• Molecules and Cells
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• 제25권1호
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• pp.142-147
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• 2008

We recently used degenerate PCR and locus-specific PCR methods to identify the endogenous retroviruses (ERV) in the bovine genome. Using the ovine ERV classification system, the bovine ERVs (BERVs) could be classified into four families. Here, we searched the most recently released bovine genome database with the partial nucleotide sequence of the pro/pol region of the BERV ${\beta}3$ family. This allowed us to obtain and analyze the complete genome of BERV ${\beta}3$. The BERV ${\beta}3$ genome is 7666 nucleotides long and has the typical retroviral organization, namely, 5'-long terminal repeat (LTR)-gag-pro-pol-env-LTR-3'. The deduced open reading frames for gag, pro, pol and env of BERV ${\beta}3$ en- code 507, 271, 879 and 603 amino acids, respectively. BERV ${\beta}3$ showed little amino acid similarity to other betaretroviruses. Phylogenetic analysis showed that it clusters with HERV-K. This is the first report describing the genetic structure and sequence of an entire BERV.

• 대한수의학회지
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• 제43권1호
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• pp.95-102
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• 2003

Because Staphylococcus aureus (S. aureus) has variable number of short sequence repeat region in coagulase gene, it has been used to investigate the relatedness of S. aureus isolates. In this study, we isolated S. aureus strains from 20 dairy farms with bovine mastitis from September 2000 to August 2001. PCR-RFLP analysis of coagulase gene revealed 10 different patterns. Most of the S. aureus isolates showed only one coagulase gene RFLP pattern per farm. However, there were several S. aureus clones spreading between dairy farms. All the farms showed poor management conditions of milking machine and milker, indicating that managements for mastitis control program include use of proper milking matching, premilking sanitation, and segregation in the S. aureus infection herd. Our data suggest that PCR-RFLP analysis of coagulase gene might be applicable for the epidemiological investigations of S. aureus isolated from bovine mastitis cows.

• Journal of Korean Biological Nursing Science
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• 제10권2호
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• pp.147-153
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• 2008

Purpose: Methicillin Resistant Staphylococcus aureus (MRSA) has become a major clinical problem and one of the major nosocomial pathogen worldwide. The aim of the study was to investigate the epidemiological characteristics of genotypes of MRSA isolated in the A-hospital ICU. Methods: In the period between December 2007 and May 2008, MRSA was isolated from ICU patients and its surrounding environment. Polymerase Chain Reaction (PCR) was conducted for the detection of MRSA gene. The incidence of MRSA in the clinical isolates of Staphylococcus aureus was examined by using a multiplex PCR. The spa gene of Staphylococcus aureus encodes protein A and is used for typing of MRSA. We used sequence typing of the spa gene repeat region to study the epidemiology of MRSA at a hospital. Results: Two different genotypes of MRSA were identified with 90 isolated from the patients and its surrounding environments in the ICU. Conclusion: This study may contribute to the development of effective strategies for preventing nosocomial infections. Genotyping may have more general application for the study of MRSA epidemic outbreak in hospital and community infection.

• 한국통신학회논문지
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• 제33권9C호
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• pp.683-690
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• 2008

반복적인 신뢰 전파 알고리듬을 low-density parity-check(LDPC) 부호에 적용하는 경우 패리티-검사를 이용한 기존 복호 중단 기법은 높은 signal-to-noise ratio(SNR) 영역에서 반복 복호 수를 줄이는 것을 가능케 한다. 그러나 재전송 요청이 빈번한 Hybrid-ARQ(H-ARQ) 시스템에서는 낮은 SNR 영역에 적합한 복호 중단 기법이 없기 때문에 복호에 실패하는 경우 많은 양의 불필요한 반복 복호가 수행된다. 본 논문에서는 결국 복호에 실패하게 될 LDPC 부호 블록들을 복호 초기 단계에서 발견하기 위하여 신뢰 전파 복호에서 임시 부호어의 신드롬 무게를 이용한 중단 기법을 제안한다. 제안된 기법은 H-ARQ 시스템을 위한 LDPC 복호기에서 구현 복잡도의 증가와 성능의 열화 없이도 연산량을 70-80% 감소시킨다.

• Biomolecules & Therapeutics
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• 제6권3호
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• pp.276-282
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• 1998

Retinoids regulate a wide variety of biological processes such as cellular proliferation and differentiation in many cell types. They have also shown to stimulate replication of several viruses including human cytomegalovirus (CMV). Retinoid signalling pathway involves two distinct subfamilies of nuclear receptors, retinoic acid receptors (RARs) and retinoid X receptors (RXRs) that bind to specific retinoic acid response elements (RAREs) in the promoter regions of retinoid-target genes. Here, we characterized RAREs in the regulatory regions of the CMV and of the hepatitis B vi.us (HBV). The viral RAREs, i.e., CMV-RARE and HBV-RARE, are composed of two consensus RARE half-sites (A/GGGTCA) arranged as a direct repeat separated by 5-bp and 1-bp, respectively. The RAREs were activated by both RAR/RXR heterodimers and RXR homodimers in transient transfection experiments. We also found that COUP-TF$\alpha$ (chicken ovalbumin upstream promoter-transcription factor u) and COUP-TF$\beta$ repressed the retinoid response of the viral elements. Further we demonstrated that previously known retinoid antagonist, SRI 1330, repressed retinoid-induced transactivation of the CMV-RARE. These results implicate Vitamin A, it's nuclear receptors and COUP-TFs as important regulators of the CMV and HBV pathogenesis and the SRl1330 as potential negative modulator of such retinoid-dependent processes.

• The Plant Pathology Journal
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• 제19권1호
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• pp.57-63
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• 2003

An insertion sequence identified as a solo long terminal repeat (LTR) of a new rice copia-like retrotransposon was detected in the ORE of the Pi-b gene from the rice cv. Nipponbare, and was designated as Osr1. Osr1 consists of a 6386 bp nucleotide sequence including 965 bp LTRs on both ends with an 82％ nucleotide sequence identity to the wheat Tarl retrotransposon on reverse transcriptase. Nucleotide divergence was noted among the individual LTRs, as well as the coding region of Osr1. Various restriction fragment length polymorphism (RFLP) of LTR were detected in indica cultivars, whereas, only a few could be detected in the japonica cultivars. The population of Osr1 is lower in the wild-type rice compared with that in the domesticated cultivars. The insertion of LTR sequence in the h-b gene in the susceptible cultivar suggested that retro-tyansposon-mediated insertional mutation might play an important role in the resistance breakdown, as well as in the evolution of resistance genes in rice.

• 대한수의학회지
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• 제60권3호
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• pp.109-116
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• 2020

This study aimed to develop a semi-nested polymerase chain reaction assay for the direct detection of Mycoplasma synoviae (M. synoviae) from clinical samples using three newly designed oligonucleotide primers specific to the variable lipoprotein haemagglutinin (vlhA) gene and differentiate M. synoviae field strains based on a nucleotide deletion or the insertion of the proline-rich repeat (PRR) region of the vlhA gene. The developed semi-nested polymerase chain reaction (PCR) assay revealed positive results in 12 out of 100 clinical samples collected from chickens showing lameness and joint swelling. Six positive samples were selected randomly for sequencing, and sequence analysis revealed 96.3-100% nucleotide identities compared to the reference sequences. Phylogenetic analysis showed that sequences of the strains in this study were closely related to WVU1853 (Spain), CK.MS.UDL.PK.2014.2 (Pakistan), and F10-2AS (USA) strains, but they were distinct from the M. synoviae-H vaccine strain sequence. M. synoviae obtained from these samples were identified as types A and C with a length of 38 and 32 amino acids, respectively. These results indicated that the specific and sensitive semi-nested PCR could be a useful diagnostic tool for the direct identification of clinical samples, and the sequence analysis of the partial vlhA gene can be useful for typing M. Synoviae.

• 대기
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• 제30권2호
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• pp.103-113
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• 2020

In this study, we analyzed and developed the monitoring system in order to confirm the effect of observations on forecast sensitivity on ensemble-based data assimilation. For this purpose, we developed the Ensemble Forecast Sensitivity to observation (EFSO) monitoring system based on Local Ensemble Transform Kalman Filter (LETKF) system coupled with Korean Integrated Model (KIM). We calculated 24 h error variance of each of observations and then classified as beneficial or detrimental effects. In details, the relative rankings were according to their magnitude and analyzed the forecast sensitivity by region for north, south hemisphere and tropics. We performed cycle experiment in order to confirm the EFSO result whether reliable or not. According to the evaluation of the EFSO monitoring, GPSRO was classified as detrimental observation during the specified period and reanalyzed by data-denial experiment. Data-denial experiment means that we detect detrimental observation using the EFSO and then repeat the analysis and forecast without using the detrimental observations. The accuracy of forecast in the denial of detrimental GPSRO observation is better than that in the default experiment using all of the GPSRO observation. It means that forecast skill score can be improved by not assimilating observation classified as detrimental one by the EFSO monitoring system.

• Archives of Pharmacal Research
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• 제28권5호
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• pp.561-565
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• 2005

Bacterial arylsulfate sulfotransferase (ASST) catalyzes the transfer of sulfate group from a phenyl sulfate ester to a phenolic acceptor. The promoter region and the transcripti on start sites of Enterobacter amnigenus astA have been determined by primer extension analysis. Northern blot analysis resolved two mRNA species with lengths of 3.3 and 2.0 kb, which correspond to the distances between the transcriptional initiation sites and the two inverted repeat sequences (IRSs). By length, the 3.3 kb RNA could comprise the three-gene (astA with dsbA and dsbB) operon. ASST has three highly conserved cysteine residues. Reducing and non-reducing SDS-PAGE and activity staining showed that disulfide bond is needed for the activity of the enzyme. To identify the cysteine residues responsible for the disulfide bond formation, a series of Cys to Ser mutants has been constructed and the enzymatic activity was measured. Based on the results, we assumed that the first cysteine (Cys349) might be involved in disulfide bond mainly with the second cysteine (Cys445) and result in active conformation.

• 미생물학회지
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• 제33권3호
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• pp.165-169
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• 1997

병원하수에서 분리한 gentamicin 저항성 세균으로부터 aacC2 유전자를 가지고 있는 R 플라스미드 pGM5와 pGM6를 선발하였다. 이들 플라스미드에서 gentamicin 저항성 유전자를 포함하는 부분을 pUC18의 BamHI 자리에 클로닝하여 재조합 플라스미드 pSY5와 pSY6를 각각 얻었다. 재조합 플라스미드의 삽입된 부분에 대한 제한효소 지도를 통해 Tn3 염기서열이 aacC2 유전자의 상류부위에 위치하는 것을 알았다. 재조합 플라스미드의 gentamicin에 대한 민감성의 비교를 통해 Tn3의 bla 유전자 부분과 3'역행중복 부위의 염기서열이 gentamicin 저항성 유전자의 발현에 중요한 역할을 담당하고 있었다.