• Asian-Australasian Journal of Animal Sciences
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• v.27 no.5
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• pp.743-748
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• 2014

The objective of this study was to determine the molecular characteristics of the horse vascular endothelial growth factor alpha gene ($VEGF{\alpha}$) by constructing a phylogenetic tree, and to investigate gene expression profiles in tissues and blood leukocytes after exercise for development of suitable biomarkers. Using published amino acid sequences of other vertebrate species (human, chimpanzee, mouse, rat, cow, pig, chicken and dog), we constructed a phylogenetic tree which showed that equine $VEGF{\alpha}$ belonged to the same clade of the pig $VEGF{\alpha}$. Analysis for synonymous (Ks) and non-synonymous substitution ratios (Ka) revealed that the horse $VEGF{\alpha}$ underwent positive selection. RNA was extracted from blood samples before and after exercise and different tissue samples of three horses. Expression analyses using reverse transcription-polymerase chain reaction (RT-PCR) and quantitative-polymerase chain reaction (qPCR) showed ubiquitous expression of $VEGF{\alpha}$ mRNA in skeletal muscle, kidney, thyroid, lung, appendix, colon, spinal cord, and heart tissues. Analysis of differential expression of $VEGF{\alpha}$ gene in blood leukocytes after exercise indicated a unimodal pattern. These results will be useful in developing biomarkers that can predict the recovery capacity of racing horses.

• Bioinformatics and Biosystems
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• v.2 no.1
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• pp.24-27
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• 2007

Human cell regulatory mechanism is one of suspicious problems among biologists. Here we tried to uncover the human breast cancer cell regulatory mechanism from gene expression data (Marc J. Van de vijver, et. al., 2002) using a module network algorithm which is suggested by Segal, et. al.(2003) Finally, we derived a module network which consists of 50 modules and 10 tree depths. Moreover, to validate this candidate network, we applied a GO enrichment test and known transcription factor-target relationships from Transfac(R) (V. Matys, et. al, 2006) and HPRD database (Peri, S. et al., 2003).

• Mycobiology
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• v.36 no.4
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• pp.211-216
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• 2008

During our studies on the diverse endophytic fungi resident on conifer needles, many species of Cladosporium previously unreported in Korea were encountered. In this paper, we report on two species of Cladosporium from the needles of pine trees (Pinus spp.). Based on analyses of internal transcribed spacer gene sequence, and cultural and micromorphological characteristics, they were identified as C. oxysporum and C. sphaerospermum. Both species have not been hitherto reported in Korea.

• Journal of KIISE:Databases
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• v.34 no.6
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• pp.546-553
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• 2007

As ontologies are used widely, interest for semantic similarity search is also increasing. In this paper, we suggest a query evaluation scheme for k-nearest neighbor query, which retrieves k most similar objects to the query object. We use the best match method to calculate the semantic similarity between objects and use the signature tree to index annotation information of objects in database. The signature tree is usually used for the set similarity search. When we use the signature tree in similarity search, we are required to predict the upper-bound of similarity for a node; the highest similarity value which can be found when we traverse into the node. So we suggest a prediction function for the best match similarity function and prove the correctness of the prediction. And we modify the original signature tree structure for same signatures not to be stored redundantly. This improved structure of signature tree not only reduces the size of signature tree but also increases the efficiency of query evaluation. We use the Gene Ontology(GO) for our experiments, which provides large ontologies and large amount of annotation data. Using GO, we show that proposed method improves query efficiency and present several experimental results varying the page size and using several node-splitting methods.

• Genes and Genomics
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• v.40 no.11
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• pp.1181-1197
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• 2018

Tropical plant rubber tree (Hevea brasiliensis) is the sole source of commercial natural rubber and low-temperature stress is the most important limiting factor for its cultivation. To characterize the gene expression profiles of H. brasiliensis under the cold stress and discover the key cold stress-induced genes. Three cDNA libraries, CT (control), LT2 (cold treatment at $4^{\circ}C$ for 2 h) and LT24 (cold treatment at $4^{\circ}C$ for 24 h) were constructed for RNA sequencing (RNA-Seq) and gene expression profiling. Quantitative real time PCR (qRT-PCR) was conducted to validate the RNA-Seq and gene differentially expression results. A total of 1457 and 2328 differentially expressed genes (DEGs) in LT2 and LT24 compared with CT were respectively detected. Most significantly enriched KEGG pathways included flavonoid biosynthesis, phenylpropanoid biosynthesis, plant hormone signal transduction, cutin, suberine and wax biosynthesis, Pentose and glucuronate interconversions, phenylalanine metabolism and starch and sucrose metabolism. A total of 239 transcription factors (TFs) were differentially expressed following 2 h or/and 24 h of cold treatment. Cold-response transcription factor families included ARR-B, B3, BES1, bHLH, C2H, CO-like, Dof, ERF, FAR1, G2-like, GRAS, GRF, HD-ZIP, HSF, LBD, MIKC-MADS, M-type MADS, MYB, MYB-related, NAC, RAV, SRS, TALE, TCP, Trihelix, WOX, WRKY, YABBY and ZF-HD. The genome-wide transcriptional response of rubber tree to the cold treatments were determined and a large number of DEGs were characterized including 239 transcription factors, providing important clues for further elucidation of the mechanisms of cold stress responses in rubber tree.

• Toxicological Research
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• v.23 no.1
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• pp.19-24
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• 2007

We demonstrate that paclitaxel, an antitumor agent derived from yew tree, inhibits LPS- and $IFN-{\gamma}$-induced NF-kB/Rel activation in RAW 264.7 cells. Previously, paclitaxel ($>10{\mu}M$) has been known to induce iNOS gene expression in macrophages. However, in the previous report we described that the pretreatment of macrophages with low concentration of paclitaxel ($0.1{\mu}M$) for 8 h inhibited LPS-induced iNOS gene expression. Pretreatment of RAW 264.7 cells with paclitaxel significantly inhibited NF-kB/Rel transcriptional activation. Electrophoretic mobility shift assay further confirmed that pretreatment of macrophages with paclitaxel inhibited NF-kB/Rel DNA binding. Taxotere, a semisynthetic analog of paclitaxel, also inhibited LPS- and $IFN-{\gamma}$-induced iNOS gene expression. Collectively, these series of experiments indicate that paclitaxel inhibits iNOS gene expression by blocking NF-kB/Rel activation.

• Clinical and Experimental Pediatrics
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• v.54 no.6
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• pp.272-275
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• 2011

A recently recognized connective tissue disorder, Loeys-Dietz syndrome (LDS) is a genetic aortic aneurysm syndrome caused by mutations in the transforming growth factor-receptor type I or II gene (TGFBR1 or TGFBR2). They have distinctive phenotypic abnormalities including widely spaced eyes (hypertelorism), bifid uvula or cleft palate, and arterial tortuosity with aortic aneurysm or dissection throughout the arterial tree. LDS is characterized by aggressive and rapid progression of aortic aneurysm. Therefore, the patients with distinct phenotype, marked aortic dilatation and aneurysm at early age should be suspected to be affected by LDS and rapid TGFBR gene analysis should be done. We report one child diagnosed as LDS due to typical phenotypes and two novel missense mutations of the TGFBR2 gene (c.1526G>T and c.1528A>T).

• Communications for Statistical Applications and Methods
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• v.16 no.6
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• pp.915-923
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• 2009

The gene which is related in the disease of the human has been searched among numerous genes in GWA(Genome-Wide Association) research. However, most current statistical methods used to detect gene-gene interactions in disease association studies cannot be easily applied to handle the whole genome association study(GWAS) due to heavy computing. Therefore SNPHarvester is developed to find the main gene group among numerous genes. This research finds the superior gene groups which are related with the economic traits of the Korean beef cattle, not that of human, among sets of SNPs by using SNPHarvester, and also finds the superior genotypes which can enhance various qualities of Korean beef among SNP groups.

• Journal of Forest and Environmental Science
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• v.24 no.1
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• pp.15-25
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• 2008

Social and scientific changes, i.e., global warming, desertification, pollution, biodiversity, bioenergy, plant variety protection, biotechnology, timber demand, reforestation in North Korea, and etc., were reviewed for new strategy of forest tree breeding in Korea. Diversified breeding goals, globalization of breeding target species, multidisciplinary research approaches, manpower networking, establishment of new administrative and research units in KFS and KFRI were proposed. Principles suggested for new tree breeding strategy are: 1) multi-disciplinary approach in settlement of objectives, breeding methods, and etc., 2) expansion of target trees including foreign species, 3) fulfillment of both domestic and international demands for forest tree breeding, 4) establishment of breeding program well-grounded on genetic resources conservation, 5) acknowledgement of breeding products (i.e., variety, technique, gene, and etc.) as goods, and 6) provision of more research opportunities for young scientists. Lastly, ongoing tree breeding project in Indonesia and NTFP R&D Center at the College of Forest and Environmental Sciences, Kangwon National University were introduced as examples of desirable breeding projects based on target species diversification, multidisciplinary approach, and manpower networking.

• Korean Journal of Ichthyology
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• v.22 no.4
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• pp.273-278
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• 2010

Partial nucleotide sequences of nuclear protein-coding recombination activating gene 1 (RAG1) gene of two Abbottina and five Microphysogobio species residing in Korea were analyzed to elucidate the molecular phylogenetic position of A. springeri Banarescu and Nalbant. In RAG1 tree A. rivularis was clearly separated from the monophyletic lineage composed of A. springeri, Biwia zezera and Microphysogobio species. Within this lineage B. zezera showed sister-group relationship to the monophyletic group composed of A. springeri and five Microphysogobio species. Thus, our phylogenetic tree revealed the polyphyletic nature of two Abbottina species from Korea, which result is well congruent with the previous phyletic assumption based on osteological features. The current classification of Abbottina and Microphysogobio based on morphological criteria, such as the presence or absence of papillae on lips and size of swim bladder with or without encapsulation, does not reflect their true evolutionary history.