• 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.

• 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 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 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.

• The Korean Journal of Mycology
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• v.32 no.2
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• pp.148-151
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• 2004

This study was carried out to elucidate phylogenetic relationship of a yellow lump, Phellinus linteus by comparing the nuclear ribosomal intergenic spacer (IGS) I region with that of other genera of basidiomycetes retrieved from Genbank. IGS I region of Phellinus linteus was 730 bp long and sequence homology was conserved in the 5' region, in particular $1{\sim}280\;bp$, and decreased in the direction toward the 3' end. ITS region was widely studied in phylogenies related to basidiomycetes, but IGS region was not well understood yet. Our study indicated that IGS region can be a good tool in phylogenetic study of basidiomycetes.

• Korean Journal of Microbiology
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• v.38 no.1
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• pp.7-12
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• 2002

The intergenic spacer (IGS) region of the ribosomal DNA of species in Fusarium section Liseola was analyzed by amplification and subsequent digestion with several restriction enzymes. The length of the amplified IGS region was about 2.6 Kb in all strains except F.moniliforme 12 Which was about 2.9 Kb. The enzymes, EcoRI, HincII, SalI, HindIII, PstI and SmaI, digested the IGS region and nine haplotypes were identified among 11 strains. In the dendrogram based on PCR-RFLP of IGS region combined the results of section Liseola in this study and section Elegans in previous study, variation in the IGS appears to offer considerable potential to resolve intraspecific relationship as well as interspecies or intersection.

• The Plant Pathology Journal
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• v.16 no.5
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• pp.252-256
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• 2000

The 16S-23S rRNA intergenic spacer regions (ISRs) were sequenced and analyzed to design specific primer for identification of Pectobacterium chrysanthemi. Two types ISRs, large and small ISRs, were identified from three strains (ATCC 11663, KACC 10163 and KACC 10165) of P. chrysanthemi and Pectobacterium carotovorum subsp. carotovorum ATCC 15713.Large ISRs contained transfer RNA-Ile(tRNA$^{Ile}$)and tRNA$^{Ala}$, and small ISRs contained tRNA$^{Glu}$. Size of the small ISRs of P. chrysanthemi ranged on 354-356 bp, while it was 451 bp in small ISR of P. carotovorum subsp. carotovorum ATCC 15713. From hypervariable region of small ISRs, species-specific primer for P. chrysanthemi with 20 bp length (CHPG) was designed from hypervariable region of small ISRs, which was used as forward promer to detect P. chrysanthemi strains with R23-1R produced PCR product of about 260bp size (CHSF) only from P. chrysanthemi strains, not from other Pectobacterium spp. and Erwinia spp. Direct PCR from bacterial cell without extracting DNA successfully amplified a specific fragment, CHSF, from P. chrysanthemi ATCC 11663. The limit of PCR detection was 1${\pm}10^2$ cfu/ml.

• 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).