• Animal cells and systems
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• 제4권1호
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• pp.77-85
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• 2000

This study has demonstrated the molecular variation of 5S rRNA genes in 15 Allium subgenus Rhizirideum and 1 Allium subg. Allium. For cloning of the 5S rRNA genes, PCR products were obtained from amplification with oligonucleotide primers which were derived from the conserved coding region of 5S rRNA genes. These amplified PCR products were cloned and identified by FISH and sequence analysis. The 5S rRNA loci were primarily located on chromosomes 5 and/or 7 in diploid species and various chromosomes in alloploid species. The size of the coding region of 5S rRNA genes was 120 bp in all the species and the sequences were highly conserved within Allium species. The sizes of nontranscribed spacer (NTS) region were varied from 194 bp (A. dektiude-fustykisum, 2n=16) to 483 bp (A. sativum). Two kinds of NTS regions were observed in A. victorialis var. platyphyllum a diploid, A. wakegi an amphihaploid, A. sacculiferum, A. grayi, A. deltoide-fistulosum and A. wenescens all allotetraploids, while most diploid species showed only one NTS region. The species containing two components of NTS region were grouped with different diploid species in a phylogenetic tree analysis using the sequences of 5S rRNA genes and adjacent non-coding regions.

• 한국수산과학회지
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• 제36권3호
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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.

• 미생물학회지
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• 제26권4호
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• pp.312-317
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• 1988

The genes for ribosomal RNA in Rhizobium meliloti and Bradyrhizobium japonicum were analyzed by southern hybridization of BamHI, EcoRI, HindIII digested chromosomal DNA with purified 5' $^{32}P$-labeled 16S and 23S rRNA. The big differences in the hybridization pattern of both rhizobia were found. The comparative results were discussed in relation to the copy number and conservativity of restriction sites in the rRNA genes of both rhizobia.

• 한국약용작물학회지
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• 제16권3호
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• pp.195-198
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• 2008

Karyotypic analysis and FISH (fluorescence in situ hybridization) with 45S and 5S rRNA genes were carried out in Persicaria tinctoria H Gross. The somatic metaphase chromosomes were ranged from 2.25 ${\mu}m$ to 1.50 ${\mu}m$ in length. Chromosome number was 2n = 4x = 40 with the basic number of x = 10. The chromosome complement of the species consisted of 16 pairs of metacentrics (chromososomes 1,2,3,4,6,7,8,9, 10, 11, 12, 13, 15, 18, 19 and 20) and 4 pairs of submetacentrics (chromosome 5, 14, 16 and 17). The karyotype formula was K(2n) = 4x = 32 m + 8 sm. In FISH analysis, three pairs of 45S rRNA gene loci on the terminal region of submetacentrics (chromosomes 5, 16 and 17) and two pairs of 5S rRNA gene loci on the centromeric region of metacentrics (chromosomes 9 and 11) were detected, respectively.

• Journal of Microbiology and Biotechnology
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• 제27권1호
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• pp.112-121
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• 2017

Edwardsiella tarda is a gram-negative pathogenic bacterium in aquaculture that can cause hemorrhagic septicemia in fish. Many secreted proteins have already been identified as virulent factors of E. tarda. Moreover, since virulent phenotypes are based on the expression regulation of virulent genes, understanding the expression profile of virulent genes is important. A quantitative RT-PCR is one of the preferred methods for determining different gene expressions. However, this requires the selection of a stable reference gene in E. tarda, which has not yet been systematically studied. Accordingly, this study evaluated nine candidate reference genes (recA, uup, rpoB, rho, topA, gyrA, groEL, rpoD, and 16S rRNA) using the Excel-based programs BestKeeper, GeNorm, and NormFinder under different culture conditions. The results showed that 16S rRNA was more stable than the other genes at different culture growth phases. However, at the same culture time, topA was identified as the reference gene under the conditions of different strains, different culture media, and infection, whereas gyrA was identified under the condition of different temperatures. Thus, in experiments, the expression of gapA and fbaA in E. tarda was analyzed by RT-qPCR using 16S rRNA, recA, and uup as the reference genes. The results showed that 16S rRNA was the most suitable reference gene in this analysis, and that using unsuitable reference genes resulted in inaccurate results.

• 생태와환경
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• 제55권4호
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• pp.352-359
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• 2022

국내 서식하는 수서 생물(식물플랑크톤, 동물플랑크톤, 저서대형무척추동물, 어류)에 대한 eDNA 연구에 주요 이용되는 유전자인 12S rRNA와 16S rRNA, 18S rRNA, COI, CYTB를 대상으로 속(Genus) 수준의 등록 현황을 조사하였다. 그 결과 식물플랑크톤과 동물플랑크톤은 18S rRNA에서 가장 높은 등록 속 비율을 보였으며, 저서무척추동물은 COI에서 가장 높은 등록 속 비율을 확인하였다. 어류에서는 18S rRNA를 제외한 모든 유전자에서 90%에 가까운 높은 비율을 보였다. 분류군에 따른 우점 생물의 상위 20속에 대한 유전자 등록 현황은 식물플랑크톤은 18S rRNA에서 19속이, 저서무척추동물은 COI에서 18개 속이 등록되어 있었다. 어류에서는 12S rRNA, 16S rRNA, CYTB에서 상위 20의 모든 유전자 염기서열이 존재함을 확인하였다. 본 자료 분석을 통하여 각 분류군별 eDNA 연구에 적합한 유전자 데이터베이스의 양적인 정보를 파악하였다.

• 생명과학회지
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• 제22권2호
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• pp.167-176
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• 2012

발효가 진행중인 멸치액젓에서 단백질분해효소를 생산하는 3종의 호염성 세균을 분리하였다. 분리된 FAM 10, FAM 114, 그리고 FAM 115는 각각 소금농도가 2~4%, 10%, 6%에서 최적 세포성장이 관찰되었으며, 18~22% 소 금농도까지 생육이 가능했다. 단백질분해효소 생산을 위한 최적 소금농도는 FAM 10은 6%, FAM 114와 FAM 115는 10%로 나타났다. FAM 10의 단백질분해효소 활성은 10%까지 첨가하면 서서히 저하되며, 14% 소금농도에서는 효소활성이 없는 반면, FAM 114와 FAM 115의 경우, 14%까지 효소활성을 나타냈으며 18%에서는 활성을 관찰할 수 없었다. 이러한 결과로부터 분리된 3종의 미생물이 중간 정도의 호염성 세균임을 증명하였다. 16S rRNA 유전자와 16S-23S 유전자 사이 공간(IGS) 서열, 생화학적 실험, 그람염색을 이용하여 비교 분석한 결과, FAM 10, FAM 114, 그리고 FAM 115는 각각 Salinivibrio sp., Halobacillus sp., 그리고 Halobacillus sp.임을 동정하였다. Salinivibrio sp. FAM 10에는 191번째 서열부터 약간 다른 2가지 종류의 16S rDNA와 16S-23S IGS내에 tRNA 유전자가 없는 형태, 이소루이신/알라닌, 글루탐산/라이신/발린을 운반하는 tRNA 유전자들을 함유하는 4가지 종류의 다른 16S-23S IGS가 존재하였다. Hablobacillus sp. FAM 114와 FAM 115는 완전히 동일한 16S rRNA 유전자 서열을 가지고 있었으며, 여러 Halobacillus sp.와 99% 서열동일성을 보여주었다. IGS의 경우, tRNA 유전자가 없는 IGS와 이소루이신/알라닌을 운반하는 tRNA 유전자들을 함유하는 3가지 16S-23S IGS가 존재하였으며, Halobacillus aidingensis와 Halobacillus sp. JM-Hb의 IGS와 99% 서열동일성을 보여주었다.

• Ocean Science Journal
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• 제41권4호
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• pp.315-318
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• 2006

Three Synechococcus strains were isolated from seawater near the Ieodo Ocean Research Station (IORS), and their 16S rDNA genes and the internal transcribed spacer (ITS) between the 16S and 23S rRNA genes were sequenced to investigate their phylogenetic relationships. Phylogenetic trees based on the 16S rDNA and ITS sequences showed that they clustered in the main MC-A Synechococcus group (subcluster 5.1), but formed branches differentiating them from the described clades. As the IORS is located in an area affected by diverse water masses, high Synechococcus diversity is expected in the area. Therefore, the IORS might be a good site to study the diversity, physiology, and distribution of the Synechococcus group.

• 한국어병학회지
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• 제22권3호
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• pp.391-400
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• 2009

Genetic identification of 17 fish-derived Aeromonas strains was attempted using 5 housekeeping genes. 16S rRNA, gyrB, rpoD, dnaJ and recA genes from the 17 strains were amplified, and total of 85 amplicons were sequenced. DNA sequences of the strains and type strains of the 17 Aeromonas homology groups were used for genetic identification and phylogenetic analyses. None of the strains was identified as a single species using the 16S rRNA gene, showing the same identities (average = 99.7%) with several Aeromonas species. According to gyrB, rpoD, dnaJ, and recA, 9 strains and RFAS-1 used in this study were identified as A. hydrophila and A. salmonicida, respectively. However, the other strains were closely related to 2 or more Aeromonas species (i.e., A. salmonicida, A. veronii, A. jandaei, A. media and A. troda) depending on the genetic marker used. In this study, gyrB, rpoD, dnaJ and recA gene sequences proved to be advantageous over 16S rRNA for the identification of field Aeromonas isolates obtained from fish. However, there are discrepancies between analyses of different phylogenetic markers, indicating there are still difficulties in genetic identification of the genus Aeromonas using the housekeeping genes used in this study. Advantages and disadvantages of each housekeeping gene should be taken into account when the gene is used for identification of Aeromonas species.

• 대한의생명과학회지
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• 제10권4호
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• pp.333-339
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• 2004

A multiplex PCR assay targeting the yst and 16S rRNA genes of Yersinia enterocolitica was developed to specifically identify pathogenic Y. enterocolitica from pure culture. Simultaneous amplification of 145 and 416 bp fragments of the yst and 16S rRNA genes of Y. enterocolitica was obtained using the primer pairs in a single reaction. Validation of the assay was performed with the reference Yersinia strains and other members of the family Enterobacteriaceae. The defined primer pairs amplified the targeted sequence from only pathogenic Y. enterocolitica strains, whereas none of the other bacterial species yielded any amplified fragments. Within an assay time of 4 h, this assay offers a very specific, reliable, and inexpensive alternative to the conventional phenotypic assays used in clinical laboratories to identify pathogenic Y. enterocolitica.