• Asian-Australasian Journal of Animal Sciences
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• v.19 no.3
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• pp.329-334
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• 2006

Adipocyte-specific secretory factor (ADSF)/resistin, a hormone, is a small cysteine-rich protein secreted from adipose tissue and has been implicated in modulating adipogenesis in humans and rodents. The objective of this study was to clone a gene encoding ADSF/resistin and to characterize its function in Korean Native Cattle (Hanwoo). The coding sequence was 330 base pairs and it encoded a protein of 109 amino acids. An NCBI BLAST-search revealed the cloned cDNA fragment shared significant homology (82%) with the cDNA encoding the human ADSF/resistin. The nucleotide sequence homology of the Hanwoo sequence was 73% and 64% for the rat and mouse, respectively. A 654 bp ADSF/resistin gene promoter was cloned and putative binding sites of transcription factors were identified. Tissue distribution of ADSF mRNA was examined in liver, skeletal muscles (tenderloin, biceps femoris), subcutaneous fat, and perirenal fat by RT-PCR. ADSF mRNAs were detected in fat tissues but not in liver and muscles, suggesting that ADSF/resistin expression may be induced during adipogenesis. Although, the physiological function of ADSF/resistin in the cow remains to be determined, these data indicate ADSF is related to the adipocyte phenotype and may have a possibly regulatory role in adipocyte function.

• Journal of Computing Science and Engineering
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• v.11 no.4
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• pp.121-129
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• 2017

Feature selection has been widely established as an efficient technique for microarray data analysis. Feature selection aims to search for the most important feature/gene subset of a given dataset according to its relevance to the current target. Unsupervised feature selection is considered to be challenging due to the lack of label information. In this paper, we propose a novel method for unsupervised feature selection, which incorporates embedded learning and $l_{2,1}-norm$ sparse regression into a framework to select genes in microarray data analysis. Local tangent space alignment is applied during embedded learning to preserve the local data structure. The $l_{2,1}-norm$ sparse regression acts as a constraint to aid in learning the gene weights correlatively, by which the proposed method optimizes for selecting the informative genes which better capture the interesting natural classes of samples. We provide an effective algorithm to solve the optimization problem in our method. Finally, to validate the efficacy of the proposed method, we evaluate the proposed method on real microarray gene expression datasets. The experimental results demonstrate that the proposed method obtains quite promising performance.

• Korean Journal of Microbiology
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• v.35 no.1
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• pp.28-34
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• 1999

Fragmentation vectors are used to analyze function and genomic structure of a gene of interest by creating deletion derivatives of large fragments of genomic DNA cloned as yeast artificial chromosomes (YACs). Herein, we developed a new hicistronic fragmentation vector that contains internal ribosomal entry sile (IRES) of encephalomyocarditis vin~s (EMCV) and $\beta$-galactosidase as a reporter gene. This vector system provides a novcl loo1 to analyze expression patterns of a gene of interest due to simultaneous expression of a target gene as well as $\beta$-galactosidase driven from a single message. In addition, the bicistronic fragmentation vector contains four rare-cutting restriction enzyme sites in the polycloning sites which can be used to conveniently insert any kinds of genes and therefore facilitates targeting DNA scgments into YAC by means of homologous recombination. This approach establishes a paradigm for manipulation of mammalian DNA segments and characterization of expression and regulatory regions of mammalian gene cloned as YAC.

• Clinical and Experimental Reproductive Medicine
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• v.47 no.1
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• pp.68-76
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• 2020

Objective: Since sperm abnormalities are known to be a major reason for recurrent pregnancy loss (RPL), any defects in DNA structure and chromatin condensation can place embryos at risk in the early stage of development and implantation. As antioxidants such as vitamin C may play a protective role against the destruction of protamine genes in sperm chromatin, this study was conducted to evaluate the effects of vitamin C on chromatin and the expression of protamine genes in the male partners of couples with RPL. Methods: Twenty male partners of couples with RPL were selected as the intervention group and received vitamin C supplementation (250 mg daily for 3 months). Healthy fertile men (n = 20) were included as controls. Sperm chromatin, DNA integrity, and the expression levels of protamine genes were evaluated before and after treatment. Results: Significant differences were found in sperm morphology, protamine deficiency, and apoptosis between the two groups and before and after vitamin C administration. A significant change was found in mRNA levels of PRM1, PRM2, and the PRM1/PRM2 ratio after treatment. Conclusion: Daily oral administration of vitamin C may improve human sperm parameters and DNA integrity by increasing protamine gene expression levels in the male partners of couples with RPL. The beneficial effects of vitamin C supplementation as an antioxidant for the male partners of couples with RPL could lead to improved pregnancy outcomes in these cases.

• Journal of Physiology & Pathology in Korean Medicine
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• v.19 no.6
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• pp.1585-1593
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• 2005

The genetic effects of restraint stress challenge on HPA axis and the therapeutic effect of Boshimgeonbi-tang on the stress were studied with cDNA microarray analyses, RT-PCR on hypothalamus using an immobilization-stress mice as an animal model. Male CD-1 mice were restrained in a tightly fitted and ventilated vinyl holder for 2hrs once a day, and this challenge was repeated for seven· consecutive days. In the change of body weight it showed that the Boshimgeonbi-tang is effected recovery on weight loss caused by the immobilization-stress. Seven days later, total RNA was extracted from the organs of the mouse, body-labeled with $CyDye^{TM}$ fluorescence dyes and then hybridized to CDNA microarray chip. Scanning and analyzing the array slides were carried out using GenePix4000 series scanner and GenePix $Pro^{TM}$ analyzing program, respectively. The expression profiles of 109 genes out of 6000 genes on the chip were significantly modulated in hypothalamus by the immobilization stress. Energy metabolism-, lipid metabolism-, apoptosis-, stress protein, transcriptional factor, and signal transduction-related genes were transcriptionally activated whereas DNA repair-, protein biosysthesis-, and structure integrity-related genes were down-regulated in hypothalamus. The 58 genes were up-regulated by the mRNA expression folds of 1.5 to 7.9. and the 51 genes were down-regulated by 1.5 - 5.5 fold. The 11 genes among them were selected to confirm the expression profiles by RT-PCR. The mRNA expression levels of Tnfrsf1a (apoptosis), Calm2 (cell cycle), Bag3 (apoptosis), Ogg1 (DNA repair), Aatk (apoptosis), Dffa (apoptosis), Fkbp5 (protein folding) were restored to the normal one by the treatment of Boshimgeonbi-tang.

• Fisheries and Aquatic Sciences
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• v.15 no.3
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• pp.221-231
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• 2012

The marine medaka Oryzias dancena choriogenin H gene (odChgH) and its mRNA expression during estradiol-$17{\beta}$ (E2) exposure were characterized. At the amino acid level, the choriogenin H protein is predicted to possess the conserved repetitive N-terminal region, as well as zona pellucida (ZP) and Trefoil factor family (TFF) domains. At the genomic level, odChgH has an eight-exon organization with a distribution pattern of transcription factor binding sites in the 5'-upstream region, which is commonly found in other estrogen-responsive genes. The tissue distribution pattern of odChgH mRNA was found to be gender-specific, whereby females showed a higher expression level and wider tissue distribution than did males. During embryonic development, odChgH mRNA was robustly detected from the stage of visceral blood vessel formation. Experimental E2 exposure of males resulted in odChgH mRNA being induced not only in the liver, but also in other several tissues. The E2-mediated induction was fairly dose-dependent. The basal expression levels of hepatic odChgH mRNA were lower in males that were acclimated to 30 ppt salinity than in those acclimated to 0 or 15 ppt salinity. In contrast, the inducibility of odChgH mRNA during E2 exposure was greater in seawater-acclimated fish than in brackish water- or freshwater-acclimated fish.

• Proceedings of the Korean Society for Applied Microbiology Conference
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• 2004.06a
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• pp.257-257
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• 2004

• International Journal of Industrial Entomology and Biomaterials
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• v.11 no.2
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• pp.113-117
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• 2005

A chymotrpsin gene homologue was cloned from the mulberry longicorn beetle, Apriona germari. The A. germari chymotrypsin cDNA contains an ORF of 950 nucleotides capable of encoding a 283 amino acid polypeptide with a predicted molecular mass of 29151 Da and pI of 9.38. The A. germari chymotrypsin has conserved six cysteine residues and active triad formed by His, Asp and Ser. The deduced amino acid sequence of the A. germari chymotrypsin cDNA was closest in structure to the Anthonomus grandis chymotrypsin. Northern blot analysis revealed that A. germari chymotrypsin showed the midgut-specific expression.

• Genomics & Informatics
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• v.6 no.4
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• pp.202-209
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• 2008

Biological pathways are known as collections of knowledge of certain biological processes. Although knowledge about a pathway is quite significant to further analysis, it covers only tiny portion of genes that exists. In this paper, we suggest a model to extend each individual pathway using a microarray expression data based on the known knowledge about the pathway. We take the Rosetta compendium dataset to extend pathways of Saccharomyces cerevisiae obtained from KEGG (Kyoto Encyclopedia of genes and genomes) database. Before applying our model, we verify the underlying assumption that microarray data reflect the interactive knowledge from pathway, and we evaluate our scoring system by introducing performance function. In the last step, we validate proposed candidates with the help of another type of biological information. We introduced a pathway extending model using its intrinsic structure and microarray expression data. The model provides the suitable candidate genes for each single biological pathway to extend it.

• Proceedings of the SCSK Conference
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• 2003.09a
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• pp.741-762
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• 2003

Ginsenosides, the major active ingredients of ginseng, show a variety of biomedical efficacies such as anti-aging, anti oxidation and anti-inflammatory activities. To understand the effects of compound K (20-O-D-glucopyranosyl-20 (S)-protopanaxadiol), one of the major metabolite of ginsenosides on the skin, we assessed the expression level of ∼ 100 transcripts in compound K-treated HaCaT cells using cDNA microarray analysis. Compound K treatment induced differential expression of 21 genes, which have been reported to be involved in the organization of ECM structure as well as defense responses in human skin cells. One of the most interesting findings is 2-fold increase in hyaluronan synthase2 (HAS2) gene expression by compound K. We found that change in expression of HAS2 gene represents a specific response of HaCaT cells to compound K because hyaluronan synthase 1, 3 was not changed by treatment with compound K. We also demonstrated that the compound K effectively induced hyaluronan synthesis in human skin cells and hairless mouse skin. The human clinical study indicates that topical application of compound K-containing oil-in-water emulsion showed improvement of xerosis, wrinkle and fine lines in the aged skin. We concluded that compound K has anti-aging effects by the induction of HAS2 gene expression and following hyaluronan synthase.