• Journal of Microbiology and Biotechnology
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• 제18권5호
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• pp.815-820
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• 2008

Two culture-independent methods, namely ribosomal DNA libraries and denaturing gradient gel electrophoresis (DGGE), were adopted to examine the microbial community of a Malaysian light crude oil. In this study, both 16S and 18S rDNAs were PCR-amplified from bulk DNA of crude oil samples, cloned, and sequenced. Analyses of restriction fragment length polymorphism (RFLP) and phylogenetics clustered the 16S and 18S rDNA sequences into seven and six groups, respectively. The ribosomal DNA sequences obtained showed sequence similarity between 90 to 100% to those available in the GenBank database. The closest relatives documented for the 16S rDNAs include member species of Thermoincola and Rhodopseudomonas, whereas the closest fungal relatives include Acremonium, Ceriporiopsis, Xeromyces, Lecythophora, and Candida. Others were affiliated to uncultured bacteria and uncultured ascomycete. The 16S rDNA library demonstrated predomination by a single uncultured bacterial type by >80% relative abundance. The predomination was confirmed by DGGE analysis.

• 약학회지
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• 제37권5호
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• pp.504-510
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• 1993

Human insulin gene is consisted of the polymorphic region with the repeating units, the regulatory sequence, the structural gene including the intervening sequence, and 3'-flanking region. The polymerase chain reaction, which amplifies the target DNA between two specific primers, has been performed for the amplification of human insulin gene and simple one-step cloning of it into Escherichia coli. Out of 1727 nuceotides compared, only 4 sites were variable: 5'-regulatory region(G2101$\rightarrow$AGG); IVS I(T2401$\rightarrow$A); Exon II(C2411 deletion); IVS II(A2740 dejection). The variations at the G2101 and T2401 were the same as those found in one American allele. The other two variations were observed only in the specific Korean allele. And, the enzyme digestion patterns among normal, insulin dependent diabetes mellitus, and non-insulin dependent diabetes mellitus were the same. On the other hand, PCR method showed the possibility of the quickaccess for the polymorphic region in terms of the restriction fragment length of polymorphism.

• Parasites, Hosts and Diseases
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• 제34권4호
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• pp.259-266
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• 1996

형태학적 제3군 가시아메바의 taxonomic validity는 아직 확실하지 않다. 이번 연구에서 제3군에 속하는 6종의 가시 아메바 즉 A. culbertsoni A. healyi A. palestinensis. A. pustulosa, A. royreba 및 A. lenticulata의 type strain들의 동위효소. 미토콘트리아 DNA 및 small subunit(ssu) rDNA의 Restriction Fragment Length Polymorphism(RFLP) 양상을 비교하여 이들의 taxonomic validity를 검토하였다. 미토콘드리아 DNA의 RFLP 양상은 분리주간에 서로 심한 차이를 보였다. A. palestinensis와 A. pustulosc는 거의 동일한 rDNA RFLP(추정 염기 치환율 2.6%) 및 동위효소의 양상을 보여 A. palestinensis와 A. pustulosc는 같은 종으로 판단되었다. 그외의 종들은 서로 아주 다양한 rDNA RFLP 및 동위효소의 양상을 나타내어 독립종으로 인정되었다.

• BMB Reports
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• 제33권3호
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• pp.208-212
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• 2000

In order to develop a specific genetic marker for the Korean native cattle (Hanwoo), an arbitrarily-primed polymerase chain reaction (AP-PCR) analysis of 6 different cattle breeds was attempted. Eight different arbitrary primers, each longer than 20-mer nucleotides, were used. In comparison to the AP-PCR patterns, several distinctive DNA bands that are specific for a certain breed were detected. When the primer Kpn-X was employed, a 280bp DNA fragment was found to be specific only for Hanwoo. In an individual analysis of Hanwoo, this AP-PCR marker was observed in 123 head of cattle among the 153 that were tested (80.4%). Nucleotide sequencing revealed that this fragment has a short microsatellite sequence of tandem repeat, $A(G)_{1-2}\;(C)_{1-3}AGAG$. According to the analysis of AP-PCR band patterns, Hanwoo was discovered to be genetically most closely-related with Holstein among the various cattle breeds.

• 한국미생물학회:학술대회논문집
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• 한국미생물학회 2002년도 추계학술대회
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• pp.15-21
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• 2002

Terminal-restriction fragment length polymorphism (T-RFLP) analysis has been optimized by using in vitro model community composed of genomic DNAs of known bacterial strains and has been applied to assess the bacterial community structure in marine sediments. The specific fluorescence-labeled terminal restriction fragments (T-RFs) between 39 and 839 base long specifying each strain were precisely measured for known bacterial strains. The addition of a co-solvent (dimethylsulfoxide or glycerol) into PCR reactions has reduced differential PCR amplification. Comparative bacterial community structure was investigated for pristine and polluted sediments. A complex T-RFLP pattern showing complex bacterial community structure was obtained in the pristine sediment, whereas simple T-RFLP pattern (low bacterial diversity) was shown in polluted sediments where caged aquaculture has been conducted for several years. The results of T-RFLP analysis were compared with that of cloning and sequencing 16S rDNA clones from the same sediments. Sequence analysis of 16S rDNA clones (72) of the pristine sediment revealed a diverse collection of lineages, largely of the class Proteobacteria ($6\%$ alpha subdivision, $46\%$ gamma subdivision, $13\%$ delta subdivision, and $3\%$ epsilon subdivision), Nitrospina $(8\%)$, high G+C gram positive $(8\%)$, Verrucomicrobia $(7\%)$, and Planctomycetes $(6\%)$. In the contaminated sediments, 17 $(59\%)$ of the 16S rDNA clones (29) were related to Campylobacter and symbiont of Rimicaris exoculata belonging to epsilon subdivision of Proteobacteria. The results obtained indicated that T-RFLP analysis is a rapid and precise technique for comparative bacterial community analysis.

• BMB Reports
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• 제29권1호
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• pp.45-51
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• 1996

Most expressed HLA loci exhibit a remarkable degree of allelic polymorphism, which derives from sequence differences predominantly localized to discrete hypervariable regions of the amino-terminal domain of the molecule. In this study, the HLA-DRB1 genotypes were determined in eighteen control cell lines and 112 unrelated Koreans using the PCR-SSP (Polymerase Chain Reaction-Sequence Specific Primer) technique. 29 specific primer pairs in assigning the DRB1 gene were used. The results of control cells correlated well with the data which was previously reported. The heterozygosity and homozygosity of the DRB1 gene were 0.786 and 0.214, respectively. In a total of 41 different DRB1 alleles and 83 genotypes, the most frequent allele and genotype were DRB1*04 and DRB1*0901/1501, respectively. This study shows that the PCR-SSP technique is relatively simple, fast and a practical tool for the determination of the HLA-DRBI genotypes. Moreover, these results-allele and genotype frequency and heterozygosity of the HLA DRB1 gene-could be useful for database study before being applied to individual identification and transplantation immunity.

• 한국생물공학회:학술대회논문집
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• 한국생물공학회 2000년도 추계학술발표대회 및 bio-venture fair
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• pp.119-122
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• 2000

Biological science is being revolutionized by the availability of much sequence information from many genome project With the advanced technology at hand, main trend in biological research is rapidly changing from a structural DNA analysis to understanding cellular function of the DNA sequences. Combined with mechanics, computer, bioinformatics and other advanced technologies, DNA chip technology provides numerous applications because of its robustness, accuracy, and automation. DNA chip is expected to become an indispensable tool in fields of biology, biotechnology, drug discovery, and other application areas. DNA chip can be used for mutation and polymorphism detection, gene expression monitoring and phenotypic analysis as well. If DNA chip is used for the development of pharmaceutical products, it can considerably reduce the cost and time for the entire process of drug discovery and development, and can also contribute in developing personal drugs.

• 한국자원식물학회:학술대회논문집
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• 한국자원식물학회 2018년도 추계학술대회
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• pp.25-25
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• 2018

The Fukushima Daiichi Nuclear Power Plant accident in March 2011 caused severe radioactive contamination in the surrounding environment. Since the accident, much attention has been paid to the biological and genetic consequences of organism inhabiting the contaminated area. The effect of radiation exposure on genetic mutation rates is little known, especially for low doses and in situ conditions. Evaluating DNA mutation by low levels of radiation dose is difficult due to the rare mutation event and lack of sequence information before the accident. In this study, correlations with air dose levels and somatic DNA mutation rates were evaluated using Next Generation Sequencer for the clonal plant, Phyllostachys edulis. This bamboo is known to spread an identical clone throughout Japan, and it has the advantage that we can compare genetic mutation rate among identical clone growing different air dose levels. We collected 94 samples of P. edulis from 14 sites with air dose rates from $0.04{\sim}7.80{\mu}Gy/h$. Their clonal identity was confirmed by analysis using 24 microsatellite markers, and then, sequences among samples were compared by MIG sequence. The sequence data were obtained from 2,718 loci. About ~200,000 bp sequence (80 bp X 2,718 loci) were obtained for each sample, and this corresponds to about 0.01% of the genome sequence of P. edulis. In these sequences, 442 loci showed polymorphism patterns including recent origin mutation, old mutation, and sequence errors. The number of mutations per sample ranged from 0 to 13, and did not correlate with air dose levels. This result indicated that DNA mutations have not accumulated in P. edulis living in the air doses levels less than $10{\mu}Gy/h$. Our study also suggests that mutation rates can be assessed by selecting an appropriate experimental approach and analyzing with next generation sequencer.

• BMB Reports
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• 제36권5호
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• pp.427-432
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• 2003

Jute is the principal coarse fiber for commercial production and use in Bangladesh. Therefore, the development of a high-yielding and environmental-stress tolerant jute variety would be beneficial for the agro economy of Bangladesh. Two molecular fingerprinting techniques, random-amplified polymorphic DNA (RAPD) and amplified-fragment length polymorphism (AFLP) were applied on six jute samples. Two of them were cold-sensitive varieties and the remaining four were cold-tolerant accessions. RAPD and AFLP fingerprints were employed to generate polymorphism between the cold-sensitive varieties and cold-tolerant accessions because of their simplicity, and also because there is no available sequence information on jute. RAPD data were obtained by using 30 arbitrary oligonucleotide primers. Five primers were found to give polymorphism between the varieties that were tested. AFLP fingerprints were generated using 25 combinations of selective-amplification primers. Eight primer combinations gave the best results with 93 polymorphic fragments, and they were able to discriminate the two cold-sensitive and four cold-tolerant jute populations. A cluster analysis, based on the RAPD and AFLP fingerprint data, showed the population-specific grouping of individuals. This information could be useful later in marker-aided selection between the cold-sensitive varieties and cold-tolerant jute accessions.

• 보존과학연구
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• 통권25호
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• pp.47-74
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• 2004

We investigated the nucleotide substitution and insertion polymorphism of the hypervariable region Ⅰ and Ⅱ in mt DNA by sequencing ancient DNA from 51 ancient bones and teeth excavated at Nuk-do and Yimdang-dong in Korea. It revealed 35 sequence types from the ancient Korean. Of these, different sequences were 34 sequences. There were 19 and 38 base substitutions in HVI and HVⅡ, respectively. Some substitutions were characteristic of East Asian populations as compared with data reported on Caucacianpopulations,16051, 16150, 16172, 16223 in region I and 73, 263 in region II were noted as polymorphic sites, respectively. These were distributed evenly along the control region, though the frequency of each site was variable. Nucleotide substitution rather than insertion and deletion was the prevalent pattern of variation. Insertion of cytosine between312 and 315 in region HVⅡ were detected up to 98% in 51 ancient bone samples. This sequence data represents a phylogenetic tree using NTI DNA Suite computer program. The phylogenetic tree showed that mt DNA sequences of Nuk-do bones were relative to west Siberian and Indonesian. The usefulness of mt DNA sequencing in ancient Korean population excavated atarchaeological sites is based on biological and historical evidence for origin and migration of ancient Korean.