• International Journal of Contents
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• 제14권1호
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• pp.34-38
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• 2018

With the rapid growth of genomic data, new requirements have emerged that are difficult to handle with big data storage and analysis techniques. Regardless of the size of an organization performing genomic data analysis, it is becoming increasingly difficult for an institution to build a computing environment for storing and analyzing genomic data. Recently, cloud computing has emerged as a computing environment that meets these new requirements. In this paper, we analyze and compare existing distributed and parallel NGS (Next Generation Sequencing) analysis based on cloud computing environment for future research.

• Asian-Australasian Journal of Animal Sciences
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• 제6권4호
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• pp.541-547
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• 1993

A phage clone containing the partial ${\alpha}_{S1}$-casein gene was isolated from a bovine genomic library by using mixed probes of ovine ${\alpha}_{S1}$-, ${\beta}$- and ${\kappa}$-casein cDNAs. Restriction enzyme mapping analysis for 14.6 kb revealed that the map was in conflict with the report of Meade et al. (1990), especially in the 3'-end fragment. Sequence analysis of 12.6 kb revealed a high AT/GC ratio (1.64); we have identified eight exon sequences according to the bovine ${\alpha}_{S1}$-casein cDNA sequence. The same exon/intron splice junction sequence was observed between these exons. We suggest that the bovine ${\alpha}_{S1}$-casein gene night contain a minimum of 18 exons and the full length is approximately 18-19 kb.

• Archives of Pharmacal Research
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• 제13권1호
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• pp.69-73
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• 1990

As a part of the study to elucidate the mechanism by which transcription of LDH A-gene is regulated by cAMP, we aimed to isolated rat LDH A gene and characterize cAMP-reponsive element (CRE). We have screened $1.2{\times}10^6$ recombinant phages of rat Charon 4A genomic library and isolated 33 positive clones among which we identified 12 different LDH A gene-related clones. By the results of restriction enzyme mapping, Southern blotting, and nucleotide sequence analyses, we concluded that the 12 LDH A gene-related clones were intronless and frequently mutated LDH A-pseudogenes. In this report, we present the characteristic features of the 12 rat liver LDH A-pseudogenes.

• Journal of Microbiology and Biotechnology
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• 제20권12호
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• pp.1637-1646
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• 2010

The bacterium Deinococcus radiodurans is one of the most resistant organisms to ionizing radiation and other DNA-damaging agents. Although, at present, 30 Deinococcus species have been identified, the whole-genome sequences of most species remain unknown, with the exception of D. radiodurans (DRD), D. geothermalis, and D. deserti. In this study, comparative genomic hybridization (CGH) microarray analysis of three Deinococcus species, D. radiopugnans (DRP), D. proteolyticus (DPL), and D. radiophilus (DRPH), was performed using oligonucleotide arrays based on DRD. Approximately 28%, 14%, and 15% of 3,128 open reading frames (ORFs) of DRD were absent in the genomes of DRP, DPL, and DRPH, respectively. In addition, 162 DRD ORFs were absent in all three species. The absence of 17 randomly selected ORFs was confirmed by a Southern blot. Functional classification showed that the absent genes spanned a variety of functional categories: some genes involved in amino acid biosynthesis, cell envelope, cellular processes, central intermediary metabolism, and DNA metabolism were not present in any of the three deinococcal species tested. Finally, comparative genomic data showed that 120 genes were Deinococcus-specific, not the 230 reported previously. Specifically, ddrD, ddrO, and ddrH genes, previously identified as Deinococcus-specific, were not present in DRP, DPL, or DRPH, suggesting that only a portion of ddr genes are shared by all members of the genus Deinococcus.

• 대한약리학회지
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• 제24권1호
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• pp.1-10
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• 1988

카테콜아민 생합성에 관여하는 마지막 효소인 phenylethanolamine N-methyltransferase는 Norepinephrine을 epinephrine으로 전환시키는 중요한 효소이다. PNMT효소의 발현은 epinephrine 신경세포의 발현에 필수적이다. 따라서 PNMT유전자를 크로닝하여 그 구조를 결정하고, 유전자 발현연구를 하는 것은 상당히 중요한 일이다. 그러나 최근에 저자가 bovine cDNA를 처음으로 분리하여 그 구조를 보고한 것 외에는 아직까지 인간 PNMT cDNA나, 전체 genomic DNA의 분리 보고는 없다. 이에 저자들은 인간 PNMT유전자의 전체구조와 여러 종(species) 사이의 진화적인 관계를 규명하기 위해서 human genomic library(Charon 4A)를 만들고, 이 library 이용하여 bovine cDNA를 probe로 13.1 Kb길이의 genomic clone을 분리 크로닝하는데 성공하였다. 이 유전자는 두개의 EcoRI site가 포함되어 있어서, EcoRI제한효소에 의해서 7.5 Kb, 5.0 Kb,0.6 Kb로 분리되었으며, Southern과 dot blot 실험 에서 보면 5.0 Kb와 0.6 Kb에 exon이 흩어져 존재하고 있으며, 7.5 Kb는 flanking sequence로 판명되었다.

• 미생물학회지
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• 제54권3호
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• pp.188-199
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• 2018

다양한 미생물학 연구 분야의 발전에 힘입어 유전체역학은 발전되어 왔다. 예를 들어, 대용량서열화 기술의 발전으로 미생물 유전체의 수는 급속도로 증가해 오고 있다. 이러한 풍부한 유전체 데이터는 전에는 보지 못한 보다 더 정확한 미생물종의 동정에 도움을 주는 균주종 타이핑에 새로운 기회를 제공한다. 유전체역학은 유전체에 일반적인 유전자를 찾고 표기하는 것 뿐만 아니라 항균 저항성 유전자를 찾을 수 있다. 균주종 타이핑과 항균 저항성 유전자 찾기는 각각 종을 구분하고 유전체내의 유전자 위치를 결정하는 유전체 역학의 방법들로 시간에 따른 변화가 없는 측면이다. 이에 반하여, 하나의 숙주가 어떤 숙주를 감염시켰는지 알아내기 위해서는 감염된 숙주들 사이의 시간에 따른 동적인 전염 경로를 추론해야 한다. 이렇게, 균주종 타이핑, 항균 저항성 유전자 찾기, 전염 계통수 추론을 통하여 유전체역학의 궁극적인 목표 중 하나인 미생물성 전염병을 보다 효율적으로 감시할 수 있을 것으로 기대된다. 그리고, 대용량서열화 기술 중, 3세대 서열화기술 중 하나인 옥스포드 나노포어 MinION의 보다 나은 휴대성과 빠른 서열화의 성능 덕분에 유전체역학은 더 많은 발전을 거듭할 것으로 보인다. 이에, 본 연구는 항균 저항성 유전자를 찾고 전염병 경로를 추론하는 계산적인 방법에 대하여 살펴보고, 미생물 유전체역학에서 MinION이 응용된 예들에 대하여 논하였다.

• Molecules and Cells
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• 제42권8호
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• pp.604-616
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• 2019

Phosphoserine phosphatase (PSPH) is one of the key enzymes of the L-serine synthesis pathway. PSPH is reported to affect the progression and survival of several cancers in an L-serine synthesis-independent manner, but the mechanism remains elusive. We demonstrate that PSPH promotes lung cancer progression through a noncanonical L-serine-independent pathway. PSPH was significantly associated with the prognosis of lung cancer patients and regulated the invasion and colony formation of lung cancer cells. Interestingly, L-serine had no effect on the altered invasion and colony formation by PSPH. Upon measuring the phosphatase activity of PSPH on a serine-phosphorylated peptide, we found that PSPH dephosphorylated phospho-serine in peptide sequences. To identify the target proteins of PSPH, we analyzed the protein phosphorylation profile and the PSPH-interacting protein profile using proteomic analyses and found one putative target protein, IRS-1. Immunoprecipitation and immunoblot assays validated a specific interaction between PSPH and IRS-1 and the dephosphorylation of phospho-IRS-1 by PSPH in lung cancer cells. We suggest that the specific interaction and dephosphorylation activity of PSPH have novel therapeutic potential for lung cancer treatment, while the metabolic activity of PSPH, as a therapeutic target, is controversial.

• Journal of Genetic Medicine
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• 제2권2호
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• pp.71-77
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• 1998

Comparative genomic hybridization (CGH) can now be applied to detect the origin of extra or missing chromosomal material in cases with common unbalanced aberrations and in prenatal investigations. This method has been used in 13 cases of fetal samples for this study; 3 for amniocytes, 2 for cord blood and 8 for abortus tissues. These samples were previously subjected to GTG-banding. Our study showed aneuploidy in 8 cases, and partial monosomy, partial trisomy or marker chromosome in the remaining 5. The CGH disclosed further small genetic imbalances in 4 of all 13 cases: a prenatal sample showing del(20)(q13) by GTG confirmed a loss of the segment 20p13-pter by CGH; a marker chromosome manifested normal CGH profile; chromosome der(?)(?;15) found in an abortus sample by GTG turned out to be a loss of 15pter-q14 (partial monosomy) and a gain of 10pter-q22 (partial trisomy); the der(15) shown by GTG represented partial trisomy of 3q24-qter. These findings show that CGH is very useful and efficient for cytogenetic investigations of clinical cases.

• 한국동물번식학회:학술대회논문집
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• 한국동물번식학회 2002년도 춘계학술발표대회 발표논문초록집
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• pp.64-64
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• 2002

Peroxiredoxins (Prxs) possess protective activity against oxygen radicals generated by thiol-catalyzed oxidative systems. We already reported the genomic structure and its expression of mouse Prx Ⅰ, Ⅱ, and 1-Cys Prx. However, the Prx Ⅲ has not been determined. That was initially defined transiently expressed gene, mouse MER5, of murine erythroleukaemia cell differentiation. In addition, this protein was recently redefined a member of the thiol-specific antioxidant gene family. (omitted)

• 대한수의학회지
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• 제39권1호
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• pp.90-95
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• 1999

A species-specific 760 base pair(bp) BamHI to EcoRI DNA fragment(fMG-2) of lipoprotein gene was isolated from a Mycoplasma gallisepticum(M gallisepticum) genomic library. Based on the DNA sequence data of fMG-2, a pair of 25bp primers was synthesized. When used in the polymerase chain reaction(PCR), 732bp DNA products were amplified from 6 standard strains and 10 field isolates of M gallisepticum, but not from 2 Mycoplasma synoviae and 7 other Mycoplasma species. The lower detection limit was 100fg of the genomic DNA. Identity of the PCR products was confirmed by comparison of patterns of restriction endonuclease analysis with AseI, DraI, EcoRV and SspI.