• 대한수의학회지
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• 제60권1호
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• pp.1-7
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• 2020

We investigated the genotypes of Leptospira spp. detected in symptomatic dogs in Thailand. During April to December 2012, 6 out of 41 client-owned dogs were diagnosed with leptospirosis based on polymerase chain reaction tests. All of the infected dogs showed clinical symptoms related to leptospirosis. Direct genotyping of the causative agent of the canine leptospirosis was conducted from the archival DNA samples extracted from urine or blood of those 6 infected dogs. Sequencing of the partial 16S rRNA and lipL32 genes from all samples identified Leptospira (L.) interrogans as the infecting species. Multilocus sequence typing tests were successful for 2 out of 6 samples. The sequence type (ST) was identified as ST50 for both samples where the profile corresponded to L. interrogans species and Bataviae serogroup. The presence of this genotype of Leptospira has never been reported in Thailand. Thus, our findings showed the existence of ST50 L. interrogans serogroup Bataviae and the ability to cause leptospirosis in dogs in Thailand.

• 한국식품위생안전성학회지
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• 제29권4호
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• pp.316-321
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• 2014

The aim of study was to investigate the virulence profile of Escherichia coli O157:H7 bacteriophages isolated from sewage and livestock stools. Among 23 E. coli O157:H7 bacteriophages, 14 strains were isolated from sewage and 9 were from animal stools collected from 10 livestock farms in Korea. For each bacteriophage DNA sample, the presence of stx1, stx2, eae, aafII, ial, elt, estI, estII, astA, afa, and cnf was examined by polymerase chain reaction. The detection rate of eae, stx2, estI, astA, and ial was 100%, 69.6%, 13.0%, 13.0%, 8.7%, respectively. While all E. coli O157:H7 bacteriophages isolated from stools carried eae+stx2, stx2+eae, eae+astA, eae, stx2+eae+estI, eae+estI, stx2+eae+ial, and eae+ial were observed in bacteriophages isolated from sewage. As several plasmid-carrying virulence factors (estI, astA, and ial) were found in E. coli O157:H7 bacteriophages obtained from sewage and stools, the microbial safety of bacteriophages should be investigated in further study.

• 고려인삼학회:학술대회논문집
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• 고려인삼학회 2002년도 학술대회지
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• pp.467-476
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• 2002

A large number of individual ginseng plants have been selected in the farmer's fields to develop new ginseng varieties with desirable traits since 1970s. Among them, Hwangsukjong with green stem and yellow berry was selected as a ginseng germplasm. The phenotype of Hwangsukjong is quite different from Jakyungjong that has violet stem and red berry and has been cultivated in most of ginseng fields. Therefore, Hwangsukjong was crossed with Jakyungjong to clarify the inheritance of stem color and then the characteristics of $F_1\;and\;F_2$ hybrids were investigated. $F_1$ hybrid plants were similar to Jakyungjong in most of aerial part characters and showed hybrid vigor in fresh weight of root and weight of 100 seeds. In $F_2$ generation, the stem color was segregated in a ratio of 3 violet to 1 green. From this result, it was elucidated that violet color was controlled by single dominant gene. In another experiment, DNA was extracted from parents (Jakyungjong and Hwangsukjong) and $F_1$ hybrid. For each primer evaluated, multiple band profile was produced comprising from one to five major bands plus a varying number of minor bands and amplified bands were detected among most primers. In case of UBC primer number 13, 17, 30, 31, and 43, band patterns of parents and $F_1$ hybrid were very similar, but the others were not. Especially, in {\sharp}1$, {\sharp}4$, and {\sharp}33$, specific band was produced in Hwangsukjong and $F_1$ hybrid while in {\sharp}6$, another specific band was produced in Jakyungjong and $F_1$ hybrid. Therefore, $F_1$ hybrid had all specific bands at these primers. So, these selective markers could be used for identification of characteristics of $F_2$ hybrids

• Genomics & Informatics
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• 제18권4호
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• pp.42.1-42.9
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• 2020

Chromatin immunoprecipitation coupled with high-throughput DNA sequencing (ChIP-Seq) is a powerful technology to profile the location of proteins of interest on a whole-genome scale. To identify the enrichment location of proteins, many programs and algorithms have been proposed. However, none of the commonly used peak calling programs could accurately explain the binding features of target proteins detected by ChIP-Seq. Here, publicly available data on 12 histone modifications, including H3K4ac/me1/me2/me3, H3K9ac/me3, H3K27ac/me3, H3K36me3, H3K56ac, and H3K79me1/me2, generated from a human embryonic stem cell line (H1), were profiled with five peak callers (CisGenome, MACS1, MACS2, PeakSeq, and SISSRs). The performance of the peak calling programs was compared in terms of reproducibility between replicates, examination of enriched regions to variable sequencing depths, the specificity-to-noise signal, and sensitivity of peak prediction. There were no major differences among peak callers when analyzing point source histone modifications. The peak calling results from histone modifications with low fidelity, such as H3K4ac, H3K56ac, and H3K79me1/me2, showed low performance in all parameters, which indicates that their peak positions might not be located accurately. Our comparative results could provide a helpful guide to choose a suitable peak calling program for specific histone modifications.

• 한국정보통신학회논문지
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• 제25권7호
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• pp.903-909
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• 2021

예쁜꼬마선충(Caenorhabditis elegans)은 염기서열이 완전히 밝혀진 동물로 유전자 기능 분석, 동물 행동 연구 등 다양한 연구 분야에 사용되는 대표적인 생물 종이다. 그동안 선충을 이용해 물의 오염 여부를 판별하기 위한 바이오 모니터링 시스템에 대한 여러 연구들이 있었다. 본 논문은 하천의 수질 오염의 원인이 되는 화학물질을 식별하기 위해 선충의 수영 행동이 활용 가능한 지를 보여주기 위해 기계학습 기반의 바이오 모니터링 시스템을 제안한다. 선충의 수영 행동을 대표하기 위해 선충을 대상으로 가지 길이 유사성(Branch Length Similarity) 엔트로피를 계산한다. 그리고 BLS 엔트로피의 조합인 BLS 엔트로피 프로파일을 클러스터링 알고리즘을 사용해 몇 가지 패턴으로 유형화하여 데이터 집합을 만든다. 0.1ppm 농도의 포름알데히드, 벤젠, 톨루엔이 첨가된 아레나에서 선충의 수영 행동을 촬영하고 개발한 히든 마코프 모델(Hidden Markov Model: HMM)의 성능을 검증한다.

• Animal Bioscience
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• 제36권11호
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• pp.1632-1646
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• 2023

Objective: The objective of the present study was to investigate the effect of dietary betaine (BT) supplementation on the hepatic transcriptome profiles in broiler chickens raised under heat stress (HS) conditions. Methods: A total of 180 (21-d-old) Ross 308 male broiler chicks were allotted to 1 of 3 treatment groups with 6 replicated cages in a completely randomized design. One group was kept under thermoneutral conditions at all times and was fed a basal diet (PC). Other 2 groups were exposed to a cyclic heat stress condition. One of the 2 groups under heat stress conditions was fed the basal diet as a negative control (NC), whereas the other group was fed the basal diet supplemented with 0.2% BT. All chickens were provided with diets and water ad libitum for 21 d. Following the experiment, the liver samples were collected for RNA sequencing analysis. Results: Broiler chickens in NC and BT group had decreased (p<0.05) growth performance. In the transcriptome analysis, the number of differentially expressed genes were identified in the liver by HS conditions and dietary BT supplementation. In the comparison between NC and PC treatments, genes related to energy and nucleic acid metabolism, amino acid metabolism, and immune system were altered by HS, which support the reason why heat-stressed poultry had decreased growth performance. In the comparison between NC and BT treatments, genes related to lipid metabolism, carbohydrate metabolism, and immune system were differently expressed under HS conditions. Conclusion: HS negatively impacts various physiological processes, including DNA replication, metabolism of amino acids, lipids, and carbohydrates, and cell cycle progression in broiler chickens. Dietary BT supplementation, however, offers potential counteractive effects by modulating liver function, facilitating gluconeogenesis, and enhancing immune systems. These findings provide a basis for understanding molecular responses by HS and the possible benefits of dietary BT supplementation in broiler chickens exposed to HS.

• 한국버섯학회지
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• 제10권3호
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• pp.109-114
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• 2012

느타리 버섯류의 새로운 품종을 개발하기 위하여 고품질의 짙은 회색느타리 신품종을 육성하였다. 2003년부터 2004년까지 느타리 유전자원의 특성검정을 하였다. 2008년에 육종모본수한과 '농기201호'의 단핵체간 교잡하여 04-154 교잡주를 육성하였다. 이 교잡주 04-154와 품종 '청풍'의 단핵체와 다시 교잡하여 우수한 Po2008-275를 선발하여 특성검정, 확대재배를 실시하여 농작물 직무육성 신품종 선정심의회에서 '구슬'로 명명되었다. 주요특성으로 균사 생장 적온이 $25{\sim}30^{\circ}C$이며 버섯 원기형성 및 발생 온도는 $10{\sim}16^{\circ}C$이였다. 자실체의 갓 색깔은 짙은 회색으로 자연 상태에서 봄, 가을에 재배가 알맞은 특성을 가지고 있다. 균사체 배양기간은 25~30일이며 균 긁기 후 초발이소요일수는 3~5일로 온도가 높을수록 단축된다. 자실체 형태는 얕은 깔때기형이다. 대굵기는 $16.8{\pm}1.6mm$, 대길이는 $51.0{\pm}4.4mm$로 다른 느타리 종에 비해 자실체 대가 굵고 다소 짧은 편이다. 자실체 수량은 상자 당($43{\times}43{\times}11cm$) 1,545g으로 04-154 계통친이 100일 때 '구슬' 137, '청풍'이 146이었다. 가변특성으로는 감자배지와 버섯완전배지에서 균사를 배양한 결과 버섯완전배지에서 생장이 양호하였다. 또한 3종류의 primer를 이용하여 새로운 품종 '구슬'과 모균주에 대한 DNA profile을 분석한 결과 primer URP 1, primer URP 2, primer URP 5에서 양친주의 주요 밴드를 가지며 대조구인 '춘추2호'와는 뚜렷하게 구분되었다. 신품종 느타리 '구슬'은 소비자들이 가장 선호하는 짙은 회색의 갓을 나타내어 고품질을 요구하는 소비자를 만족시키는데 기여 할 것으로 기대된다.

• 한국작물학회지
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• 제52권1호
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• pp.81-88
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• 2007

본 연구는 농진청 종자은행에 보존된 한국, 중국 및 일본 재래종 콩과 한국 야생콩의 SSR profile 작성과 그들의 유전적 구조 해석을 위해 9개의 SSR 마커에 의해 분석되었다. 1. DNA profiling은 유전자좌별로 2,855(Satt458)점$\sim$4,368(Satt197)점이 분석되어 35,655건이 데이터베이스화되었다. 2. 총 대립인자수는 267개였고 유전자좌당 평균 29.6개의 높은 다형성을 나타냈다. 유전자좌별 대립인자 수는 21개(Satt532 및 Satt141)부터 58개(Sat_074)까지 나타났다. 자원내력별 대립인자수는 한국 야생콩에서 196개로 가장 많은 것으로 나타난 반면, 일본 재래종 콩에서는 가장 적은 115개로 나타났다. 3. 집단에 따른 유전자좌별 대립인자의 범위로 한국 재래종 콩이 가장 많은 5개의 유전자좌(Sat_074, Satt141, Satt286, Satt545, Satt458)에서 다음으로는 한국 야생콩이 4개의 유전자좌(Satt187, Satt532, Satt245, Satt197)에서 가장 넓은 것으로 나타났다. 그러나 대립 인자수면에서는 한국 재래종 콩이 5개의 유전자좌(Sat_074, Satt141, Satt197, Satt545, Satt458)에서 가장 많은 대립인자수를 나타냈고, 한국 야생콩은 나머지 4개의 유전자좌(Satt187, Satt532, Satt245, Satt286)에서 가장 많은 대립인자수를 나타냈다. 4. 대립인자 분포에 있어 전체적으로 한국 야생콩 집단은 재래종 집단들에 비해 고른 분포를 나타냈고 대립인자의 크기가 큰쪽(high ladder)에서보다 작은쪽(low ladder)에서 높은 분포를 나타냈다. 5. 재래종 집단들 간에 대립인자 분포를 살펴보면, 한국 집단은 Satt286(202 bp, 232 bp)에서, 중국집단은 Satt197(171 bp)와 Satt458(173 bp)에서 그리고 일본집단은 Sat_074(244 bp)와 Satt458(170 bp)에서 매우 높은 것으로 나타났다.

• International Journal of Oral Biology
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• 제32권1호
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• pp.35-43
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• 2007

Tooth loss in elderly is mainly caused by alveolar bone loss via severe periodontitis. Although the severity of periodontitis is known to be affected by age, the aging process or the genetic changes during the aging of periodontal tissue cells are not well characterized. In this study, we investigated the effect of in vitro aging on the change of gene expression pattern in periodontal fibroblasts. Gingival fibroblasts (GF) and periodontal ligament fibroblasts (PDL) were obtained from two young patients and replicative senescence was induced by sequential subcultivation. When more than 90% cells were positively stained with senescence-associated ${\beta},-galactosidase$, those cells were regarded as aged cells. In aged GF and PDL, the level of phosphorylated retinoblastoma (RB) and $p16^{INK4A}$ protein was significantly decreased and increased, respectively. However, the protein level of p53 and p21, well known senescence-inducing genes, did not increase in aged GF and PDL. Although $p27^{Kip1}$ and $p15^{INK4B}$, another cyclin-dependent kinase inhibitors, were reported to be involved in replicative senescence of human cells, they were decreased in aged GF and PDL. Because senescent cells showed flattened and enlarged cell shape and are known to have increased focal adhesion, we examined the protein level of several integrins. Aged GF and PDL showed increased protein level of integrin ${\alpha}2$, ${\alpha}v$, and ${\beta}1$. When the gene expression profiles of actively proliferating young cells and aged cells were compared by cDNA microarray of 3,063 genes and were confirmed by reverse transcription-polymerase chain reaction, 7 genes and 15 genes were significantly and commonly increased and decreased, respectively, in aged GF and PDL. Among them, included are the genes that were known to be involved in the regulation of cell cycle, gene transcription, or integrin signaling. The change of gene expression pattern in GF and PDL was minimally similar to that of oral keratinocyte. These results suggest that $p16^{INK4A}/RB$ might be involved in replicative senescence of periodontal fibroblasts and the change of gene expression profile during aging process is cell type specific.

• IMMUNE NETWORK
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• 제11권5호
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• pp.258-267
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• 2011

Background: Current management strategies attempt to diagnose rheumatoid arthritis (RA) at an early stage. Transcription profiling is applied in the search for biomarkers for detecting early-stage disease. Even though gene profiling has been reported using several animal models of RA, most studies were performed after the development of active arthritis, and conducted only on the peripheral blood and joint. Therefore, we investigated gene expression during the initial phase of collagen-induced arthritis (CIA) before the arthritic features developed in the thymus in addition to the peripheral blood and synovium. Methods: For gene expression analysis using cDNA microarray technology, samples of thymus, blood, and synovium were collected from CIA, rats immunized only with type II collagen (Cll), rats immunized only with adjuvant, and unimmunized rats on days 4 and 9 after the first immunization. Arrays were scanned with an Illumina bead array. Results: Of the 21,910 genes in the array, 1,243 genes were differentially expressed at least 2-fold change in various organs of CIA compared to controls. Among the 1,243 genes, 8 encode T-cell receptors (TCRs), including CD3${\zeta}$, CD3${\delta}$, CD3${\varepsilon}$, CD8${\alpha}$, and CD8${\beta}$ genes, which were down-regulated in CIA. The synovium was the organ in which the genes were differentially expressed between CIA and control group, and no difference were found in the thymus and blood. Further, we determined that the differential expression was affected by adjuvant more than Cll. The differential expression of genes as revealed by real-time RT-PCR, was in agreement with the microarray data. Conclusion: This study provides evidence that the genes encoding TCRs including CD3${\zeta}$, CD3${\delta}$, CD3${\varepsilon}$, CD8${\alpha}$, and CD8${\beta}$ genes were down-regulated during the initial phase of CIA in the synovium of CIA. In addition, adjuvant played a greater role in the down-regulation of the CD3 complex compared to CII. Therefore, the down-regulation of TCR gene expression occurred dominantly by adjuvant could be involved in the pathogenesis of the early stage at CIA.