• Genomics & Informatics
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• 제5권4호
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• pp.179-187
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• 2007

An increasing number of primate genomes are being sequenced. A direct comparison of repeat elements in human genes and their corresponding chimpanzee orthologs will not only give information on their evolution, but also shed light on the major evolutionary events that shaped our species. We have developed REPEATOME to enable visualization and subsequent comparisons of human and chimpanzee repeat elements. REPEATOME (http://www.repeatome.org/) provides easy access to a complete repeat element map of the human genome, as well as repeat element-associated information. It provides a convenient and effective way to access the repeat elements within or spanning the functional regions in human and chimpanzee genome sequences. REPEATOME includes information to compare repeat elements and gene structures of human genes and their counterparts in chimpanzee. This database can be accessed using comparative search options such as intersection, union, and difference to find lineage-specific or common repeat elements. REPEATOME allows researchers to perform visualization and comparative analysis of repeat elements in human and chimpanzee.

• Genomics & Informatics
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• 제5권2호
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• pp.88-91
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• 2007

Repetitive sequences such as SINE, LINE, and LTR elements form a major part of eukaryotic genomes. A literature search tool that summarizes the information contained within repeat elements would provide biologists in the field of genomics with a useful tool for analyzing genomic sequence features. We developed a java program designed to make literature access easier by using two search engines simultaneously. RepWeb is a web-based search system that provides a user friendly interface for searching the reference data and journals for information related to repeat elements by using the search engines, Google Scholar and PubMed, simultaneously. It provides an interface that displays the repeat element- related biological information, and includes useful functions such as the production of a repeat tree, clickable links to PubMed and Google Scholar, exporting, and sorting a field into date, author, journal and title.

• 한국농공학회논문집
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• 제53권6호
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• pp.153-163
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• 2011

This research describe improved algorithm that is able to decide terminal criterion of Evolutionary Structural Optimization (ESO), reducing load of calculation to search load path of concrete beam, and apply to agricultural facilities. The ESO method is that make to discrete structure, structural analyze each element stress through FEM. And repeat generation with next material condition to become for most suitable composing. Individual element introduces concept of zero stiffness, but zero stiffness decisions are gone to direction of exclusion. In this stduy, improve algorithm to be convergence by 'Rule of Alive or Die' in arrival because is most suitable. Also, existing terminal criterion lack consistency because that used depend on experience of researcher. This research procedure is fellowed. First, all modulus of elasticity assume a half of elasticity modulus of material, Second, structural analysis by FEM, Third, apply to the remove ratio and restoration ratio for the 'rule of alive or die'. Forth, reconstruct the element and material conditions. And repeat the first to forth process. The terminal time of evolutional procedure is the all elastic modulus of element changed to blank value or elasticity modulus value of original. Therefore, in this study, consist the algorithm for programming, and apply to the agricultural facilities with concrete.

• Molecules and Cells
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• 제24권1호
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• pp.148-151
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• 2007

Porcine endogenous retroviruses (PERVs) in the pig genome represent a potential risk of infection in pig-to-human transplantation and are transmitted vertically. The solitary long terminal repeat (LTR) elements of the PERVs affect the replication properties of the individual viruses via their repeat sequences and by encoding a set of specific transcription factors. We examined the promoter activities of solitary LTR elements belonging to the PERV-A and -B families of the Korean domestic pig (KDP) using luciferase reporters. Three of the LTR structures (of PERV-A5-KDP, PERV-A7-KDP, PERV-A8-KDP) had different promoter activities in human HCT116 cells and monkey Cos7 cells, and potential negatively and positively acting regions affecting transcription were identified by deletion analysis. These data suggest that specific sequences in the U3 region of a given LTR element can affect the activities of promoter or enhancer elements in the PERV.

• Molecules and Cells
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• 제26권4호
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• pp.387-395
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• 2008

A novel Tc1-like transposable element has been identified as a new DNA transposon in the mud loach, Misgurnus mizolepis. The M. mizolepis Tc1-like transposon (MMTS) is comprised of inverted terminal repeats and a single gene that codes Tc1-like transposase. The deduced amino acid sequence of the transposase-encoding region of MMTS transposon contains motifs including DDE motif, which was previously recognized in other Tc1-like transposons. However, putative MMTS transposase has only 34-37% identity with well-known Tc1, PPTN, and S elements at the amino acid level. In dot-hybridization analysis used to measure the copy numbers of the MMTS transposon in genomes of the mud loach, it was shown that the MMTS transposon is present at about $3.36{\times}10^4$ copies per $2{\times}10^9$ bp, and accounts for approximately 0.027% of the mud loach genome. Here, we also describe novel MMTS-like transposons from the genomes of carp-like fishes, flatfish species, and cichlid fishes, which bear conserved inverted repeats flanking an apparently intact transposase gene. Additionally, BLAST searches and phylogenetic analysis indicated that MMTS-like transposons evolved uniquely in fishes, and comprise a new subfamily of Tc1-like transposons, with only modest similarity to Drosophila melanogaster (foldback element FB4, HB2, HB1), Xenopus laevis, Xenopus tropicalis, and Anopheles gambiae (Frisky).

• 대한기계학회논문집A
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• 제30권3호
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• pp.310-317
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• 2006

Currently most practical vibration and structural problems in automotive suspensions require the use of the finite element method to obtain their structural responses. When the finite element model has a very large number of degrees of freedom the harmonic and dynamic analyses are computationally too expensive to repeat within a feasible design process time. To alleviate the computational difficulty, this paper presents a moment-matching based model order reduction (MOR) which reduces the number of degrees of freedom of the original finite element model and speeds up the necessary simulations with the reduced-size models. The moment-matching model reduction via the Arnoldi process is performed directly to ANSYS finite element models by software mor4ansys. Among automotive suspension components, a knuckle is taken as an example to demonstrate the advantages of this approach for vibration simulation. The frequency and transient dynamic responses by the MOR are compared with those by the mode superposition method.

• 사상체질의학회지
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• 제21권1호
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• pp.227-236
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• 2009

1. Objectives As a basic trial for identification of Sasang constitutional gene marker, we genotyped and analysed statistical relationships of STR(short tandem repeat) alleles and its distribution in each constitution. 2. Methods After obtaining basic constitutional data with questionnaire (QSCC II), decision of constitution was made by 3 different constitution specialists' diagnosis, and only the samples of specialists' agreement of each constitution by discussion were taken into this research. Using multiplex PCR kit, total 146 constitutional samples were amplified in 16 autosomal STR marker, genotyped, and analysed statistically. Among 16 markers, 15 were analysed in this study excluding the amelogenin marker is used for in gender identification. 3. Results and Conclusions It is difficult to determine the relationship between constitution and STR marker as the sample size is small, however, Penta D and vWA were shown to be related statistically with constitution. It has been know that STRs has no genetic informations, however there are some recent research results showing STRs as a regulatory element, relationship between microsatellite instability and repeat number and size, and post-transcriptional sigualing. STRs which is not known about its function currently, are proposed to have function and/or regulatory activities anyhow with Sasang constitution. It is believed that the results of this study can halp determine and deatify the markers related to Sasang Constitutional Medicien.

• Journal of Microbiology
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• 제38권4호
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• pp.239-244
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• 2000

The cats gene encodes the major catalase in Sreptomyces coelicolor, whose production increases upon H$_2$O$_2$treatment. Besides the previously identified primary promoter (catApl), a minor promoter (catAp2) was newly assigned by S1 nuclease mapping. The catAp2 transcript was observed transiently upon entry into the stationary phase in liquid culture and upon differentiation on solid plates, whereas the level of catApl transcription did not chance significantly during this growth transition. ThecatApl promoter was transcribed by the major vegetative RNA polymerase holoenzyme containing $\sigma$$\^$HrdB/, whereas the catAp2 was transcribed in vitro by the holoenzyme containing $\sigma$$\^$R/ that is activated under oxidative conditions. The cia-element regulating the H$_2$O$_2$-inducibility of catApl was identified within the 23 bp inverted repeat sequence located between -65 and -43 of the catApl promoter. We roamed this sequence HRE (H$_2$O$_2$-responsive Element). The distal half of the inverted repeat was more crucial for H$_2$O$_2$-dependent induction of the catApl transcript than the proximal half. HRE most likely serves as a binding site for the H$_2$O$_2$-responsive repressor CatR.

• 한국식품위생안전성학회지
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• 제32권3호
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• pp.199-205
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• 2017

인수공통 감염증의 하나인 톡소포자충의 검출을 위해서는 대부분은 ELISA 법이 사용 되고 있으나, 충체가 사멸된 후에도 양성반응이 나타나는 등 사용에 제한이 있다. 반면 유전자 검출법은 현재 감염상태를 확인 할 수 있기 때문에 식중독 원인조사 등에 적합하다고 판단되어 이를 활용하여 본 연구를 진행하였다. 톡소포자충의 유전정보를 통해 529 repeat region의 염기서열을 얻고, 프라이머 및 TaqMan 프로브를 설계하여 real-time PCR을 이용한 검출법을 개발하였다. 검출한계(lower limit of detection) 및 적정곡선을 확인한 결과 10 genomic DNA copy가 검출한계로 확인되었고, 정량을 위한 곡선은 $10^1{\sim}10^6$ DNA copies까지 0.999의 $R^2$ 값을 나타내었다. 개발된 검출법의 증폭효율을 비교하기 위해 B1 gene 타겟 프라이머 세트와 타입별 검출한계를 비교한 결과, type 1, 2, 3 톡소포자충에서 같거나 더 나은 검출한계를 보였다. 또한 식품에서 주로 분리되는 식중독 세균 14종 및 원충 3종에 대해 특이도를 비교한 결과, 모두 음성으로 나타났다. 개발된 검출법을 식육검체에 적용하였을 때 type 1, 2, 3에서 모두 원활한 검출결과를 보여 증폭방해물질이 존재하지 않은 것으로 확인되었다. 본 연구를 통해 개발된 유전자검출법은 국내 유통 중인 식육에서 인수 공통감염 원충의 하나인 톡소포자충의 감염 여부를 확인하는 사전적 모니터링의 방법으로 활용될 예정이다.

• 한국식물병리학회:학술대회논문집
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• 한국식물병리학회 1995년도 Proceedings of special lectures on Molecular Biological Approaches to Plant Disease National Agricultural Science and Technology Institute Suwon, Korea
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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.