• 한국양식학회지
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• 제16권1호
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• pp.8-14
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• 2003

To generate expressed sequence tags for genomics research involving genetic linkage analysis, to examine gene expression profiles in muscles of channel catfish in a non-normalized muscle cDNA library, to compare gene expression in young and mature channel catfish muscles using the EST reagents and gene filters to demonstrate the feasibility of functional genomics research in small laboratories. 102 randomly picked cDNA clones were analyzed from the catfish muscle cDNA library. Of the sequences generated, 90.2% of ESTs was identified as known genes by identity comparisons. These 92 clones of known gene products represent transcriptional products of 24 genes. The 10 clones of unknown gene products represent 8 genes. The major transcripts (70.1% of the analyzed ESTs) in the catfish muscle are from many major genes involved in muscle contraction, relaxation, energy metabolism and calcium binding such as alpha actin, creatine kinase, parvalbumin, myosin, troponins, and tropomyosins. Gene expression of the unique ESTs was comparatively studied in the young and adult catfish muscles. Significant differences were observed for aldolase, myostatin, myosin light chain, parvalbumin, and an unknown gene. While myosin light chain and an unknown gene (CM 192) are down-regulated in the mature fish muscle, the aldolase, myostatin, and parvalbumin are significantly up-regulated in the mature fish muscle. Although the physiological significance of the changes in expression levels needs to be further addressed, this research demonstrates the feasibility and power of functional genomics in channel catfish. Channel catfish muscle gene expression profiles provide a valuable molecular muscle physiology blueprint for functional comparative genomics.

• Asian-Australasian Journal of Animal Sciences
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• 제25권10호
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• pp.1481-1492
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• 2012

The interaction of the genes involved in intestinal development is the molecular basis of the regulatory mechanisms of intestinal development. The objective of this study was to identify the significant pathways and key genes that regulate intestinal development in Landrace piglets, and elucidate their rules of operation. The differential expression of genes related to intestinal development during suckling time was investigated using a porcine genome array. Time sequence profiles were analyzed for the differentially expressed genes to obtain significant expression profiles. Subsequently, the most significant profiles were assayed using Gene Ontology categories, pathway analysis, network analysis, and analysis of gene co-expression to unveil the main biological processes, the significant pathways, and the effective genes, respectively. In addition, quantitative real-time PCR was carried out to verify the reliability of the results of the analysis of the array. The results showed that more than 8000 differential expression transcripts were identified using microarray technology. Among the 30 significant obtained model profiles, profiles 66 and 13 were the most significant. Analysis of profiles 66 and 13 indicated that they were mainly involved in immunity, metabolism, and cell division or proliferation. Among the most effective genes in these two profiles, CN161469, which is similar to methylcrotonoyl-Coenzyme A carboxylase 2 (beta), and U89949.1, which encodes a folate binding protein, had a crucial influence on the co-expression network.

• 대한수의학회지
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• 제40권2호
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• pp.301-310
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• 2000

The antimicrobial susceptibility, genotypes of enterotoxins(LT, STa) and pili(K88, 987P), and plasmid profiles were investigated with 102 Escherichia coli isolated from piglets showing diarrhea in Korea. Almost of them were susceptible to ceftiofur(99%), cefquinone(97.1%). However they showed resistance to bacitracin(100%), streptomycin(98%), vancomycin(97%), trimethoprim/sulfamethoxazole(87.2%), tetracycline(84.3%) in antimicrobial susceptibility test. Moreover, all of the isolates demonstrated resistance to more than 2, and 78% of them were resistant to more than 8 of total 17 drugs. Multiplex PCRs for genotyping of enterotoxins(LT, STa) and pili(K88, 987P) were established with primers designed based on sequences from Genebank. Seventeen strains(16.6%) of the isolates had STa gene, 11 strains(10.8%) of them had both STa and LT genes, and 18 strains(17.8%) had K88 gene. But none of the isolates harbored a gene exclusively encoding LT. The gene encoding 987P pili was not found in all isolates. Fifty-four strains of 102 isolates(52.9%) had plasmid with various sizes ranging from 125kb to 1.1kb. Numbers of plasmid per isolates were also various, from 1 to 9. Distinctive relationship between plasmid profiles and genotypes of enterotoxins and pili in the isolates was not found. These results might provide the basic knowledge to establish strategies for the treatment and prevention of colibacillosis in piglets.

• Journal of Periodontal and Implant Science
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• 제52권2호
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• pp.127-140
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• 2022

Purpose: In dental avulsion, delayed replantation usually has an uncertain prognosis. After tooth replantation, complex inflammatory responses promote a return to periodontal tissue homeostasis. Various types of cytokines are produced in the inflammatory microenvironment, and these cytokines determine the periodontal tissue response. This study aimed to identify the gene expression profiles of replanted teeth and evaluate the functional differences between immediate and delayed replantation. Methods: Maxillary molars from Sprague-Dawley rats were extracted, exposed to a dry environment, and then replanted. The animals were divided into 2 groups according to the extra-oral time: immediate replantation (dry for 5 minutes) and delayed replantation (dry for 60 minutes). Either 3 or 7 days after replantation, the animals were sacrificed. Periodontal soft tissues were harvested for mRNA sequencing. Hallmark gene set enrichment analysis was performed to predict the function of gene-gene interactions. The normalized enrichment score (NES) was calculated to determine functional differences. Results: The hallmark gene sets enriched in delayed replantation at 3 days were oxidative phosphorylation (NES=2.82, Q<0.001) and tumor necrosis factor-alpha (TNF-α) signaling via the nuclear factor kappa light chain enhancer of activated B cells (NF-κB) pathway (NES=1.52, Q=0.034). At 7 days after delayed replantation, TNF-α signaling via the NF-κB pathway (NES=-1.82, Q=0.002), angiogenesis (NES=-1.66, Q=0.01), and the transforming growth factor-beta signaling pathway (NES=-1.46, Q=0.051) were negatively highlighted. Conclusions: Differentially expressed gene profiles were significantly different between immediate and delayed replantation. TNF-α signaling via the NF-κB pathway was marked during the healing process. However, the enrichment score of this pathway changed in a time-dependent manner between immediate and delayed replantation.

• 한국정보과학회논문지:소프트웨어및응용
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• 제33권8호
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• pp.681-691
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• 2006

유전자 데이타의 클러스터링은 방대한 유전자 정보를 발현 정도에 따라 비슷한 그룹으로 나누어 분석하는 방법으로 유전자의 기능을 분석하는데 사용되어 왔다. 클러스터링의 한 종류인 퍼지 클러스터링은 하나의 샘플이 소속정도에 따라 여러 그룹에 동시에 소속되도록 나누는 방법으로, 하나의 유전자 데이타는 여러가지 유전 정보를 가칠 수 있기 때문에 유전자 발현 데이타의 분석에 보다 적절한 방법이다. 그러나 보통 클러스터링 방법은 초기 값에 민감하고, 지역해에 빠질 수 있는 단점을 갖는다. 이런 단점을 해결하기 위해 본 논문에서는 진화 연산을 이용한 퍼지 클러스터링 방법을 제안한다. 이때, 적합도 평가를 위해서 모든 데이타에 대해 동일한 기준을 적용하는 베이지안 검증방법의 단점을 개선하여, 데이타의 특성 을 고려하여 결정된 적용적 ${\alpha}$-cut 기반 평가방법을 사용한다. SRBCT 데이타와 효모 세포주기 데이타를 이용해 실험을 하고 결과를 분석하여 제안하는 방법의 유용성을 확인하였다.

• Journal of Microbiology and Biotechnology
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• 제8권5호
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• pp.517-522
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• 1998

The cry1 gene content of a collection of Bacillus thuringiensis strains, which include new isolates from Malaysia and Indonesia, was determined by a multiplex PCR using a set of eight oligonucleotide forward primers specific to cry1Aa, cry1Ab, cry1Ac, cry1Ba, cry1Ca, cry1Da, cry1Ea, and cry1Fa genes, and two reverse primers, one specific to cry1Ab and the other common to the remaining cry1 genes. Two-thirds of the 59 strains screened were cry1 positive and contained one to four different genes. The cry gene profiles correlated well with toxicities of the strains to lepidopteran insects. The method can be used for rapid screening of a large number of new isolates as the total DNA extracted by boiling cells from single colonies can be used directly in the PCR. However, it is not suitable for follow-up monitoring of specific commercial strains after application in the field as the PCR product profiles of these strains could not be differentiated from those of new isolates.

• 대한수의학회지
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• 제39권6호
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• pp.1091-1098
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• 1999

Antimicrobial susceptibility, plasmid profiles and distribution of toxA gene were investigated in Pasteurella multocida isolated from pneumonic lung lesions of swine. The bacteria were highly susceptible to norfloxacin, cabenicillin, enrofloxacin and chloramphenicol, but resistant to colistin, sulfamethoxawle/trimethoprime, bacitracin, streptomycin. Sixty percentage of the isolates was resistant more than 2 drugs used in this experiment and 21 strains (23.6%) were resistant more than 5 drugs. This phenomenon meant that they had highly multi-drugs resistance. In the analysis of plasmid profiles, nineteen strains (47.5%) of 40 P multocida isolates harbored plasmids, ranging from 53.3kb to 2.49kb in size and the plasmid profiles could be classified into 5 groups. However, there was no relationship between the size and the profile of plasmid and the resistance pattern of antimicrobial agents. Thirty strains of 39 P multocida isolates (77%) investigated by PCR harbored toxA gene. This result suggested involvement of the ToxA protein expressed from the gene in pneumonic pasteurellosis of swine.

• 한국수정란이식학회:학술대회논문집
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• 한국수정란이식학회 2005년도 제5회 발생공학 국제심포지엄 및 학술대회
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• pp.108-108
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• 2005

• Asian Pacific Journal of Cancer Prevention
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• 제13권8호
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• pp.3605-3609
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• 2012

Lung cancer seriously threatens human health, so it is important to investigate gene expression changes in affected individuals in comparison with healthy people. Here we compared the gene expression profiles between smokers with and without lung cancer. We found that the majority of the expressed genes (threshold was set as 0.1 RPKM) were the same in the two samples, with a small portion of the remainder being unique to smokers with and without lung cancer. Expression distribution patterns showed that most of the genes in smokers with and without lung cancer are expressed at low or moderate levels. We also found that the expression levels of the genes in smokers with lung cancer were lower than in smokers without lung cancer in general. Then we detected 27 differentially expressed genes in smokers with versus without lung cancer, and these differentially expressed genes were foudn to be involved in diverse processes. Our study provided detail expression profiles and expression changes between smokers with and without lung cancer.

• KSBB Journal
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• 제20권3호
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• pp.220-227
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• 2005

독소루비신 생합성 유전자의 발현을 촉진시키는 유전자인 dnrI와 다나루비신으로부터 독소루비신으로의 생전환에 관여하는 유전자인 doxA를 ermE 프로모터가 포함된 pSE34에 도입하였을 때 각각 5.5배, 2.5배의 독소루비신 생산성 증가가 이루어졌다. 독소루비신 생합성 유전자군의 발현패턴 분석을 위한 DNA microarray system을 구축하였고, 고생산 균주의 독소루비신 생합성 유전자 발현 패턴을 DNA microarray를 통해 확인하였다. 독소루비신 생합성 유전자군의 세포성장에 따른 발현패턴을 분석한 결과, 독소루비신 생산성 증가에 따라 생합성 유전자의 발현도 증가함을 확인할 수 있었고, pSE34를 통해 도입해준 donA, dnrI 유전자의 경우 전체 생합성 유전자의 평균보다 높은 수준의 발현량을 보여줌으로써, ermE 프로모터에 의해 발현이 극대화되었음을 확인할 수 있었다. 독소루비신 내성 유전자의 경우 다른 독소루비신 생합성 유전자들에 비해 발현정도가 크게 증가했고, DnrI 의해 조절을 받는 다른 유전자들의 발현 수준과 비교하였을 때 TDP-daunosamine을 생합성의 첫 번째 단계에 관여하는 dnmL 유전자는 그 발현양의 증가가 크지 않았다. 따라서 DNA microarray 시스템 분석 결과, 독소루비신 생산성 극대화를 위해서는 dnrI, doxA, drrA, drrB, drrC, dnmL 등의 유전자들의 안정적 발현이 매우 중요하고도 핵심적인 인자임이 확인되었다.