• Journal of Plant Biology
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• v.39 no.1
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• pp.49-55
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• 1996

We have studied the DNA of Allium sativum L. with respect to highly repetitive sequences. Fast reassociated DNA fragments expected to be highly repetitive sequences based on $C_{o}t$ curve were isolated and characterized. Their copy numbers were approximately $10^{5}~10^{7}$ per haploid genome. Nucleotide sequences analysis of six candidates reveals that their G/C content were low, 25-40% and typical patterns of repeating sequences exist. Repeat sequences were used as probes to access restriction fragment length polymorphism (RFLP) of genomic DNAs of four local clones, Tanyang, Mungyong, So san, and Uisong. The hybridization pattern were very similar among these four local clones.clones.

• Korean Journal of Ecology and Environment
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• v.33 no.3 s.91
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• pp.206-212
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• 2000

Since some cyanobacterial isolates under selective culturing conditions are lacking of characteristic specialized cells or showing altered morphology, the morpho-taxonomic criteria are not accurate enough to discriminate between species. Instead of morphological parameters, a method based on the single or the combination of repetitive oligonucleotides in a single PCR, repetitive oligonucleotides-primed PCR (ROP-PCR), was applied to generate DNA profiles for members of the cyanobacterial genera Anabaena and Oscillatoria, both of which are responsible for causing poisonous blooms in various freshwater systems. ROP-PCR performed on 10 isolates of the cyanobacteria with ERIC and REP sequences from gram-negative bacteria, STRR1A and LTRR sequences derived from cyanobacterial genome, and eukaryotic repetitive sequences, led to the identification of distinct genotypes, and provided specific and repeatable DNA fingerprints for cyanobacterial isolates. Grouping analysis of cyanobacterial isolates showed a signifiant difference depending on the primer used in PCR.

• Proceedings of the Zoological Society Korea Conference
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• 1999.10b
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• pp.89.2-89
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• 1999

No Abstract, See Full Text

• BMB Reports
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• v.45 no.2
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• pp.126-131
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• 2012

We have previously identified a DNA silent region located downstream of the 3'-end of the ${\beta}^{major}$ globin gene (designated B1-559) that contains a B1 retrotransposon, consensus binding sites for erythroid specific transcription factors and shares the capacity to act as promoter in hematopoietic cells interacting with ${\beta}$-globin gene LCR sequences in vitro. In this study, we have cloned four new non-polyA RNA transcripts being detected upon blockade of murine erythroleukemia (MEL) cell differentiation to erythroid maturation by methylation inhibitors and demonstrated that two of them share high structural homology with sequences of B1 element found within the B1-559 region. Although it is not clear yet whether and how these RNAs interfere with induction of erythroid maturation, these data provide evidence for the first time showing that methylation inhibitors can activate silent repetitive DNA sequences in MEL cells and may have implications in cancer chemotherapy using demethylating drugs as antineoplastic agents.

• Korean Journal of Fisheries and Aquatic Sciences
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• v.44 no.4
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• pp.352-358
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• 2011

The presence of ISKNV-like viruses in various freshwater ornamental fish species imported from Asia was confirmed by polymerase chain reaction(PCR) amplification of the ATPase(adenosine triphosphatase) gene. Interestingly, molecular analyses of the Open Reading Frame 25(ORF25) region of these isolates based on the ISKNV(Infectious spleen and kidney necrosis virus) genome revealed the presence of various repetitive sequences. ORF25 repeat sequence length had no effect on cumulative mortality of rock bream Oplegnathus fasciatus challenged with tissue homogenates of infected pearl gourami, Trichogaster leeri; silver gourami, Trichogaster microlepis; blue gourami, or Trichogaster trichopterus. All isolates induce cumulative mortalities after 12 days of infection, confirming that ORF25 polymorphism did not affect the pathogenicity of ornamental fish megalocytiviruses that cross infect rock bream, a seawater fish. Also, no statistically significant differences in spleen index or viral copy number in infected tissues was detected between isolates with varying ORF25 repeat sequence lengths. However, further studies are necessary to fully characterize the functional characteristics of these polymorphisms in megalocytivirus disease in ornamental fishes.

• Genomics & Informatics
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• v.12 no.4
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• pp.261-267
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• 2014

MicroRNAs (miRNAs) are known for their role in mRNA silencing via interference pathways. Repetitive elements (REs) share several characteristics with endogenous precursor miRNAs. In this study, 406 previously identified and 1,494 novel RE-derived miRNAs were sorted from the GENCODE v.19 database using the RepeatMasker program. They were divided into six major types, based on their genomic structure. More novel RE-derived miRNAs were confirmed than identified as RE-derived miRNAs. In conclusion, many miRNAs have not yet been identified, most of which are derived from REs.

• Korean Journal Plant Pathology
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• v.12 no.4
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• pp.389-394
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• 1996

도열병균, Magnaporthe grisea, 균주간의 유전적 유연관계를 분석하고 그들의 유전에 관한 '기본 정보를 얻고자 DNA polymorphism 분석을 실시하였다. 기주가 다른 도열병 균주들이 공시되었고 cloning에 의해 벼 도열병균 KJ201레이스 균주로부터 생성된 임의 선발 genomic clone들이 공시균주들간의 polymorphism을 밝히기 위해 사용되었던 바 그중 repectitive sequence를 보유한 repeated copy clone 하나가 선발되었다. Clone pMJ6에 의해 밝혀진 repetitive sequence는 Southern hybridization시 벼 분리균주에는 약 30개, 다른 기주 분리균에도 20∼33개의 밴드를 형성하였다. 반면 피 분리균주에는 단지 두 개의 밴드만을 나타내 분리기주가 다른 균주간에 뚜렷한 polymorphism이 존재하였으며 parsimony 분석에서도 역시 아주 먼 cluster를 형성하여 피 분리균은 다른 기주 분리균과 유전적으로 상당히 먼 것으로 추정되었다. 공시균의 genomic DNA를 HindIII로 처리했을 때 pMJ6에 의한 밴드양상은 공시균을 EcoRI으로 처리했을 때의 MGR probe의 밴드 양상과 유사하여 이 repeated copy clone이 도열병균주간의 유전적 유연관계를 분석하는데 MGR 못지않게 유용할 것으로 보인다.

• Journal of Microbiology and Biotechnology
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• v.22 no.1
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• pp.13-24
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• 2012

The genetic diversity of plant growth-promoting rhizobacterial (PGPR) fluorescent pseudomonads associated with the sugarcane (Saccharum officinarum L.) rhizosphere was analyzed. Selected isolates were screened for plant growthpromoting properties including production of indole acetic acid, phosphate solubilization, denitrification ability, and production of antifungal metabolites. Furthermore, 16S rDNA sequence analysis was performed to identify and differentiate these isolates. Based on 16S rDNA sequence similarity, the isolates were designated as Pseudomonas plecoglossicida, P. fluorescens, P. libaniensis, and P. aeruginosa. Differentiation of isolates belonging to the same group was achieved through different genomic DNA fingerprinting techniques, including randomly amplified polymorphic DNA (RAPD), amplified ribosomal DNA restriction analysis (ARDRA), repetitive extragenic palindromic (REP), enterobacterial repetitive intergenic consensus (ERIC), and bacterial repetitive BOX elements (BOX) analyses. The genetic diversity observed among the isolates and rep-PCR-generated fingerprinting patterns revealed that PGPR fluorescent pseudomonads are associated with the rhizosphere of sugarcane and that P. plecoglossicida is a dominant species. The knowledge obtained herein regarding the genetic and functional diversity of fluorescent pseudomonads associated with the sugarcane rhizosphere is useful for understanding their ecological role and potential utilization in sustainable agriculture.

• Korean Journal of Food Science and Technology
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• v.37 no.4
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• pp.611-617
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• 2005

Dispersed repetitive DNA elements in genomes of microorganisms differ among and within species. Because distances between repetitive sequences vary depending on bacterial strains, genomic fingerprinting with interspersed repetitive sequence-based probes can be used to distinguish unrelated organisms. Among well-known bacterial repetitive sequences, Repetitive Extragenic Palindromic (REP) sequence has been used to identify environmental bacterial species and strains. We applied REP-PCR to detect and differentiate four major Gram-negative food-borne bacterial pathogens, E. coli, Salmonella, Shigella, and Vibrio. Target DNA fragments of these pathogens were amplified by REP-PCR method. PCR-generated DNA fragments were separated on 1.5% agarose gel. Dendrograms for PCR products of each strain were constructed using photo-documentation system. REP-PCR reactions with primer pairs REP1R-I and REP2-I revealed distinct REP-PCR-derived genomic fingerprinting patterns from E. coli, Salmonella, Shigella, and Vibrio. REP-PCR method provided clear distinctions among different bacterial species containing REP-repetitive elements and can be widely used for typing food-borne Gram-negative strains. Results showed established REP-PCR reaction conditions and generated dendrograms could be used with other supplementary genotyping or phenotyping methods to identify isolates from outbreak and to estimate relative degrees of genetic similarities among isolates from different outbreaks to determine whether they are clonally related.

• Proceedings of the Korean Society of Plant Pathology Conference
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• 1995.06b
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• pp.1-19
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• 1995

The plasmid pJEL 101 contains a highly repetitive element from the genome of Xanthomonas oryae pv. oryzae that has properties of an insertional element. The insertional nature of the element, hereto referred to as IS203, was confirmed by molecular analyses of the element and three related elements that were isolated from X. oryzae. The related sequences were isolated on the basis of transposition to the transposon-trapping vector pL3SAC and hybridization with pJEL101. The trapped elements (IS203a, IS203b, and IS203c) were each composed of 1,055 base pairs with 25 base terminal inverted repeats. The elements caused a three base pair target site duplication at the site of insertion in the sacRB gene. The sequence of pJEL 101 has 96% base pair identity with IS203a and 99% identity with IS203a and IS203c but lacks three nucleotides of the consensus left terminal repeat. IS203b has the same DNA sequences as IS203c but is inserted ito the sacRB gene in the opposite orientation. The longest open reading frame of IS203a could code for a protein of 318 amino acids and molecular weight of 37, 151. A search of the Genbank database revealed that IS203 has 51% identity with 909 nucleotides of IS4551 from Escherichia coli. The predicted protein of ORF1 has 40% and 30% amino acid identity to the ORF1 of Tn4551 and the transposase of IS30, respectively.