 간염으로 진단되어 인터페론(interferon ${\alpha}$-2b, 10 $MU/m^2$ 또는 pegylated interferon $1.5{\mu}g/kg$)으로 6개월 간 치료를 받은 33명 중 치료에 반응이 없어 치료 종결 후 6~12개월 뒤부터 라미부딘(3 mg/kg/일, 최고 100 mg/일)으로 치료를 한 8명(남 6명, 여 2명)을 대상으로 라미부딘의 치료 효과를 분석하였다. 임상적 소견에 대해 의무기록지를 후향적으로 검토하였다. 결 과: 인터페론 치료 시작 시 나이는 4.9${\pm}$3.1세, 라미부딘 치료 시작 시 나이는 6.1${\pm}$3.2세였다. 인터페론 치료 전 혈청 ALT는 148.1${\pm}$105.8 IU/L였고, HBV-DNA PCR log값은 6.95${\pm}$0.70 copies/mL였다. 인터페론 치료 후 ALT는 143.1${\pm}$90.4 IU/L였고, DNA PCR log값은 6.46${\pm}$2.08 copies/mL로 치료 전과 차이가 없었고(p> 0.05), 2명에서 HBeAg 음전이 있었다. 모든 환자에서 라미부딘 치료 후 7.4${\pm}$2.1개월에 ALT가 정상화되고, 이미 HBeAg이 음전된 2명을 제외한 6명에서 7.9${\pm}$2.1개월에 HBeAg 혈청전환이 있었다. HBV DNA는 2.4${\pm}$2.8개월에 7명(87.5%)에서 음성화되었다. 2명은 라미부딘치료 종결 후 3년 이상 재발이 없으며, 5명은 완전 반응상태로 24.4${\pm}$9.1개월간 복용 중이다. 1명은 12개월간 라미부딘을 복용하여 혈청 ALT가 정상화되고 HBeAg 혈청전환이 있었으나 바이러스 돌파현상이 발생하여 치료를 중단하였다. 결 론: 연구 대상 환자 수가 적었지만 인터페론 치료에 반응이 없었던 만성 B형 간염 환자에서 라미부딘의 치료는 매우 효과적이었다.

• BMB Reports
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• 제43권2호
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• pp.133-139
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• 2010

We have performed analyses using ancient DNA extracted from 25 excavated human bones, estimating around the 1st century B.C. Ancient human bones were obtained from Nukdo Island, which is located off of the Korean peninsula of East Asia. We made concerted efforts to extract ancient DNA of high quality and to obtain reproducible PCR products, as this was a primary consideration for this extensive kind of undertaking. We performed PCR amplifications for several regions of the mitochondrial DNA, and could determine mitochondrial haplogroups for 21 ancient DNA samples. Genetic information from mitochondrial DNA belonged to super-haplogroup M, haplogroup D or its sub-haplogroups (D4 or D4b), which are distinctively found in East Asians, including Koreans or Japanese. The dendrogram and principal component analysis based on haplogroup frequencies revealed that the Nukdo population was close to those of the East Asians and clearly distinguished from populations shown in the other regions. Considering that Nukdo is geologically isolated in the southern part of the Korean peninsula and is a site of commercial importance with neighboring countries, these results may reflect genetic continuity for the habitation and migration of ethnic groups who had lived in a particular area in the past. Therefore, we suggest that phylogenetic analyses of ancient DNA have significant advantages for clarifying the origins and migrations of ethnic groups, or human races.