• BMB Reports
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• v.39 no.3
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• pp.247-252
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• 2006

A rapid method for the detection of Hepatitis E Virus (HEV) was developed by utilizing nano-gold labeled oligonucleotide probes, silver stain enhancement and the microarray technique. The 5'-end -$NH_2$ modified oligonucleotide probes were immobilized on the surface of the chip base as the capture probe. The detection probe was made of the 3'-end -SH modified oligonucleotide probe and nano-gold colloid. The optimal concentrations of these two probes were determined. To test the detection sensitivity and specificity of this technique, a conservative fragment of the virus RNA was amplified by the RT-PCR/PCR one step amplification. The cDNA was hybridized with the capture probes and the detection probes on microarray. The detection signal was amplified by silver stain enhancement and could be identified by naked eyes. 100 fM of amplicon could be detected out on the microarray. As the results, preparation of nano-gold was improved and faster. Development time also was shortened to 2 min. Thus, considering high efficiency, low cost, good specificity and high sensitivity, this technique is alternative for the detection of HEV.

• KSBB Journal
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• v.24 no.5
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• pp.432-438
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• 2009

Here, we demonstrated simple nucleic acid, RNA, concentration method using polymer micro chip containing glass bead ($100\;{\mu}m$). Polymer micro chip was fabricated by PDMS ($1.5\;cm\;{\times}\;1.5\;cm$, $100\;{\mu}m$ in the height) including pillar structure ($160\;{\mu}m\;(I)\;{\times}\;80\;{\mu}m\;(w)\;{\times}\;100\;{\mu}m\;(h)$, gap size $50\;{\mu}m$) for blocking micro bead. RNA could be adsorbed on micro glass bead at low pH by hydrogen bonding whereas RNA was released at high pH by electrostatic force between silica surface and RNA. Amount of glass beads and flow rate were optimized in aspects of adsorption and desorption of RNA. Adsorption and desorption rate was measured with real time PCR. This concentrated RNA was applied to amplification micro chip in which NASBA (Nucleic Acid Sequence Based Amplification) was performed. As a result, E.coli O157 : H7 in the concentration of 10 c.f.u./10 mL was successfully detected by these serial processes (concentration and amplification) with polymer micro chips. It implies this simple concentration method using polymer micro chip can be directly applied to ultra sensitive method to measure viable bacteria and virus in clinical samples as well as environmental samples.

• Journal of Animal Reproduction and Biotechnology
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• v.38 no.3
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• pp.177-187
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• 2023

Background: The grading of Hanwoo (Korean native cattle) is based on four economic traits, and efforts have been continuously made to improve the genetic traits associated with these traits. There is a technology to predict the expected grade based on the 4 economic genetic SNP characteristics of Korean cattle calves using single nucleotide polymorphism (SNP) technology. Selection of highly proliferative, self-renewing, and differentiating satellite cells from cattle is a key technology in the cultured meat industry. Methods: We selected the Hanwoo with high and low-scored of genomic estimated breeding value (GEBV) by using the Hanwoo 50K SNP bead chip. We then isolated the bovine satellite cells from the chuck mass. We then conducted comparative analyses of cell proliferation, immunocytochemistry, qRT-PCR at short- and long-term culture. We also analyzed the differentiation capability at short term culture. Results: Our result showed that the proliferation was significantly high at High scored GEBV (Hs-GEBV) compared to Low scored GEBV (Ls-GEBV) at short- and long-term culture. The expression levels of Pax3 were significantly higher in Hs-GEBV bovine satellite cells at long-term culture. However, there were no significant differences in the expression levels of Pax7 between Hs- and Ls-GEBV bovine satellite cells at short- and long- term culture. The expression levels of MyoG and MyHC were significantly high at Ls-GEBV bovine satellite cells. Conclusions: Our results indicated that selection of bovine satellite cells by Hanwoo 50K SNP bead chip could be effective selection methods for massive producing of satellite cells.

• Food Science of Animal Resources
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• v.30 no.6
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• pp.918-922
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• 2010

Due to the large amount of beef imported from the USA to Korea, Korean consumers have become increasingly interested in the country of origin since it can affect market prices. Previously, Bos indicus and Bos taurus-specific markers were developed for the purpose of cattle breed identification, specifically discrimination of Australian beef. In this study, six SNP markers derived from Illumina 50K bovine SNP chip data were used for the discrimination between Korean cattle (Hanwoo) and imported beef from USA. PCR-RFLP genotyping methods were also developed, which indicates that these markers can be applied relatively easily compared to other markers. Taking into account a discrimination rate of 55% based on MC1R marker between Hanwoo and imported beef from USA, two additional markers, SNPs 23803 and 34776, were ideal and resulted in probability of identification of 0.942 and probability of misjudgment of 0.03. Therefore, the markers developed in this study can greatly contribute to the correct discrimination between beef from USA and Hanwoo beef.

• Journal of the Korean Chemical Society
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• v.48 no.5
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• pp.483-490
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• 2004

We have developed a novel polymerase chain reaction (PCR)-microchip gel electrophoresis (MGE) method based on the sieving gel mixture of commercially available poly(vinylpyrrolidone) (PVP) and hydroxy ethyl cellulose (HEC) for the rapid detection and diagnosis of the orf virus (ORFV) from Korean indigenous goat. After amplification of 594-bp DNA fragment from the B2L gene of ORF virus, the amplicon was analyzed by the MGE separation. The glass microfluidic chip (64 mm total length (36 mm effective length)${\times}$90 ${\mu}$m width${\times}$20 ${\mu}$m depth) allowed the fast detection and diagnosis of ORFV in the mixture of 1.0% PVP ($M_r$ 360,000) and 1.0% HEC ($M_r$250,000) as a sieving matrix with better resolution and reproducibility of DNA fragments. Under the electric field of 277.8 V/cm, the 594-bp DNA was analyzed within 4 min. Compared to traditional slab gel electrophoresis, the PCR-MGE method was twenty times faster and an effective clinical method for the quantitative analysis of ORFV.

• Clinical and Experimental Reproductive Medicine
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• v.39 no.2
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• pp.87-93
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• 2012

Objective: Lin28 has been known to control the proliferation and pluripotency of embryonic stem cells. The purpose of this study was to determine the downstream effectors of Lin28 in mouse embryonic stem cells (mESCs) by RNA interference and microarray analysis. Methods: The control siRNA and Lin28 siRNA (Dharmacon) were transfected into mESCs. Total RNA was prepared from each type of transfected mESC and subjected to reverse transcription-polymerase chain reaction (RT-PCR) analysis to confirm the downregulation of Lin28. The RNAs were labeled and hybridized with an Affymetrix Gene-Chip Mouse Genome 430 2.0 array. The data analysis was accomplished by GenPlex 3.0 software. The expression levels of selected genes were confirmed by quantitative real-time RT-PCR. Results: According to the statistical analysis of the cDNA microarray, a total of 500 genes were altered in Lin28-downregulated mESCs (up-regulated, 384; down-regulated, 116). After differentially expressed gene filtering, 31 genes were selected as candidate genes regulated by Lin28 downregulation. Among them, neuropeptide Y5 receptor and oocyte-specific homeobox 5 genes were significantly upregulated in Lin28-downregulated mESCs. We also showed that the families of neuropeptide Y receptor (Npyr) and oocyte-specific homeobox (Obox) genes were upregulated by downregulation of Lin28. Conclusion: Based on the results of this study, we suggest that Lin28 controls the characteristics of mESCs through the regulation of effectors such as the Npyr and Obox families.

• Parasites, Hosts and Diseases
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• v.49 no.4
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• pp.341-347
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• 2011

Acanthamoeba infection is difficult to treat because of the resistance property of Acanthamoeba cyst against the host immune system, diverse antibiotics, and therapeutic agents. To identify encystation mediating factors of Acanthamoeba, we compared the transcription profile between cysts and trophozoites using microarray analysis. The DNA chip was composed of 12,544 genes based on expressed sequence tag (EST) from an Acanthamoeba ESTs database (DB) constructed in our laboratory, genetic information of Acanthamoeba from TBest DB, and all of Acanthamoeba related genes registered in the NCBI. Microarray analysis indicated that 701 genes showed higher expression than 2 folds in cysts than in trophozoites, and 859 genes were less expressed in cysts than in trophozoites. The results of real-time PCR analysis of randomly selected 9 genes of which expression was increased during cyst formation were coincided well with the microarray results. Eukaryotic orthologous groups (KOG) analysis showed an increment in T article (signal transduction mechanisms) and O article (posttranslational modification, protein turnover, and chaperones) whereas significant decrement of C article (energy production and conversion) during cyst formation. Especially, cystein proteinases showed high expression changes (282 folds) with significant increases in real-time PCR, suggesting a pivotal role of this proteinase in the cyst formation of Acanthamoeba. The present study provides important clues for the identification and characterization of encystation mediating factors of Acanthamoeba.

• Reproductive and Developmental Biology
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• v.32 no.2
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• pp.71-79
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• 2008

Surface-enhanced laser desorption and ionization time-of-flight mass spectrometry (SELDI-TOF MS) is one of the recently developed proteomic technologies which is based on capturing proteins and peptides by chemically modified surfaces and highly sensitive for the analysis of complex biological samples. In the present study, to gain insights into oocyte maturation and early embryo development, SELDI-TOF-MS was used to find the protein candidates that are specifically or prominently expressed in porcine oocytes at the in vitro matured metaphase II (MIIl) and germinal vesicle (GV) stages. By selected CM10 chip, 16 candidates were found to be up-regulated in GV stage oocytes compared with in MII stage oocytes, their molecular weights were 8,180 (2 candidates), 10,226 (5 candidates), 15,767 (5 candidates) and 16,770 (4 candidates) Da respectively. And the expression of 29 candidates were higher in MII than in GV stage oocytes, their molecular weight were 10,832 (3 candidates), 17,743 (8 candidates), 20,122 (3 candidates), 22,131 (3 candidates), 24,857 (7 candidates) and 33,507 (5 candidates) Da, respectively. The expression of selected 13 candidates (0.2 and 1.0 % error tolerances) were analyzed using real time RT-PCR. The proteins that differentially regulated during oocyte in vitro maturation in the pigs may be potential biomarkers of oocyte maturation and quality.

• Korean Journal of Poultry Science
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• v.40 no.3
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• pp.223-234
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• 2013

Poultry industry is abounding day by day as it engrosses less cost of investment per bird as compared to large animals. Poultry have the most copious genomic tool box amongst domestic animals for the detection of quantitative trait loci (QTL) and marker assisted selection (MAS). Use of multiple markers and least square techniques for mapping of QTL affecting quality and production traits in poultry is in vogue. Examples of genetic tests that are available to or used in industry programs are documented and classified into causative mutations (direct markers), linked markers in population-wide linkage disequilibrium (LD) with the QTL (LD markers), and linked markers in population wide equilibrium with the QTL (LE markers). Development of genome-wide SNP assays, role of 42 K, 60 K (Illumina) and 600 K (Affymetrix$^{(R)}$ Axim$^{(R)}$) SNP chip with next generation sequencing for identification of single nucleotide polymorphism (SNP) has been documented. Hybridization based, PCR based, DNA chip and sequencing based are the major segments of DNA markers which help in conducting of MAS in poultry. Economic index-marker assisted selection (EI-MAS) provides platform for simultaneous selection for production traits while giving due weightage to their marginal economic values by calculating predicted breeding value, using information on DNA markers which are normally associated with relevant QTL. Understanding of linkage equilibrium, linkage dis-equilibrium, relation between the markers and gene of interest are quite important for success of MAS. This kind of selection is the most useful tool in enhancing disease resistance by identifying candidate genes to improve the immune response. The application of marker assisted selection in selection procedures would help in improvement of economic traits in poultry.

• Korean Journal of Head & Neck Oncology
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• v.23 no.1
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• pp.21-25
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• 2007

Background：Squamous cell carcinoma(SCC)of the palatine tonsils represents approximately 15-23% of all intraoral SCC. The most frequently reported risk factors for oropharyngeal cancer are smoking and alcohol. In a recent overview of HPV and tonsillar squamous cell carcinoma(TC), 51% contained HPV DNA, and HPV-16 being the most frequent type. We aimed to clarify whether HPV directly effects on the oncogenesis and biologic behavior of TC by comparison with infection prevalence, and physical status of virus. Material and Method：We used HPV genotyping DNA chip(Biocore, Korea, Seoul) arrayed by multiple oligonucleotide probes of L1 sequence of 26 types of HPV and HPV genotypes are identified by fluorescence scanner. The copy numbers of HPV E2 and E6 open reading frames(ORF) were assessed using a TaqMan-based 5'-exonuclease quantitative real-time PCR assay. The ratio of E2 to E6 copy numbers was calculated to determine the physical status of HPV-16 viral gene. Results：We observed a significant difference in HPV prevalence between 52 TCs and 69 CFTs(73.1% vs. 11.6%), and most of the HPVs were type 16(87.2%)and non-episomal(94.1%) state. Conclusions：This study regarding HPV infection prevalence and mechanism in the largest population of palatine tonsillar squamous cell carcinoma with chronic follicular tonsillitis revealed significant difference pf HPV prevalence between TC and CFT. Most of HPV were 16 type and integrated or mixed, HPV-16 integration could be directly related to tonsillar carcinogenesis.