• Genomics & Informatics
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• 제5권1호
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• pp.10-18
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• 2007

Numerous studies have reported that genes with similar expression patterns are co-regulated. From gene expression data, we have assumed that genes having similar expression pattern would share similar transcription factor binding sites (TFBSs). These function as the binding regions for transcription factors (TFs) and thereby regulate gene expression. In this context, various analysis tools have been developed. However, they have shortcomings in the combined analysis of expression patterns and significant TFBSs and in the functional analysis of target genes of significantly overrepresented putative regulators. In this study, we present a web-based A Functional Clustering Analysis Tool for Predicted Transcription Regulatory Elements and Gene Ontology Terms (FCAnalyzer). This system integrates microarray clustering data with similar expression patterns, and TFBS data in each cluster. FCAnalyzer is designed to perform two independent clustering procedures. The first process clusters gene expression profiles using the K-means clustering method, and the second process clusters predicted TFBSs in the upstream region of previously clustered genes using the hierarchical biclustering method for simultaneous grouping of genes and samples. This system offers retrieved information for predicted TFBSs in each cluster using $Match^{TM}$ in the TRANSFAC database. We used gene ontology term analysis for functional annotation of genes in the same cluster. We also provide the user with a combinatorial TFBS analysis of TFBS pairs. The enrichment of TFBS analysis and GO term analysis is statistically by the calculation of P values based on Fisher’s exact test, hypergeometric distribution and Bonferroni correction. FCAnalyzer is a web-based, user-friendly functional clustering analysis system that facilitates the transcriptional regulatory analysis of co-expressed genes. This system presents the analyses of clustered genes, significant TFBSs, significantly enriched TFBS combinations, their target genes and TFBS-TF pairs.

• Asian-Australasian Journal of Animal Sciences
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• 제30권7호
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• pp.920-929
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• 2017

Objective: The bursa of Fabricius (BF) is a central humoral immune organ belonging specifically to avians. Recent studies had suggested that miRNAs were active regulators involved in the immune processes. This study was to investigate the possible differences of the BF at miRNA level between two genetically disparate duck breeds. Methods: Using Illumina next-generation sequencing, the miRNAs libraries of ducks were established. Results: The results showed that there were 66 differentially expressed miRNAs and 28 novel miRNAs in bursa. A set of abundant miRNAs (i.e., let-7, miR-146a-5p, miR-21-5p, miR-17~92) which are involved in immunity and disease were detected and the predicted target genes of the novel miRNAs were associated with duck high anti-adversity ability. By gene ontology analysis and enriching KEGG pathway, the targets of differential expressed miRNAs were mainly involved in immunity and disease, supporting that there were differences in the BF immune functions between the two duck breeds. In addition, the metabolic pathway had the maximum enriched target genes and some enriched pathways that were related to cell cycle, protein synthesis, cell proliferation and apoptosis. It indicted that the difference of metabolism may be one of the reasons leading the immune difference between the BF of two duck breeds. Conclusion: This data lists the main differences in the BF at miRNAs level between two genetically disparate duck breeds and lays a foundation to carry out molecular assisted breeding of poultry in the future.

• Bulletin of the Korean Chemical Society
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• 제30권12호
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• pp.2993-2998
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• 2009

An enzyme-linked immunosorbent assay (ELISA)-on-a-chip (EOC) biosensor combined with cell concentration technology based on immuno-magnetic separation (IMS) was investigated for use as a potential tool for early screening of Listeria monocytogenes (L. monocytogenes) in food products. The target analyte is a well-known pathogenic foodborne microorganism and outbreaks of the food poisoning typically occur due to contamination of normal food products. Thus, the aim of this study was to develop a rapid and reliable sensor that could be utilized on a daily basis to test food products for the presence of this pathogenic microorganism. The sensor was optimized to provide a high detection capability (e.g., 5.9 ${\times}\;10^3$ cells/mL) and, to eventually minimize cultivation time. The cell density was condensed using IMS prior to analysis. Since the concentration rate of IMS was greater than 100-fold, this combination resulted in a detection limit of 54 cells/mL. The EOC-IMS coupled analytical system was then applied to a real sample test of fish intestines. The system was able to detect L. monocytogenes at a concentration of 2.4 CFU/g after pre-enrichment for 6 h from the onset of cell cultivation. This may allow us to monitor the target analyte at a concentration less than 1 CFU/g within a 9 h-cultivation provided a doubling time of 40 min is typically maintained. Based on this estimation, the EOC-IMS system can screen and detect the presence of this microorganism in food products almost within working hours.

• 미생물학회지
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• 제41권3호
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• pp.168-176
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• 2005

갯벌 퇴적물에 존재하는 병원성 해양미생물인 Vibrio vulnificus를 신속하고 정확하게 검출하기 위해 PCR, Southern hybridization 방법과 real-time PCR을 수행하여 검출 민감도를 비교하였다. 갯벌 퇴적물로부터 bead beater를 이용한 물리적 방법으로 DNA 조추출액을 얻고 상용화된 키트 (Geneclean turbo Kit)를 이용하여 부식물질(humic substances)을 제거하였다. 병원성에 관련된 3 종의 유전자(hemolysin, vvhA; phosphomannomutase, pmm; metalloprotease, vvpE)를 대상으로 설계한 프라이머 셋을 동시에 사용하는 multiplex PCR 방법과 Southern hybridization과 병행한 방법(PCR/Southern hybridization)을 수행하였다. Real-time PCR은 hemolysin 유전자(vvhA)에 특이한 프라이머와 TaqMan 탐침을 사용하였다. 전처리하지 않은 갯벌 퇴적물의 경우, PCR/Sourthern hybridization과 real-time PCR 방법의 검출 민감도는 퇴적물 1 g 당 약 $10^2$ 개의 세포 수준이었다. 농후처리액(APW; alkaline peptone water)으로 $35^{\circ}C$에서 $2{\~}3$시간, 8시간 중균 배양할 경우 갯벌 퇴적물 1 g 당 $2{\~}10$개 세포가 존재할 때 PCR/Southern hybridization 방법과 real-time PCR 방법으로 각각 검출할 수 있었다. 전처리 과정을 포함하여 real-time PCR은 $6{\~}7$시간, PCR/Sourthern hybridization은 약 36시간이 소요되었다.

• Korean Chemical Engineering Research
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• 제50권6호
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• pp.1027-1033
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• 2012

일반적인 SMB 공정은 여러 개의 크로마토그래피 컬럼을 갖는 4개의 구역으로 구성되어 있다. SMB는 회분식 크로마토그래피와는 달리 연속적으로 이성분계 물질 분리가 가능한 것이 가장 큰 장점이다. SMB 공정을 이용하여 목적 물질의 높은 생산성과 높은 순도의 물질을 얻어낼 수 있다. 이러한 SMB의 특징을 더욱 부각시키려는 연구들이 현재 진행되고 있다. 본 연구에서는 기존 SMB 공정에 온도의 변화를 추가한 Thermal Simulated Moving Bed Concentrator (TSMBC) 공정의 모사를 연구하였다. TSMBC의 장점으로는 온도의 변화를 통하여 등온 흡착식의 조작을 가할 수 있으며, 목적 물질에 따른 적용 분야가 다양하다는 것이다. 본 연구에서는 환경 친화적 공정으로 TSMBC의 적용 가능성을 시험하기 위해서 페놀 폐수로부터 순수한 용매인 물을 얻어내고 용질인 페놀은 농축시키는 모사 과정을 연구하였다. 고정상과 목적물질인 DOWEX $1{\times}4$와 페놀을 선정하고 고정상에 대한 페놀의 등온 흡착식을 측정하였다. 모사 과정에서는 총 세 가지 종류의 컬럼을 사용하였고 주입 시료 대비 2.29배, 2.28배, 그리고 1.31배의 목적 물질 농축을 확인할 수 있었다. 그러나 solvent port에서 용질의 배출도 발견되어 DOWEX $1{\times}4$ 고정상이 상온에서 갖는 페놀의 흡착식에 대한 한계점을 확인하였다.

• Journal of Ginseng Research
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• 제38권1호
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• pp.1-7
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• 2014

Background: Although ginsenosides such as Rg1, Rb1 and Rg3 have shown promise as potential nutraceuticals for cognitive impairment, their use has been limited due to high production cost and low potency. In particular, the process of extracting pure Rg3 from ginseng is laborious and expensive. Methods: We described the methods in preparing ginseol k-g3, an Rg3-enriched fraction, and evaluated its effects on scopolamine-induced memory impairment in mice. Results: Ginseol k-g3 (25-200 mg/kg) significantly reversed scopolamine-induced cognitive impairment in the passive avoidance, but not in Y-maze testing. Ginseol k-g3 (50 and 200 mg/kg) improved escape latency in training trials and increased swimming times within the target zone of the Morris water maze. The effect of ginseol k-g3 on the water maze task was more potent than that of Rg3 or Red ginseng. Acute or subchronic (6 d) treatment of ginseol k-g3 did not alter normal locomotor activity of mice in an open field. Ginseol k-g3 did not inhibit acetylcholinesterase activity, unlike donezepil, an acetylcholinesterase inhibitor. Rg3 enrichment through the ginseol k-g3 fraction enhanced the efficacy of Rg3 in scopolamine-induced memory impairment in mice as demonstrated in the Morris water maze task. Conclusion: The effects of ginseol k-g3 in ameliorating scopolamine-induced memory impairment in the passive avoidance and Morris water maze tests indicate its specific influence on reference or long-term memory. The mechanism underlying the reversal of scopolamine-induced amnesia by ginseol k-g3 is not yet known, but is not related to anticholinesterase-like activity.

• 한국식품영양과학회지
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• 제29권6호
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• pp.1016-1024
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• 2000

본 연구는 식품에 존재하는 L. monocytogenes균의 신속한 검출방법을 조사하기 위하여 hlyA 유전자 primer 를 사용하여 PCR 기법으로 행하였으며 primer의 특이성과 PCR의 민감성, L. monocytogenes균의 검출을 위한 최적조건 및 우유 및 소고기의 적용시험을 각각 조사하였다 PCR 특이성 실험에서는 L. monocytogenes 20주에 대한 PCR 분석 결과 모두 713 bp 크기의 PCR products를 확인할 수 있었고, Listeria spp. 및 다른 세균에서는 동일한 Poducts가 증폭되지 않으므로써 hiyA based primer의 L. monocytogenes에 대한 PCR 특이성이 관찰되었다. PCR 분석법의 민감도는 L. monocytogenes ATCC 19111의 1 pg DNA와 2.4$\times$$10^4$cell 수준에서 target DNA가 증폭되었다. Tailing의 제거와 민감도를 높이기 위하여 PCR cycle 수에 따른 최적조건을 조사한 결과 20~30 cycle 정도의 PCR clcyle 수가 좋은 것으로 나타났으며 민감도는 20 cycle PCR amplification을 행한 후 한번 더 10~15 cycle로 처리했을 때 훨씬 증가하였다. 한편, 우유(10 mL)와 쇠고기 절편(10g)에 0~$10^{7}$ CFU/mL 또는 g 수준으로 L. monocytogenes를 신속하게 검출하기 위하여 PCR을 적용한 결과, 우유시료에서는 2번 PCR을 반복함으로써 2 cells까지 검출할 수 있었고, 쇠고기 절편은 LEB로 35$^{\circ}C$에서 24시간 증균하여 PCR합으로써 2.6$\times$$10^2$cell가지 검출할 수 있었다.

• Asian-Australasian Journal of Animal Sciences
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• 제32권9호
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• pp.1458-1468
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• 2019

Objective: As one of the most important metabolic organs, the liver plays vital roles in modulating the lipid metabolism. This study was to compare miRNA expression profiles of the Large White liver between two different developmental periods and to identify candidate miRNAs for lipid metabolism. Methods: Eight liver samples were collected from White Large of 70-day fetus (P70) and of 70-day piglets (D70) (with 4 biological repeats at each development period) to construct sRNA libraries. Then the eight prepared sRNA libraries were sequenced using Illumina next-generation sequencing technology on HiSeq 2500 platform. Results: As a result, we obtained 346 known and 187 novel miRNAs. Compared with the D70, 55 down- and 61 up-regulated miRNAs were shown to be significantly differentially expressed (DE). Gene ontology and Kyoto encyclopedia of genes and genomes enrichment analysis indicated that these DE miRNAs were mainly involved in growth, development and diverse metabolic processes. They were predicted to regulate lipid metabolism through adipocytokine signaling pathway, mitogen-activated protein kinase, AMP-activated protein kinase, cyclic adenosine monophosphate, phosphatidylinositol 3 kinase/protein kinase B, and Notch signaling pathway. The four most abundantly expressed miRNAs were miR-122, miR-26a and miR-30a-5p (miR-122 only in P70), which play important roles in lipid metabolism. Integration analysis (details of mRNAs sequencing data were shown in another unpublished paper) revealed that many target genes of the DE miRNAs (miR-181b, miR-145-5p, miR-199a-5p, and miR-98) might be critical regulators in lipid metabolic process, including acyl-CoA synthetase long chain family member 4, ATP-binding casette A4, and stearyl-CoA desaturase. Thus, these miRNAs were the promising candidates for lipid metabolism. Conclusion: Our study provides the main differences in the Large White at miRNA level between two different developmental stages. It supplies a valuable database for the further function and mechanism elucidation of miRNAs in porcine liver development and lipid metabolism.

• 한국식품위생안전성학회지
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• 제34권3호
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• pp.290-295
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• 2019

최근 한국에서 발생한 Salmonella로 인한 식중독 사고는 2018년 9월 학교급식에서 제공된 초콜릿 무스 케이크가 원인이 되었다. 이 연구의 목적은 Salmonella Typhimurium이 인위적으로 접종된 무스케이크와 티라미수에서 3M Molecular Detection Assay 2 - Salmonella와 식품공전에 등재된 방법인 분리배지와 real-time PCR을 비교하는 것이었다. 무스케이크 2종과 티라미수 2종 25 g에 225 mL BPW를 넣고 $37^{\circ}C$에서 24시간 동안 증균 배양하였다. 배양 후, 3M Molecular Detection Assay 2 - Salmonella, 분리배지 그리고 real-time PCR로 분석하였다. 초콜릿 무스 케이크를 제외하고 3가지 방법은 유사한 결과를 보였다. 초콜릿 무스 케이크에서 분리배지와 3M Molecular Detection Assay 2 - Salmonella는 모든 접종수준에서 동일한 결과를 나타낸 반면 real-time PCR은 $10^4CFU/25g$ 수준에서 1번의 양성결과를 제외하고 모두 검출되지 않았다. 초콜릿 무스에 S. Typhimurium을 $10^2CFU/25g$ 수준으로 접종하였을때, real-time PCR를 이용한 검출은 15%에서는 부분적인 음성을 나타냈고, 20-100% 함량의 초콜릿 무스에서는 모두 음성이었다. Real-time PCR로는 chocolate이 15% 이상 함유된 식품에서의 Salmonella균 검출이 불가능하였지만, LMAP 기반의 3M Molecular Detection Assay 2으로는 chocolate 농도에 관계없이 검출이 가능하였다.

• Animal Bioscience
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• 제34권11호
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• pp.1739-1748
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• 2021

Objective: In recent years, long noncoding RNAs (lncRNAs) have been identified in many species, and some of them have been shown to play important roles in muscle development and myogenesis. However, the differences in lncRNAs between Kazakh cattle and Xinjiang brown cattle remain undefined; therefore, we aimed to confirm whether lncRNAs are differentially expressed in the longissimus dorsi between these two types of cattle and whether differentially expressed lncRNAs regulate muscle differentiation. Methods: We used RNA-seq technology to identify lncRNAs in longissimus muscles from these cattle. The expression of lncRNAs were analyzed using StringTie (1.3.1) in terms of the fragments per kilobase of transcript per million mapped reads values of the encoding genes. The differential expression of the transcripts in the two samples were analyzed using the DESeq R software package. The resulting false discovery rate was controlled by the Benjamini and Hochberg's approach. KOBAS software was utilized to measure the expression of different genes in Kyoto encyclopedia of genes and genomes pathways. We randomly selected eight lncRNA genes and validated them by quantitative reverse transcription polymerase chain reaction (RT-qPCR). Results: We found that 182 lncRNA transcripts, including 102 upregulated and 80 downregulated transcripts, were differentially expressed between Kazakh cattle and Xinjiang brown cattle. The results of RT-qPCR were consistent with the sequencing results. Enrichment analysis and functional annotation of the target genes revealed that the differentially expressed lncRNAs were associated with the mitogen-activated protein kinase, Ras, and phosphatidylinositol 3-kinase (PI3k)/Akt signaling pathways. We also constructed a lncRNA/mRNA coexpression network for the PI3k/Akt signaling pathway. Conclusion: Our study provides insights into cattle muscle-associated lncRNAs and will contribute to a more thorough understanding of the molecular mechanism underlying muscle growth and development in cattle.