• Asian-Australasian Journal of Animal Sciences
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• v.16 no.12
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• pp.1816-1821
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• 2003

Reliable PCR based identification of lactobacilli has been described utilizing the sequence of 16S-23S rRNA intergenic spacer region. Those sequence comparisons showed a high degree of difference in homology among the strains of L. rhamnosus, L. casei, L. acidophilus and L. helveticus whose 16S-23S rRNA intergenic small SR's sizes were 222 bp, 222 bp, 206 bp and 216 bp respectively. The sequence of 16S-23S rRNA intergenic spacer region of L. rhamnosus ATCC 53103 revealed the close relatedness to those of L. casei strains by the homology ranges from 95.4% to 97.2%. 16S-23S rRNA intergenic spacer region nucleotide sequence of L. acidophilus showed some distant relatedness with L. rhamnosus ATCC 53103 with the homology ranges from 40.3% to 41.8% and that with L. helveticus was shown to be 30% of homology, which exists at the most distant phylogenetic relatedness. The identification of species and strain of lactobacilli was possible on the basis of these results. The common sequences among the 17 strains were CTAAGGAA located in the initiating position of the DNA and some discrepancies were found between the same strains based on these results.

• Korean Journal of Veterinary Service
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• v.27 no.1
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• pp.103-109
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• 2004

Babesia equi ema-1 5' intergenic(IG) nucleotide was PCR amplified and analyzed for restriction sites in order to identify a promoter region in this IG nucleotide sequence. B equi ema-1 5' IG specific primers identified a 1268 bp PCR product. The sequence had restriction sites for 34 restriction enzymes when analyzed by a computer program. Among them, 26 enzymes had only one restriction site, but the others had more than one sites. When four restriction enzymes (Bgll , HindⅢ, Kpn1 and BamH1) were treated to digest the 1268 bp nucleotide, they had restriction sites as expected by the computer program. Information of restriction sites in the 1268 bp IG nucleotide will be applied to select restriction enzymes for cloning the IG nucleotide to a vector.

• Journal of fish pathology
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• v.17 no.2
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• pp.91-98
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• 2004

This study was performed for the identification of Streptococcus sp. from cultured flounders (Paralichthys olivaceus) showing streptococcosis in the Jeju island. We isolated 10 strains of Streptococcus iniae from the cultured olive flounders with streptococcosis. Isolated strains were identified in S. iniae since they have formed the expected band through performing PCR assay using specific primers, Sin-1 (5'-CTAGAGTACACATGTACT(AGCT)AAG-3') and Sin-2 (5'-GGATTTTCCACTCCCATTAC-3'). In addition to 16S-23S rRNA intergenic spacers (ISR), operon structure of isolated strains showed that all strains had three 16S-23S rRNA ISR band patterns. The 16S-23S rRNA ISR sequence of isolated strains showed 96% sequence identity with S. iniae (GenBank accession number AF 048773). This paper is the first report that S. iniae is associated with streptococcosis of Olive flounder in Korea.

• Journal of Microbiology and Biotechnology
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• v.25 no.8
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• pp.1380-1389
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• 2015

Prx1, an AhpF-dependent 2-Cys peroxiredoxin (Prx), was previously identified in Vibrio vulnificus, a facultative aerobic pathogen. In the present study, transcription of the V. vulnificus prx1ahpF genes, which are adjacently located on the chromosome, was evaluated by analyzing the promoter and intergenic region of the two genes. Northern blot analyses revealed that transcription of prx1ahpF results in two transcripts, the prx1 and prx1ahpF transcripts. Primer extension analysis and a point mutational analysis of the promoter region showed that the two transcripts are generated from a single promoter. In addition, the 3' end of the prx1 transcript at the prx1ahpF intergenic region was determined by a 3'RACE assay. These results suggested that the prx1ahpF genes are transcribed as an operon, and the prx1 transcript was produced by transcriptional termination in the intergenic region. RNA secondary structure prediction of the prx1ahpF intergenic region singled out a stem-loop structure without poly(U) tract, and a deletion analysis of the intergenic region showed that the atypical stem-loop structure acts as the transcriptional attenuator to result in the prx1 and prx1ahpF transcripts. The combined results demonstrate that the differential expression of prx1 and ahpF is accomplished by the cis-acting transcriptional attenuator located between the two genes and thereby leads to the production of a high level of Prx1 and a low level of AhpF.

• Journal of Life Science
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• v.27 no.1
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• pp.89-94
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• 2017

DNA sequences of the intergenic spacer 1 and intergenic spacer 2 of the nineteen plants belonging Vitis genus were collected from the Genbank. DNA sequences of the same regions of Vitis thunbergii var. sinuata and Ampelopsis brevipedunculata var. heterophylla, both common plants in Korea, were not available in Genbank. Those two plants were collected, their genomic DNA encoding 18S rRNA, intergenic spacer 1, 5.8S rRNA, intergenic spacer 2 and part of 28S rRNA amplified and DNA sequence determined. DNA sequences of twenty-one plants including two Korean plants were aligned by the Multiple sequence comparison by log-expectation(MUSCLE) algorithm and the alignment was used to calculate neighbor-joining tree and pairwise distance. The results indicate DNA sequences of the two Korean plants are highly homologous with each other, but they are quite distantly related to the other Vitis plants. Distant relationship of the two Korean plants with the other Vitis plants might be due to independent evolution of those two plants in geographically isolated environment. Those two Korean plants are classified in different genera based on the morphology, one in Vitis genus and the other in Ampelopsis genus, providing another example of discrepancy between morphological and genetic classification.

• Journal of Animal Science and Technology
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• v.45 no.3
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• pp.473-482
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• 2003

In vivo protective and in vitro inhibitory activities of Lactobacillus casei YIT 9018. against typical enteritis causing Salmonella enteritidis KU101 and IgA level after challenge have been determined. In order to identify the strains of lactobacilli the sequences of 16S-23S rRNA intergenic spacer region were determined. All the test strains of Lactobacillus spp. inhibited Salmonella enteritidis, the intensity varied depending upon the species of lactobacilli. Effects on the survival rate of the mouse after challenge with Salmonella enteritidis KU101 on feeding Lactobacillus spp. have shown the highest survival rate in L. helveticus CU 631 followed by L. casei YIT 9018 and L. johnsonii C-4 and the lowest in control mice. The higher level of total Ig A concentration in the intestinal fluid of lactobacilli fed mice than control mice was observed. The sequences of 16S-23S rRNA intergenic spacer region of seven strains of Lactobacillus casei could be utilized as a strain identification, those sequences showed some degree of difference in homology.

• Animal cells and systems
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• v.3 no.4
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• pp.393-397
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• 1999

Length variations in human mitochondrial DNA (mtDNA) offer useful markers in the study of female aspects of human population history. One such length variation is a 9-bp deletion in the small noncoding segment located between the COII and Iysine tRNA genes (COII/tRNA/$^{Lys}$ intergenic region) which usually contain two tandemly arranged copies of a 9-bp sequence (ccccctcta) in human mtDNA. The mtDNA 9-bp deletion and polymorphic variants of expanded 9-bp repeat motif in the intergenic COII/tRNA$^{Lys}$ region have been found at varying frequencies among different human ethnic groups. We have examined the length variation of the mtDNA COII/tRNA$^{Lys}$ intergenic region from a total of 813 individuals in east Asian populations. The occurrence of the 9-bp deletion was found to be relatively homogeneous in northeast Asian populations (Chinese, 14.2%; Japanese, 14.3%: Koreans, 15.5%), with the exception of Mongolians (5.1%). In contrast, Indonesians (25.0%) and Vietnamese (23.2%) of the southeast Asian populations appeared to have relatively high frequencies of the 9-bp deletion. We identified the existence of a new expanded 9-bp repeat motif which likely resulted from a slipped mispairing insertion of six more cytosines in the intergenic COII$^{Lys}$ region. It was present at low frequencies in the Korean (2/349) and Japanese populations (2/147). Based on the results of this study, the Korean population may reflect a close genetic affinity with the Japanese and Chinese populations than the others surveyed east Asian populations.

• Journal of Microbiology
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• v.39 no.4
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• pp.265-272
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• 2001

Variation within the intergenic spacer(IGS) of the ribosomal DNA gene for twenty-two strains of E. oxysporum and its formae speciales was examined by PCR, couped with RELP analysis. The length of the amplified IGS region was about 2.6 kb in all strains except F.oxysporum f. sp. cucumer-inum from Korea and F. oxysporum f. sp. niveum. Those two strains were 2.5 kb long. Restriction digestion of IGS-RELP regions by Eco RI, NruI, HincII, SAlI, SmaI, BalIi, HindIII, XhoI and KpnI gave rise to nine IGS hapoltypes among all strains. Cluster analysis based on the presence of absence of comigrating restriction reagments show the two groups based on 44% genetic similarity. These results demonstrated that analysis of IGS showed some difference within and between F. oxysporum formae speciales.

• The Plant Pathology Journal
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• v.18 no.2
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• pp.98-101
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• 2002

Using phytoplasma universal primer pair Pl and P7, a fragment of about 1.8 kb nucleotide sequences of 16S rRNA gene and 16S-23S rRNA intergenic spacer region, and a portion of 23S rRNA gene of jujube witches'broom (JWB) and mulberry dwarf(MD) phytoplasmas were determined. The nucleotide sequences of JWB and MD were 1,850 bp and 1,831 bp long, respectively. The JWB phytoplasma sequence was aligned with the homologous sequence of MD phytoplasma. Twenty-eight base insertions and nine base deletions were found in the JWB phytoplasma sequence compared with that of MD phytoplasma. The similarity of the aligned sequences of JWB and MD was 84.8%. The near-complete 16S rRNA gene DNA sequences of JWB and MD were 1,529 bp and 1,530 bp in length, respectively, and revealed 89.0% homology. The 16S-23S rRNA intergenic spacer region DNA sequences were 263 bp and 243 bp in lengths respectively, while homology was only 70% and the conserved tRNA-lle gene of JWB and MD was located into the intergenic space region between 16S-23S rRNA gene. The nucleotide sequences were 77 bp long in both JWB and MD, and showed 97.4% sequence homology. Based on the phylogenetic analysis of the two phytoplasmas, the JWB phytoplasma belongs to the Elm yellow phytoplasma group (16S rV), whereas, the MD phytoplasma belongs to the Aster yellow group (16S rI).

• Korean Journal of Fisheries and Aquatic Sciences
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• v.36 no.3
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• pp.239-246
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• 2003

We have examined the 16S-23S rRNA intergenic spacer region (ISR) of Vibrio vulnificus KCTC 2959. ISRs were amplified by primers complementary to conserved regions of 16S and 23S rRNA genes. ISR amplicons were cloned and sequenced. Analysis of the ISR sequences showed that V. vulnificus KCTC 2959 contains five types of polymorphic ISRs. Size of ISRs ranged from 424 to 741 bp in length and the number of tRNA genes ranged from one to four. The ISRs were designated as ISR-E $(tRNA^{Glu}),\;ISR-IA\;(tRNA^{Ile}-tRNA^{Ala})$, ISR-EKV $(tRNA^{Glu}-tRNA^{Lys}-tRNA^{Val})$, ISR-IAV $(tRNA^{Ile}-tRNA^{Ala}-tRNA^{val})$ and ISR-EKAV $(tRNA^{Glu}-tRNA^{Lys}-tRNA^{Ala}-tRNA^{Val})$ based on their tRNA genes. Multiple alignment of representative sequences from different Vibrio species revealed several domains of high sequence variability. We used the sequences of variable domains to design species-specific primer for detection PCR. Specificity of the primers was examined using genomic DNA prepared from 18 different Vibrio species. The results showed that the PCR using primers designed in this study can be used to detect V. vulnificus from other Vibrio species.