• Journal of Microbiology
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• 제45권3호
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• pp.219-226
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• 2007

Insertion sequence IS1112 is a repetitive element with a relatively high number of copies in Xanthomonas oryzae pv. oryzae (Xoo), the causal agent of bacterial blight of rice (Oryza sativa L.). Three new loci of IS1112 were identified in seven Chinese strains of Xoo using a single oligonucleotide primer J3; 5'-GCTCA GGTCAGGTGGCCTGG-3' by insertion-sequence-based polymerase chain reaction (IS-PCR). Among the three new loci of IS1112, two were located in the open-reading frame region of genes fhuA and cirA, which encode TonB-dependent receptors, and the third in ISXo2, another type of insertion sequence in Xoo genome. Three variants of IS1112 were identified in those three loci based on their sequence similarities: two were identical to IS1112a and IS1112b, reported in strain PXO86 from the Philippines, while the third was a new member of IS1112, defined as IS1112d. Inserting IS1112 in gene fhuA caused three bases, GGT, to be duplicated at the target site, but inserting it in gene cirA did not cause any duplication in the target site. The diversity of IS1112 sequence and insertion loci in Xoo genome and their potential effects are discussed.

• 한국멀티미디어학회논문지
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• 제7권3호
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• pp.408-417
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• 2004

유전체 분석 과정은 여러 단계를 걸쳐 다양한 소프트웨어 분석 도구가 사용되는 복잡한 작업을 수반한다. 유전체 분석과 관련된 기존의 소프트웨어 도구들은 대부분 리눅스나 유닉스 기반 프로그램 이므로 생물학자가 이들을 설치하고 사용하는데 어려움과 불편함이 많은 실정이다. 또한, 분석의 각 단계별로 생산되는 파일은 수작업을 통한 변환을 거쳐야만 다음 단계의 입력으로 사용될 수 있다. 근래에 웹을 기반으로한 도구들이 개발되고 있으나 한번에 하나의 서열을 처리하는 방식이므로 대량의 실험 데이터를 분석하는 경우에는 반복 작업으로 인한 시간과 노력이 요구되는 단점을 갖고 있다. 본 논문에서는 유전체 분석에 필요한 여러 도구들을 웹 환경에서 하나의 그래픽 사용자 인터페이스로 통합하여 생물학자들이 보다 쉽게 서열과 기능을 분석할 수 있도록 한 WGAT(Web-based Genome Analysis Tool)를 제안한다. WGAT는 리눅스 서버에 유전체 데이터 분석프로그램을 구동하고, 클라이언트 웹 (web)에서 데이터 파일과 분석에 필요한 선택사항들을 입력함으로써 한번에 여러 단계의 분석 작업을 수작업 없이 자동으로 처리할 수 있다. WGAT시스템의 생산성을 분석하기 위하여 기존의 방식과 WGAT를 이용한 방식의 서열분석 처리 시간을 비교한 결과 서열 단편의 개수가 1000개인 경우 기존의 방식보다 20배 이상 분석 능력이 향상됨을 확인할 수 있었다.

• 대한임상검사과학회지
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• 제48권4호
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• pp.327-334
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• 2016

최근 사람과 가축에 항균제의 과도한 사용으로 감염병을 일으키는 병원성 세균들의 항균제 내성이 증가하고 있다. 본 연구에서는 PCR과 염기서열분석법을 이용하여 충청지역 일개의 대학병원에 의뢰된 임상검체와 같은 지역에서 사육된 닭으로부터 분리된 P. mirabilis 균주를 대상으로 16S ribosomal RNA methyltransferase(RMTase) 유전자와 integron을 조사하였다. 또한 Repetitive extragenic palindromic sequence-based PCR (REP-PCR)을 이용하여 P. mirabilis 균주들의 역학적 연관성 조사하였다. 총 38균주의 P. mirabilis 중에서 임상검체로부터 분리된 7균주 (18.4%)만이 RMTases 유전자를 가지고 있었는데 이들은 모두 amikacin, tobramycin, 및 gentamicin에 내성을 나타냈다. 또한 대상균주 중 23균주(60.5%)가 class 1 integron을 가지고 있는 것으로 나타났으며 class 2 및 class 3 integron은 검출되지 않았다. 본 연구에서 확인된 integrons에는 aminoglycoside 내성유전자(aadA2, aadA5, aadA7, 및 aacCA5), ${\beta}$-lactmam 내성유전자($bla_{PSE}$), erythromycin 내성유전자(ereA), lincosamides 내성유전자(linF), 및 trimethoprim 내성유전자(dfrA12, dfrA17 및 dfrA32)등이 유전자 카세트로 포함되어 있었다. 본 연구결과 RMTase 유전자는 임상검체로부터 분리된 P. mirabilis 균주에만 확산되어 있었던 반면 class 1 integrons는 임상검체와 닭으로부터 분리된 P. mirabilis 균주에 광범위하게 확산되어 있음을 확인할 수 있었다. 게다가 닭으로부터 분리된 균주 중에는 동일한 REP-PCR 밴드패턴을 보인 균주들이 있었는데 이는 닭들 사이에서 P. mirabilis 균주가 수평확산 되었음을 의미한다. P. mirabilis 균주에서 항균제 내성유전자의 확산을 막기 위해서는 내성유전자 지속적인 모니터링과 감시가 필요할 것으로 사료된다.

• Journal of Plant Biotechnology
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• 제1권2호
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• pp.109-115
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• 1999

A linkage map of Capsicum annuum L. was constructed by random amplified polymorphic DNA (RAPD) markers followed in a backcross population of an intraspecific cross between cultivars HDA210 and Yatsufusa. A total of 420 random primers were tested and 311 polymorphic bands were generated by 158 random primers. Among them, 86 Yatsufusa specific bands generated by 52 primers were examined for mapping. Most bands except three segregated in Mendelian fashion fitting the expected 1:1 ratio. The total length of the map was 533 cM distributed in 15 linkage groups. The map distance between adjacent markers ranged 0 to 32.8 cM, with an average distance of 9.1 cM (63 markers). Some markers were clustered and this may be due to the amplification of a repetitive sequence by the RAPDs. Primer pairs for a sequence characterized amplified region (SCAR) were developed and the segregation scores by the SCAR primers were in accordance with the RAPD data. Two QTL markers for number of axillary shoots and for early flowering were developed. One QTL for early flowering located in the linkage group 3 and explained 61 "io of the phenotypic variation. The other QTL for the number of axillary shoots located in the linkage group 4 explained 55 % of the phenotypic variation.tion.

• International Journal of Industrial Entomology and Biomaterials
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• 제2권1호
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• pp.87-89
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• 2001

The nucleotide sequence of the domestic silkworm (Bombyx mori) mitochondrial (mt) control region and its flanking genes was determined from PCR clones. The control region of the silkworm mt genome was located between the small ribosomal RNA gene and transfer RN $A^{Met}$. This 499 bp control region hale 95.4% A+T content. Extensive comparative analysis studies performed with similar control region of other insect genomes could not reveal a highly conserved region containing conserved motifs of animal mito-chondrial genome. The remarkable feature that found in this control region was the presence of tandem motifs containing nine repetitive sequences. The potential usefulness of this motif sequences for Bombyx species or their taxonomically related species is enhanced by its unique localization in the maternally inheritance mitochondrial molecule.e.

• Journal of Microbiology and Biotechnology
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• 제14권3호
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• pp.599-606
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• 2004

Gram-positive antagonistic bacilli were isolated from agricultural soils for possible use in biocontrol of plant pathogenic fungi, Fusarium oxysporum, Rhizoctonia solani, and/or Pythium ultimum. Among the 65 antagonistic Gram-positive soil isolates, 22 strains were identified as Bacillus species by 16S rDNA sequence analyses. Four strains, including DF14, especially exhibited multiple antagonistic properties against the three damping-off fungi. Genotypic properties of the Bacillus isolates were characterized by rapid molecular fingerprinting methods using repetitive extragenic palindromic-PCR (REP-PCR), ribosomal intergenic spacer-length polymorphisms (RIS-LP), 16S rDNA PCR-restriction fragment length polymorphisms (PCR-RFLP), and strain-specific PCR assays. The results indicated that the REP-PCR method was more valuable than the RIS-LP and 16S rDNA PCR-RFLP analyses as a rapid and reliable approach for bacilli typing and identification. The use of strain-specific primers designed based on 16S rDNA sequence comparisons enabled it to be possible to selectively detect a strain, DF14, which is being used as a biocontrol agent against damping-off fungi.

• The Plant Pathology Journal
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• 제37권3호
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• pp.243-257
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• 2021

Bacillus pumilus is the causal agent of trunk bulges disease affecting rubber and rubberwood quality and yield production. In this study, B. pumilus and other closely related species were included in B. pumilus group, as they shared over 99.5% similarity from 16S rRNA analysis. Multilocus sequence analysis (MLSA) of five housekeeping genes and repetitive elements-based polymerase chain reaction (rep-PCR) using REP, ERIC, and BOX primers conducted to analyze the diversity and systematic relationships of 20 isolates of B. pumilus group from four rubber tree plantations in Peninsular Malaysia (Serdang, Tanah Merah, Baling, and Rawang). Multi rep-PCR results revealed the genetic profiling among the B. pumilus group isolates, while MLSA results showed 98-100% similarity across the 20 isolates of B. pumilus group species. These 20 isolates, formerly established as B. pumilus, were found not to be grouped with B. pumilus. However, being distributed within distinctive groups of the B. pumilus group comprising of two clusters, A and B. Cluster A contained of 17 isolates close to B. altitudinis, whereas Cluster B consisted of three isolates attributed to B. safensis. This is the first MLSA and rep-PCR study on B. pumilus group, which provides an in-depth understanding of the diversity of these rubber-pathogenic isolates in Malaysia.

• 신재생에너지
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• 제19권4호
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• pp.46-52
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• 2023

Methane is the second most emitted greenhouse gas after carbon dioxide. Despite lower emissions than those of carbon dioxide, methane receives significant attention owing to its more than 20-fold higher global warming potential. Consequently, the importance of research on methanotrophic bacteria, microorganisms capable of converting methane gas into high-value materials, is increasingly emphasized. In the case of methanotrophic bacteria, knowledge on episomal plasmids that can be used for genetic engineering remains lacking, which poses significant challenges to the engineering process. The replication origin sequences of natural plasmids within methanotrophic bacteria have been predicted through in silico methods. The basic characteristics of the replication origin, such as a high A/T ratio, repetitive sequences, and proximity to proteins related to replication, have been used as criteria for identifying the replication origin. As a result, a region with a sequence of 18 base pairs repeated eight times could be identified. The putative replication origin sequence thus identified generally takes the form of iterons, but it also possesses unique features such as the length of the gap between iterons and the repetition of identical iteron sequences. This information can be valuable for future design of episomal plasmids applicable to methanotrophs.

• 한국지구과학회지
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• 제33권3호
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• pp.242-258
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• 2012

황해 경기만은 제4기에 반복된 해침과 해퇴로 4개의 해침-해퇴 퇴적체(DS-1, DS-2, DS-3, DS-4)를 형성하였다. 본 연구는 황해 경기만 퇴적체의 형성을 6개 퇴적단계로 나누어 설명한다. A 단계는 MIS-6 저해수면 시기로서 큰 규모의 해수면 하강으로 인해 대부분의 지역이 대기에 노출되고 광범위한 하도 침식 및 풍화작용의 영향을 받았다. 이어지는 B 단계는 MIS-5e 까지 빠른 해수면 상승과정에서 MIS-5 시퀀스의 하부 해침퇴적체가 형성되었고, 다음에 이어지는 MIS-5d부터 MIS-4 저해수면 시기까지의 C 단계에서는 MIS-5 시퀀스의 상부인 해퇴퇴적체가 만들어졌다. 다음의 D 단계는 MIS-4 저해수면 시기부터 MIS-3c 고해수면 시기까지로 하도 침식 및 하도 충전 구조로 이루어진 MIS-3 해침 퇴적체가 형성되었다. 다음의 E 단계에서는 LGM 시기까지 계속적인 해수면 하강이 있었고 외해쪽에서는 천해 기원의 MIS-3 해퇴퇴적체가 만들어진 반면에, 내륙쪽에서는 노출된 환경에서 하도 충전 퇴적체나 범람원 퇴적체가 형성되었다. 마지막 단계인 F 단계는 황해 전체적으로 홀로세 해침이 발생하였고, 이 시기에 외해쪽에서는 대륙붕 사질 퇴적체와 조석사주 퇴적체가 형성되어 고해수면 시기인 현재까지 퇴적이 일어나고 있다.

• 한국생물공학회:학술대회논문집
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• 한국생물공학회 2001년도 추계학술발표대회
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• pp.719-722
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• 2001

Silk proteins from Nephila clavipes are fibrous proteins containing repetitive sequences with both crystalline and amorphous domains. In order to obtain high-level production of silk protein, the synthetic genes had 16 contiguous units of the consensus repeat sequence of the silk protein were expressed in Escherichia coli BL21(DE3) under the strong inducible T7 promoter. For production of recombinant silk protein in large amounts, pH-stat fed-batch cultures were carried out. The recombinant silk protein was produced as soluble forms in E. coli, and the recombinant silk protein content was as high as 11% of the total protein. When cells were induced at $OD_{600}$ of 60, the amount of silk protein produced was 6.49 g/L. After simple purification steps, 9.2 mg of silk protein that was more than 80% pure was obtained from a 50 mL culture, and the recovery yield was 26.3%.