• Genomics & Informatics
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• v.21 no.3
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• pp.36.1-36.19
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• 2023

The LIM domain-containing proteins are dominantly found in plants and play a significant role in various biological processes such as gene transcription as well as actin cytoskeletal organization. Nevertheless, genome-wide identification as well as functional analysis of the LIM gene family have not yet been reported in the economically important plant sorghum (Sorghum bicolor L.). Therefore, we conducted an in silico identification and characterization of LIM genes in S. bicolor genome using integrated bioinformatics approaches. Based on phylogenetic tree analysis and conserved domain, we identified five LIM genes in S. bicolor (SbLIM) genome corresponding to Arabidopsis LIM (AtLIM) genes. The conserved domain, motif as well as gene structure analyses of the SbLIM gene family showed the similarity within the SbLIM and AtLIM members. The gene ontology (GO) enrichment study revealed that the candidate LIM genes are directly involved in cytoskeletal organization and various other important biological as well as molecular pathways. Some important families of regulating transcription factors such as ERF, MYB, WRKY, NAC, bZIP, C2H2, Dof, and G2-like were detected by analyzing their interaction network with identified SbLIM genes. The cis-acting regulatory elements related to predicted SbLIM genes were identified as responsive to light, hormones, stress, and other functions. The present study will provide valuable useful information about LIM genes in sorghum which would pave the way for the future study of functional pathways of candidate SbLIM genes as well as their regulatory factors in wet-lab experiments.

• The Journal of Korean Medicine Ophthalmology and Otolaryngology and Dermatology
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• v.21 no.3
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• pp.36-51
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• 2008

Objective : This study investigated the effects of PR(Pinelliae Rhizoma) on gene expression of lung tissue resected from asthma induced mice using intra-nasal instillation. Methods : Gene expression levels were measured using a microarray technique, and a functional analysis on these genes was conducted. Results : A total of 3270 genes were up-regulated or down-regulated, 860 genes which were lowered by induction of asthma were restored to those of naive animals, Furthermore hand, 1235 genes were lowered to normal levels, which were elevated by induction of asthma. Most of changed genes were involved in signalling pathways. Genes in which expression levels were restored by oral administration of PR were involved in MAPK pathway, focal adhesion, and regulation of actin cytoskeleton etc. Genes of which expression levels were lowered by oral administration of PR were involved in rhodopsin-like receptor activity, zinc ion binding and ATP binding. These genes were also involved in neuroactive ligand receptor interaction, the JAK-STAT signaling pathway and also the T-cell receptor signaling pathway. Conclusion : These results demonstrate the strong possibility that the mechanisms of PR on asthma are involved in neuroactive ligand receptor interaction pathway or related molecules.

• Biomedical Science Letters
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• v.10 no.2
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• pp.65-73
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• 2004

I report that single-stranded antisense as a part of large circular (LC-) genomic DNA of recombinant M13 phage exhibits enhanced stability, sequence specific antisense activity, and no need for target site search. A cDNA fragment (708 bp) of rat TNF-$\alpha$ was inserted into a phagemid vector, and TNF-$\alpha$ antisense molecules (TNF$\alpha$-LCAS) were produced as single-stranded circular DNA. When introduced into a rat monocyte/macrophage cell line, WRT7/P2, TNF$\alpha$-LCAS was able to ablate LPS-induced TNF-$\alpha$ mRNA to completion. The antisense effect of TNF$\alpha$-LCAS was shown to be sequence-specific because expressions of three control genes ($\beta$-actin, GAPDH and IL-1$\beta$) were not significantly altered by the antisense treatment. Further, TNF$\alpha$-LCAS was found to be highly efficacious as only 0.1 $\mu$g (0.24 nM) of TNF$\alpha$-LCAS was sufficient to block TNF-$\alpha$ expression in 1$\times10^5$ WRT7/P2 cells. I have also observed specific antisense activity in reduction of NF-$\kappa$B gene expression. The results suggest that an antisense sequence as a part of single-stranded circular genomic DNA has a specific antisense activity.

• Proceedings of the Korean Society of Embryo Transfer Conference
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• 2002.11a
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• pp.100-100
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• 2002

As an preliminary experiment for making transgenic animals producing human follicle stimulating hormone (hFSH), we tried to express recombinant hFSH gene in vitro. hFSH is a heterodimeric glycoprotein hormone produced in the anterior pituitary gland. The hormone is essential in the regulation of reproductive processes, such as follicular development and ovulation. Genes encoding the common gonadotrophin alpha subunit and FSH-specific beta subunit were inserted into retroviral vectors under the control of the rat beta actin promoter. Gene transfer to the Chinese hamster ovary (CHO) cells was done by infection of the retroviruses harvested from PT67 packaging cells transfected with recombinant retrovirus vector DNA. After selection with G4l8, PCR and RT-PCR analyses of the G4l8-resistant CHO cells showed successful transfer and expression of both ${\alpha}$ and ${\beta}$ fragments of the FSH gene.

• Journal of Microbiology and Biotechnology
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• v.14 no.4
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• pp.737-744
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• 2004

A multiplex polymerase chain reaction (PCR) was developed for the simultaneous detection and differentiation among Vairimorpha spp. and Nosema spp. and identification of Vairimorpha necatrix from Lepidoptera insects. Three sets of primers were selected from different genomic sequences to specifically amplify an 831 bp amplicon within the SSU rRNA gene, specific for both Vairimorpha spp. and Nosema spp. (MSSR primer); a 542 bp amplicon within the SSU rRNA gene, specific for Vairimorpha spp. (VSSU primer); and a 476 bp amplicon within the actin gene, specific for Vairimorpha necatrix (VNAG primer). Using the primers in conjunction with multiplex PCR, it was possible to detect Vairimorpha spp. and Nosema spp. and to differentiate between them. The sensitivity of this PCR assay was approximately 10 spores per milliliter. It is proposed that the multiplex PCR is a sensitive, specific, and rapid tool that can serve as a useful differential diagnostic tool for detecting Vairimorpha spp. and Nosema spp. in Lepidoptera insect.

• International Journal of Industrial Entomology and Biomaterials
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• v.23 no.1
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• pp.137-141
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• 2011

A previous data was provided information for tissuespecific expression genes by means of whole-genome oligonucleotide microarray in the silkworm. We analyzed the tissue-specific expression patterns in the hemocyte tissue on 5 days of 5th instar larvae during the development of $B.$ $mori$. Total 5 candidates pick out from the $Bombyx$ $mori$ Microarray Database (BmMDB; http://silkworm.swu.edu.cn/microarray). To verify the hemocyte-specific expression, we analyzed by semi-quantitative and real-time quantitative RT-PCR using the highly expressed endogenous $Actin$ RNA as an intrinsic reference. In this study, we confirmed that one gene-sw17255- out of 5 candidates expressed in the hemocyte tissue, which was consistent with the previous data. Circulating hemocytes in the body fluid of the $B.$ $mori$ are most powerful target organ for producing biomaterials. We need further studies to find hemocyte-specific promoter region from sw17255 gene. Finally, this result can be applied in creating transgenic silkworms as a biomedical insect.

• Journal of Microbiology
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• v.41 no.2
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• pp.121-128
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• 2003

The identification of genes involved in true hypha formation is important in the study of mechanisms underlying the morphogenetic switch in yeast. We isolated a gene responsible for the morphogenetic switch in Yarrowia lipolytica, which forms true hyphae in response to serum or N-acetylglucosamine. The isolated gene, encoding 847 amino acids, had sequence identities of 27% and 25% with the Bud6 (Aip3) proteins of Saccharomyces cerevisiae and Schizosaccharomyces pombe, respectively. Disruption of this gene, designated YIBUD6, in haploid and diploid strains significantly reduced the ability of Y. lipolytica to switch from the yeast form to the hyphal form in hypha-inducing media. It was also found that YIBud6$\Delta$ mutants were rounder than the wild type when grown in the yeast form. These results indicate that the YIBud6 protein is necessary for hyphal growth and cell polarity in both haploid and diploid Y. lipolytica cells.

• Food Science and Preservation
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• v.14 no.6
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• pp.688-694
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• 2007

To evaluate the human risk of long-term intake of genetically modified (GM) rice, we carried out RT-PCR of housekeeping genes. Housekeeping genes, which show highly uniform expression in living organisms during various stages of development and under different environmental conditions, were normalized by RT-PCR. We assessed the expression of 10 common housekeeping genes (18s rRNA, 25S rRNA, UBC, UBQ5, UBQ10, ACT11, GAPDH, eEF-$1{\alpha}$, ${\beta}$-TUB, GAPDH, ${\beta}$-actin, B2m, G6pd2, Gyk, Gus, Hprt, Cyclophlin A, Tfrc, ${\alpha}$-tubulin and RPL13A) in the liver, stomach, small intestine, large intestine, kidney and spleen of mice fed GM or non-GM rice. We found no significant differences in the expression of housekeeping genes between the two groups of mice.

• Clinical and Experimental Pediatrics
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• v.46 no.2
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• pp.167-172
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• 2003

Purpose : Pulmonary vascular hypertension is a common problem in congenital heart disease, the most common cardiac condition in childhood. However, the mechanisms responsible for this pathologic change, treatment, and prevention are poorly understood. Therefore, we studied the gene expression of vascular endothelial growth factor(VEGF) by using a hypoxic model of the pulmonary artery smooth muscle cells. Methods : The main pulmonary artery and its proximal branches of a 6 wk old Fischer rat were excised. They were cut into multiple small pieces and suspended in DMEM medium supplemented with 20% fetal bovine serum and incubated in 5% $CO_2$-95% air atmosphere. The smooth muscle cells were confirmed by immunostaining with smooth muscle myosin and ${\alpha}$-smooth muscle actin antibodies. The VEGF gene expression in the hypoxic group was compared with the one in control the group as well as the one in the starved group by RT-PCR and Northern blot hybridization. Results : There was no statistically significant difference among the control, hypoxic and starved groups. Conclusion : There are few studies of pulmonary vascular hypertension at the molecular level in Korea. Therefore, we studied the expression of VEGF gene in hypoxic pulmonary vascular smooth muscle cells. Further studies will be needed to find the difference between newly born and adult rats, or human and rat pulmonary vascular smooth muscle cells in gene expression. We hope that the study will lead to a better understanding of pulmonary vascular hypertension.

• Korean Journal of Animal Reproduction
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• v.27 no.1
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• pp.15-23
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• 2003

Lactadherin (formerly known as BA46), a major glycoprotein of the human milk fat globule membrane, is abundant in human breast milk and breast carcinomas and may prevent symptomatic rotavirus infections. In this study, under the control of tissue specific and hormonal inducible mouse whey acidic protein (WAP) promote., the expression pattern of lactadherin (Ltd) in lactogenic hormone-dependent mouse mammary epithelial cell line HC11 were tested. pLNWLtd construct containing 2.4 kilobases of the WAP promoter and 1.5 kilobases of human lactadherin gene was stably transfered into HC11 cells using retroviral vector system. Integration and expression level of the transgene was estimated using PCR and RT-PCR, respectively. Prominent induction of Ltd gene under the WAP promoter was accomplished in the presence of insulin, hydrocortisone and prolactin. Compared to the control (cells cultured with insulin alone), however we observed that the WAP promoter was leaky. These data indicate that luther studies are needed in finding an appropriate promoter other than WAP promoter because of its leakiness.