• The Plant Pathology Journal
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• 제32권6호
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• pp.584-588
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• 2016

Several Bacillus species were isolated from rice field soils, and 16S rRNA gene sequence analysis showed that Bacillus cereus was the most abundant. A strain named BC1 showed antifungal activity against Rhizoctonia solani. Bacteriophages infecting strain BC1 were isolated from the same soil sample. The isolated phage PK16 had an icosahedral head of $100{\pm}5nm$ and tail of $200{\pm}5nm$, indicating that it belonged to the family Myoviridae. Analysis of the complete linear dsDNA genome revealed a 158,127-bp genome with G + C content of 39.9% comprising 235 open reading frames as well as 19 tRNA genes (including 1 pseudogene). Blastp analysis showed that the proteins encoded by the PK16 genome had the closest hits to proteins of seven different bacteriophages. A neighbor-joining phylogenetic tree based on the major capsid protein showed a robust clustering of phage PK16 with phage JBP901 and BCP8-2 isolated from Korean fermented food.

• Journal of Microbiology
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• 제39권1호
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• pp.49-55
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• 2001

We have developed four chicken hybridomas secreting monoclonal antibodies to induce a protective immune response against the chicken disease avian coccidiosis, caused by the intestinal parasite Eimeria acervulina. Huwever, since the amount of antibodies secreted from these hybridomas is too low or sometimes they lost their ability to produce antibodies, the hybridoma method is not satisfactory in the production of large amounts of chicken monoclonal antibodies. To bypass these problems, we applied the antibody engineering technology using polymerase chain reaction. We cloned and determined the sequences of variable domains of the four chicken monoclonal antibodies, namely, 2-1, 5D11, 13C8 and 8C3. The sequences comparison to germline sequences skewed that the gene con version mechanism might contribute to developing diversification of heavy and λ-light chains in chicken antibodies. Several pseudogene families regarded as donors in gene conversion were identified at each framework region and the complementarily determining region of λ-light chains. In addition, as expected, numerous changes of nucleotide sequences such as nucleotide substitution, insertion and deletion were found predominantly in complementarity determining regions, which are likely to be somatic hypermutations as a result of affinity maturation in antibody-producing cells.

• 한국양식학회:학술대회논문집
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• 한국양식학회 2003년도 추계학술발표대회 논문요약집
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• pp.134-135
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• 2003

The geographic expansion of the toxic dinoflagellates genus Alexandrium has been shown to be world wide ranging. The members of the genus Alexandrium ocnstituted of 20-30 species did not show substantial differences in their morphology, which is mostly referred in the 'tamarensis species complex', except some species. Though rDNA sequences variations are very few and pseudogene types are so diverse that it is difficult to use them as the specific markers. In this study, we outlined Korean and Japanese A, tamarense and A. catenella regional isolates by phylogenetic analysis inferred from no cutting alignments of LSU rDNA D1-D2 and SSU rDNA sequences to group these regional isolates. The results were compared to RFLP patterns of PCR products targeted chloroplast DNA. Lastly screening of highly repeated microsatellite DNA which is frequently used for population analysis in eukaryotes was conducted. A. catenella regional strains identified by the sequencing of rDNA D1-D2 domain were divided into at least 3 groups of type E, CMC and Chinese type, divergence root may not be deep comparing with that of A. tamarense whose pseudogenes are very variable. Results of RFLP pattern and the phylogeny of the unknown gene targeting chloroplast showed that Korean and Japanese A. catenella regional isolates were divided into 3 types: Korean, Japanese and the third CMC types. Population-specific PCR amplification with Japanese A. catenella type-specific PCR primers was useful method for population analysis of A. catenella. Various types of satellite sequences such as 5 nucleotides repeats were obtained from A. tamarense and A. catenella. The 5 nucleotides repeats were primed at the both 3'and 5' ends, and these repeats were prominent as longer repeated motifs. This repeated DNA was intercalated as internal sequences containing various types subrepeats. It is expected that these satellite DNA would be a useful molecular population marker through detail comparison among Alexandrium regional isolates to trace their transferring pathway and to prevent their human-associated their regional extents.

• 미생물학회지
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• 제53권3호
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• pp.227-229
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• 2017

이 연구에서는 우포늪의 깨끗한 물에서 분리된 Spirosoma rigui KCTC $12531^T$의 완전한 게놈 서열을 분석하였다. 이 게놈은 G + C 함량이 54.4%인 5,828,404 bp으로 구성되어 있고 4,774개의 유전자와 4,647개의 단백질 코딩 유전자, 9개의 rRNA 유전자 그리고 43개의 tRNA 유전자 및 73개의 위유전자(pseudogene)를 포함하고 있다.

• 미생물학회지
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• 제53권3호
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• pp.230-232
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• 2017

이 연구에서는 자동차의 에어컨의 바이오필름환경에서 분리 된 Spirosoma aerolatum KACC $17939^T$의 완전한 게놈 서열을 분석하였다. 이 게놈은 G + C 함량이 48.3%인 7,959,595 bp으로 구성되어 있고 6,471개의 유전자와 6,471개의 단백질 코딩 유전자, 9개의 rRNA 유전자 그리고 43개의 tRNA 유전자 및 115개의 위유전자(pseudogene)를 포함하고 있다.

• Journal of Genetic Medicine
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• 제1권1호
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• pp.27-31
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• 1997

Steroid 21 hydroxylase deficiency is a major cause of congenital adrenal hyperplasia (CAH) and is caused by genetic impairment of the gene (CYP21B). In the human genome, CYP21B is located within the MHC class III region on the short arm of chromosome 6. Most of the genes in this region are highly polymorphic and crowded. Also the CYP21B gene is accompanied by its pseudogene (CYP21A) and tandemly arranged with two genes of fourth component of complement. This highly complex gene cluster in this area may predispose genetic instability of CYP21, i.e. mutations. In this study, tried to investigate the frequency of duplication and deletion of CYP21 and patterns of the genetic alterations of these genes.We also compared the genetic alteration in normal subjects with those of the CAH patients. The results showed that 15% of the normal korean population have duplication or deletion of CYP21. There was one normal subject with heterozygous deletion of CYP21B. Of the 5 CAH patients examined, 2 were found to show abnormal patterns. One was a large-scale gene conversion and the other a gene conversion associated with deletion involving both CYP21B and C4 locus II gene. Through this study, we carne to the conclusion that the duplication or even deletion of CYP21 and C4 might be quite a common event in the Korean population and these rearrangements must be regarded as polymorphisms. It could contribute to a high incidencs of CAH by providing a genetic pool of instable CYP21.

• Molecules and Cells
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• 제20권3호
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• pp.416-422
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• 2005

We previously used Southern blot analysis to detect restriction-length polymorphisms between male fertile and cytoplasmic male sterile (CMS) cytoplasms at the coxII and atp6 loci of the mtDNA of Capsicum annuum L. Two copies of atp6 were found in each male fertile and CMS pepper lines. Interestingly, one of the copies of atp6 in CMS pepper was a 3'-truncated pseudogene. The open reading frame of the coxII gene was the same in the fertile (N-) and CMS (S-) lines. However, the nucleotide sequence in the S-cytoplasm diverged from that in the N-cytoplasm 41 bp downstream of the stop codon. To develop CMS-specific sequence-characterized amplified region (SCAR) markers, inverse PCR was performed to characterize the nucleotide sequences of the 5' and 3' flanking regions of mitochondrial atp6 and coxII from the cytoplasms of male fertile (N-) and CMS (S-) pepper plants. Based on these data, two CMS-specific SCAR markers, 607 and 708 bp long, were developed to distinguish N-cytoplasm from S-cytoplasm by PCR. The CMS-specific PCR bands were verified for 20 cultivars containing either N- or S-cytoplasm. PCR amplification of CMS-specific mitochondrial nucleotide sequences will allow quick and reliable identification of the cytoplasmic types of individual plants at the seedling stage, and assessment of the purity of $F_1$ seed lots. The strategy used in this report for identifying CMS-specific markers could be adopted for many other crops where CMS is used for F1 seed production.

• 미생물학회지
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• 제54권1호
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• pp.84-86
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• 2018

이 연구에서는 5 kGy 의 감마선에 조사된 토양으로부터 분리된 Deinococcus puniceus $DY1^T$의 완전한 게놈서열을 분석하였다. 이 균주는 UVC 와 감마선에 대한 저항성을 보였으며, PacBio RS II platform 을 통해 시퀀싱을 진행하였다. 해당유전체의 분석결과 G + C 함량이 62.5%인 2,971,983 bp 크기의 원형 염색체를 확인하였으며, 해당 염색체는 2,617 개의 코딩 서열과 2,762 개의 유전자 그리고 88 개의 위유전자를 포함하고 있다.

• 원예과학기술지
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• 제31권1호
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• pp.72-79
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• 2013

Inactivation of the gene coding for dihydroflavonol 4-reductase (DFR) is responsible for the color difference between red and yellow onions (Allium cepa L.). Two inactive DFR-A alleles, DFR-$A^{PS}$ and DFR-$A^{DEL}$, were identified in our previous study. A functional marker was developed on the basis of the premature stop codon that inactivated the DFR-$A^{PS}$ allele. A derived cleaved amplified polymorphic sequences (dCAPS) primer was designed to detect the single nucleotide polymorphism, an A/T transition, which produced the premature stop codon. Digested PCR products clearly distinguished the homozygous and heterozygous red $F_2$ individuals. Meanwhile, to develop a molecular marker for detection of the DFR-$A^{DEL}$ allele in which entire DFR-A gene was deleted, genome walking was performed and approximately 3 kb 5' and 3' flanking sequences of the DFR-$A^R$ coding region were obtained. PCR amplification using multiple primers binding to the extended flanking regions showed that more of the extended region of the DFR-A gene was deleted in the DFR-$A^{DEL}$ allele. A dominant simple PCR marker was developed to identify the DFR-$A^{DEL}$ allele using the dissimilar 3' flanking sequences of the DFR-A gene and homologous DFR-B pseudogene. Distribution of the DFR-$A^{PS}$ and DFR-$A^{DEL}$ alleles in yellow onion cultivars bred in Korea and Japan was surveyed using molecular makers developed in this study. Results showed predominant existence of the DFR-$A^{PS}$ allele in yellow onion cultivars.

• 한국가금학회지
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• 제38권4호
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• pp.323-330
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• 2011

닭의 단일 클론 항체인 13C8 항체는 조류의 콕시듐증을 유발하는 것으로 알려진 Eimeria acervulina의 포자충(sporozoites) 항원에 결합하는 닭 항체이다. 그러나 닭 하이브리도마 유전자의 불안정성 때문에 분비되는 항체의 생산량이 낮은 단점이 있다. 이러한 단점을 보완하기 위해 hybridoma로 부터 항체의 중사슬 가변 부위(VH)유전자와 경사슬 가변 부위(VL) 유전자를 증폭하여 linker peptide로 연결해준 재조합 ScFv 항체 유전자를 구축하고, E. coli를 형질 전환시켜 재조합 단백질로 발현 정제하였다. ELISA 분석 결과 재조합 13C8 ScFv 항체는 세 종류의 Eimeria spp.에 대해 모두 항원 결합력을 나타내었으며, 염기서열 분석을 수행하여 germline sequence와 비교한 결과 닭 항체유전자의 다양성(diversity)은 pseudogene들의 gene conversion 기작에 의해 이루어짐을 제시해 주었다.