• Biomolecules & Therapeutics
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• v.15 no.4
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• pp.252-260
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• 2007

As it is needed to assay possible feasibility of extrapolation between in vivo and in vitro systems and to develop a new in vitro method for toxicity testing, we investigated global gene expression from both animal and cell line treated with thioacetamide (TAA) and compared between in vivo and in vitro genomic profiles. For in vivo study, mice were orally treated with TAA and sacrificed at 6 and 24 h. For in vitro study, TAA was administered to a mouse hepatic cell line, BNL CL.2 and sampling was carried out at 6 and 24 h. Hepatotoxicity was assessed by analyzing hepatic enzymes and histopathological examination (in vivo) or lactate dehydrogenase (LDH) assay and morphological examination (in vitro). Global gene expression was assessed using microarray. In high dose TAA-treated group, there was centrilobular necrosis (in vivo) and cellular toxicity with an elevation of LDH (in vitro) at 24 h. Statistical analysis of global gene expression identified that there were similar numbers of altered genes found between in vivo and in vitro at each time points. Pathway analysis identified several common pathways existed between in vivo and in vitro system such as glutathione metabolism, bile acid biosynthesis, nitrogen metabolism, butanoate metabolism for hepatotoxicty caused by TAA. Our results suggest it may be feasible to develop toxicogenomics biomarkers by comparing in vivo and in vitro genomic profiles specific to TAA for application to prediction of liver toxicity.

• Molecular & Cellular Toxicology
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• v.3 no.3
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• pp.177-184
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• 2007

As a possible feasibility of the extrapolation between in vivo and in vitro systems, we investigated the global gene expression from both mouse liver and mouse hepatic cell line treated with hepatotoxic chemical, acetaminophen (APAP), and compared between in vivo and in vitro genomic profiles. For in vivo study, mice were orally treated with APAP and sacrificed at 6 and 24 h. For in vitro study, APAP were administered to a mouse hepatic cell line, BNL CL.2 and sampling was carried out at 6 and 24 h. Hepatotoxicity was assessed by analyzing hepatic enzymes and histopathological examination (in vivo) or lactate dehydrogenase (LDH) assay and morphological examination (in vitro). Global gene expression was assessed using microarray. In high dose APAPtreated group, there was centrilobular necrosis (in vivo) and cellular toxicity with the elevation of LDH (in vitro) at 24 h. Statistical analysis of global gene expression identified that there were similar numbers of altered genes found between in vivo and in vitro at each time points. Pathway analysis identified glutathione metabolism pathway as common pathways for hepatotoxicty caused by APAP. Our results suggest it may be feasible to develop toxicogenomics biomarkers or profiles by comparing in vivo and in vitro genomic profiles specific to this hepatotoxic chemical for application to prediction of liver toxicity.

• Asian Pacific Journal of Cancer Prevention
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• v.17 no.sup3
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• pp.155-160
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• 2016

Breast cancer (BC) is the second most common cancer in the world and by far the most frequent cancer among women, with an estimated 1.67 million new cancer cases diagnosed in 2012 (25% of all cancers). Polygene expression analysis is used to predict the prognosis and determine the most appropriate treatment regimen. The objective of this study was to examine the gene expression profiles of SIRT3, HRAS, LSP1, SCUBE2 and AP2A2 in Iranian women with BC.A total of 136 patients including healthy controls were categorized into three groups based on the relapse of the disease. Expression of desired genes in formalin-fixed, paraffin embedded tissues collected from all groups of participants was analyzed via the RT PCR method. RNA extraction and cDNA synthesis were performed then real-time quantitative PCR was carried out. Gene expression analysis revealed that the expression of SIRT3 was equal among patient and control groups. LSP1 was down regulated in all patient groups relative to controls but reduced expression in the metastatic group relative to the non-metastatic one was not significant. HRAS was significantly overexpressed in total and metastatic tumor samples versus normal but not in non-metastatic cases. SCUBE2 expression showed significant over-expression in both overall tumor samples and the non-metastatic group as compared to normal tissues. Gene expression level of AP2A2 in all groups was not detectable. Our data are compatible with a tumor suppressor role of LSP1 related to potential prognostic factor for tumor recurrence and outcome. This study for the first time assayed the prognostic value and changes in the expression of SIRT3, LSP1, HRAS, SCUBE2 and AP2A2 genes in women with breast cancer in the Iranian population and findings confirmed potential biomarker and prognostic capability of these genes. Such expression profiling data can critically improve prognosis and treatment decisions in cancer patients.

• Journal of Plant Biotechnology
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• v.29 no.2
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• pp.93-98
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• 2002

A VP6 fragments was subcloned with BamHI in the binary pMBP-1 vector under Califlower Mosaic Virus (CaMV) 355 promoter and neomycin phosphotransferase II (npt II) gene. The recombinant binary vector was mobilized into Agrobacterium-tumefaciens LBA4404 by the freeze-thaw method and potato (Solanum tubensum L. cv Desiree) was transformed by modified leaf-disc cocultivation. Shoots were induced on MS medium with 0.01 mg/L NAA, 0.1 mg/L GA$_3$, 2.0 mg/L Zeatin, 100.0 mg/L kanamycin, 500.0 mg/L carbenicillin. In order to identify the copy number of VP6 into potato plant, total genomic DNA was isolated from transgenic potato and analysed by Southern blotting. Genomic DNA and total mRNA analysis demonstrated the incorporation of the foreign gene into the potato genome, as well as their transcription.

• Journal of Life Science
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• v.32 no.4
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• pp.279-284
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• 2022

This study was conducted to establish a genetic evaluation system applicable to general farms for improving cows raised on farms. The analysis used Best Linear Unbiased Prediction (BLUP) and Genomic Best Linear Unbiased Prediction (GBLUP) for 619 cows raised in Gyeonggi-do Province and compared and analyzed the accuracy of the estimated breeding value according to four traits (carcass weight, loineye muscle area, back fat thickness, and marbling). In the case of the GBLUP method, the size of the reference population was divided into different four groups and analyzed. The analysis results confirmed that the accuracy of the breeding value of each trait increased as the size of the GBLUP reference population increased. Comparing the accuracy of the breeding values estimated using the BLUP and GBLUP methods, it was confirmed that when the breeding values were estimated using the GBLUP method, they increased by 0.10, 0.09, 0.09, and 0.11 for carcass weight, eye muscle area, back fat thickness, and marbling scores, respectively. Applying the GBLUP method to the evaluation and selection of cows can enable precise and accurate individual selection, while increasing the size of the reference population can make even more accurate individual selection possible, thus increasing selection efficiency.

• Journal of Marine Life Science
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• v.6 no.1
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• pp.38-46
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• 2021

The blood clam, Tegillarca granosa, is economically important in marine bivalve and is used in fisheries industry among western Pacific Ocean Coasts especially in Korea, China, and Japan. The number of chromosomes in the blood clam is known as 2n=38, but the genome size and genetic information of the genome are not still clear. In order to predict the genomic size of the T. granosa, the in-silico analysis analysed the genomic size using short DNA sequence information obtained using the NGS Illumina HiSeq platform. As a result, the genomic size of T. granosa was estimated to be 770.61 Mb. Subsequently, a draft genome assembly was performed through the MaSuRCA assembler, and a simple sequence repeat (SSR) analysis was done by using the QDD pipeline. 43,944 SSRs were detected from the genome of T. granosa and 69.51% di-nucleotide, 16.68% trinucleotide, 12.96% tetra-nucleotide, 0.82% penta-nucleotide, and 0.03% hexa-nucleotide were consisted. 100 primer sets that could be used for genetic diversity studies were selected. In the future, this study will help identify the genetic diversity of T. granosa and population genetic studies, and further identify the classification of origin between homogenous groups.

• Journal of Microbiology and Biotechnology
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• v.17 no.8
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• pp.1242-1248
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• 2007

Genomic analysis of a hyperthermophilic archaeon, Thermococcus onnurineus NA1 [1], revealed the presence of an open reading frame consisting of 1,377 bp similar to ${\alpha}$-amylases from Thermococcales, encoding a 458-residue polypeptide containing a putative 25-residue signal peptide. The mature form of the ${\alpha}$-amylase was cloned and the recombinant enzyme was characterized. The optimum activity of the enzyme occurred at $80^{\circ}C$ and pH 5.5. The enzyme showed a liquefying activity, hydrolyzing maltooligosaccharides, amylopectin, and starch to produce mainly maltose (G2) to maltoheptaose (G7), but not pullulan and cyclodextrin. Surprisingly, the enzyme was not highly thermostable, with half-life ($t_{1/2}$) values of 10 min at $90^{\circ}C$, despite the high similarity to ${\alpha}$-amylases from Pyrococcus. Factors affecting the thermostability were considered to enhance the thermo stability. The presence of $Ca^{2+}$ seemed to be critical, significantly changing $t_{1/2}$ at $90^{\circ}C$ to 153 min by the addition of 0.5 mM $Ca^{2+}$. On the other hand, the thermostability was not enhanced by the addition of $Zn^{2+}$ or other divalent metals, irrespective of the concentration. The mutagenetic study showed that the recovery of zinc-binding residues (His175 and Cys189) enhanced the thermo stability, indicating that the residues involved in metal binding is very critical for the thermostability.

• Horticultural Science & Technology
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• v.33 no.6
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• pp.869-876
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• 2015

Wild relative species of domesticated crops are useful genetic resources for improving agronomic traits. Cytogenetic investigations based on chromosome composition provide insight into basic genetic and genomic characteristics of a species that can be exploited in a breeding program. Here, we used FISH analysis to characterize the ploidy level, chromosome constitution, and genomic distribution o f 5S and 4 5S r ibosomal DNA (rDNA) in four wild Cucurbitaceae species, namely, Citrullus lanatus (Thunb.) Mansf. var. citroides L. H. Bailey (2n = 22), Melothria japonica Maxim. (2n = 22), Sicyos angulatus L. (2n = 24), and Trichosanthes kirilowii Maxim. (2n = 66, 88, 110 cytotypes), collected in different areas of Korea. All species were diploids, except for T. kirilowii, which included hexa-, octa-, and decaploid cytotypes (2n = 6x = 66, 8x = 88, and 10x = 110). All species have small metaphase chromosomes in the range of $2-5{\mu}m$. The 45S rDNA signals were localized distally compared to the 5S rDNA. C. lanatus var. citroides and M. japonica showed one and two loci of 45S and 5S rDNA, respectively, with co-localization of rDNA signals in one M. japonica chromosome. S. angulatus showed two co-localized signals of 5S and 45S rDNA loci. The hexaploid T. kirilowii cytotype showed five signals each for 45S and 5S rDNA, with three being co-localized. This is the first report of hexaploid and decaploid cytotypes in T. kirilowii. These results will be useful in future Cucurbitaceae breeding programs.

• IMMUNE NETWORK
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• v.8 no.4
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• pp.137-142
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• 2008

Background: CD11c, also known as integrin alpha x, is one of the optimum markers of dendritic cells. However, the regulation of the CD11c expression in mouse has not been identified yet. In this study, in order to analyze the regulation of CD11c expression, the promoter of CD11c was cloned and characterized. Methods: To identify the promoter portion, various sizes of what are considered to be CD11c promoter fragments was amplified by polymerase chain reaction (PCR), using mouse genomic DNA as a template. After sequence was obtained, these fragments were transfected into various cell lines including mouse dendritic cell lines such as JAWSII and DC2.4 and L929 as control cell line.. The promoter activity of three promoter fragments was measured and compared by luciferase activity in the transfected cells. Results: Three clones with size of 1kb, 3kb and 6kb were obtained from mouse genomic DNA. Flow cytometry analysis of JAWSII cells revealed that 52% of the cells expressed CD11c, which was confirmed by RT-PCR analysis. On the contrary, L929 and DC 2.4 cells did not express CD11c. The CD11c+ JAWSII cells were enriched from 52% to 90% with cell sorter. The comparative luciferase activity analyisis demonstrated that the region responsible for tissue specific expression was contained within -3 kb and the clone with size of 3 kb particularly showed higher luciferase activity than 6 kb and 1 kb clones. Conclusion: The CD11c promoter region containing the region responsible for tissue specificity was successfully cloned and -3 kb region showed the highest activity.

• Journal of fish pathology
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• v.10 no.2
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• pp.87-95
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• 1997

Baculovirus associated with white spot syndrome (WSBV) is the causative agent of a disease with high mortalities and causes severe damage to shrimp cultures. In this study, we analyzed a recombinant clone (E3) obtained from a viral genomic library to characterize the causative agent in diseased shrimp Penaeus chinensis with white spot syndrome. According to the analysis of nucleotide sequence of E3, this clone did not showed considerable sequence homology with those of other known viruses, including baculovirus Autographa californica nuclear polyhedrosis virus (AcNPV), indicating that WSBV is a novel virus causing a serious disease in P. chinensis. Based on the sequence of E3 clone, a pair of PCR primers was designed. After 30 cycles of amplification, a specific product of the expected size was detected only if the total nucleic acids extracted from the diseased shrimp was used as a template DNA, suggesting that this method can be used to diagnose the virus infection in diseased shrimp.