• Korean Journal of Environmental Biology
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• v.36 no.2
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• pp.131-139
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• 2018

The warming of water as a result of climate change affects fish habitat. Variations in water temperature affect fish physiology almost totally. The rise in water temperature due to climate change leads to hypoxia following decreased oxygen solubility and decreased binding capacity of oxygen-carrying hemoglobin. This study was conducted to evaluate the health status of Atlantic salmon (Salmo salar) fry at elevated water temperatures($20^{\circ}C$) compared with optimum water temperature ($15^{\circ}C$). The method facilitated the detection of biomarker genes using NGS RNAseq analysis and evaluation of their expression pattern using RT-qPCR analysis. The biomarker genes included interferon alpha-inducible protein 27-like protein 2A transcript variant X3, protein L-Myc-1b-like, placenta growth factor-like transcript variant X1, fibroblast growth factor receptor-like 1 transcript variant X1, transferrin, intelectin, thioredoxin-like, c-type lectin lectoxin-Thr1-like, ladderlectin-like and calponin-1. The selected biomarker genes were sensitive to changes in water temperature based on NGS RNAseq analysis. The expression patterns of these genes based on RT-qPCR were similar to those of NGS RNAseq analysis.

• 한국균학회소식:학술대회논문집
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• 2014.10a
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• pp.11-11
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• 2014

Fungal pathogens have huge impact on health and economic wellbeing of human by causing life-threatening mycoses in immune-compromised patients or by destroying crop plants. A key determinant of fungal pathogenesis is their ability to undergo developmental change in response to host or environmental factors. Genetic pathways that regulate such morphological transitions and adaptation are therefore extensively studied during the last few decades. Given that epigenetic as well as genetic components play pivotal roles in development of plants and mammals, contribution of microbial epigenetic counterparts to this morphogenetic process is intriguing yet nearly unappreciated question to date. To bridge this gap in our knowledge, we set out to investigate histone modifications among epigenetic mechanisms that possibly regulate fungal adaptation and processes involved in pathogenesis of a model plant pathogenic fungus, Magnaporthe oryzae. M. oryzae is a causal agent of rice blast disease, which destroys 10 to 30% of the rice crop annually. Since the rice is the staple food for more than half of human population, the disease is a major threat to global food security. In addition to the socioeconomic impact of the disease it causes, the fungus is genetically tractable and can undergo well-defined morphological transitions including asexual spore production and appressorium (a specialized infection structure) formation in vitro, making it a model to study fungal development and pathogenicity. For functional and comparative analysis of histone modifications, a web-based database (dbHiMo) was constructed to archive and analyze histone modifying enzymes from eukaryotic species whose genome sequences are available. Histone modifying enzymes were identified applying a search pipeline built upon profile hidden Markov model (HMM) to proteomes. The database incorporates 22,169 histone-modifying enzymes identified from 342 species including 214 fungal, 33 plants, and 77 metazoan species. The dbHiMo provides users with web-based personalized data browsing and analysis tools, supporting comparative and evolutionary genomics. Based on the database entries, functional analysis of genes encoding histone acetyltransferases and histone demethylases is under way. Here I provide examples of such analyses that show how histone acetylation and methylation is implicated in regulating important aspects of fungal pathogenesis. Current analysis of histone modifying enzymes will be followed by ChIP-Seq and RNA-seq experiments to pinpoint the genes that are controlled by particular histone modifications. We anticipate that our work will provide not only the significant advances in our understanding of epigenetic mechanisms operating in microbial eukaryotes but also basis to expand our perspective on regulation of development in fungal pathogens.

• Journal of Sasang Constitutional Medicine
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• v.11 no.2
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• pp.185-194
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• 1999

Recently some report has been published on the classification of Sasang constitution by analysis of genetic polymorphism. In this study, to present the ideas in the study on the classification of Sasang constitution based on the genetic variation of individuals, we reviewed the previous studies dealing with relationship between genetic polymorphism and Sasang constitution and suggested new molecular biological methodologies applicable to the classification of Sasang constitution. The results were as follow; 1. In the studies on the classification of constitution by analysis of genetic polymorphism, the special genes were desirable as subjects rather than the non-functional part of genome such as inter-gene and intron. Since microsatellite is usually located in inter-gene or intron, representation of constitutions may not associated with the polymorphism of certain microsatellite. 2. It may possible that polymorphism patterns of the genes related to the expression of individuality is associated with the types of Sasang constitutions. Therefore, angiotensin converting enzyme (ACE) which known have some role in the determination the human performance is one of the candidate genes can use for the classification of Sasang constitutions. 3. It is well known that HLA types are very variable in human and closely associated with the determination of susceptibility for certain disease. The studies on the polymorphism of HLA types may applicable to the classification of Sasang constitutions. 4. DNA chip technique which developed recently for the analysis of the expression of human genes may powerful tools in the study of Sasang medicine.

• Applied Biological Chemistry
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• v.37 no.5
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• pp.361-369
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• 1994

To study the light-induced expression mechanism and protein transport into the chloroplast, a rice genomic clone (GrbcS) for the small subunit of ribulose 1,5-bisphosphate carboxylase (rbcS) was isolated and its nucleotide sequence was determined. Nucleotide sequence analysis of GrbcS revealed that the gene consists of two exons interrupted by an intron, encoding a protein of 175 amino acids including a transit peptide of 47 amino acids. These structural features of GrbcS are consistent with those of other rbcS genes from monocot species. Genomic Southern blot analysis suggested that the rbcS genes are present as a relatively small multigene family in the rice genome. Comparison of the nucleotide and deduced amino acid sequences to other rice rbcSs shows close sequence similaritiy. Conserved DNA sequences present in other light-responsive genes are also found in the 5’ upstream region of GrbcS such as G-box, 3AF1-binding site and GATA site. The possible function of these putative regulatory elements are discussed.

• Molecules and Cells
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• v.28 no.5
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• pp.423-430
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• 2009

In order to elucidate the precise phylogenetic relationships of Korean wild boar (Sus scrofa coreanus), a partial mtDNA D-loop region (1,274 bp, NC_000845 nucleotide positions 16576-1236) was sequenced among 56 Korean wild boars. In total, 25 haplotypes were identified and classified into four distinct subgroups (K1 to K4) based on Bayesian phylogenetic analysis using Markov chain Monte Carlo methods. An extended analysis, adding 139 wild boars sampled worldwide, confirmed that Korean wild boars clearly belong to the Asian wild boar cluster. Unexpectedly, the Myanmarese/Thai wild boar population was detected on the same branch as Korean wild boar subgroups K3 and K4. A parsimonious median-joining network analysis including all Asian wild boar haplotypes again revealed four maternal lineages of Korean wild boars, which corresponded to the four Korean wild boar subgroups identified previously. In an additional analysis, we supplemented the Asian wild boar network with 34 Korean and Chinese domestic pig haplotypes. We found only one haplotype, C31, that was shared by Chinese wild, Chinese domestic and Korean domestic pigs. In contrast to our expectation that Korean wild boars contributed to the gene pool of Korean native pigs, these data clearly suggest that Korean native pigs would be introduced from China after domestication from Chinese wild boars.

• Journal of Plant Biotechnology
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• v.5 no.3
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• pp.163-168
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• 2003

A routine system based on particle bombardment of embryogenic callus for recovery of fertile transgenic rice (Oryza sativa L.) plants was developed. Embryogenic callus was established within 2-3 months from calli derived from mature seeds of Korean rice cultivar, Nagdongbyeo. The callus was bombarded with the plasmid pRQ6 containing the $\beta$-glucuronidase gene (gusA) and hygromycin phosphotransferase gene (hph, conferring resistance to hygromycin B), both driven by CaMV 35S promoter. Placement of cells on an osmoticum-containing medium (0.2 M sorbitol and 0.2 M mannitol) 4 hrs prior to and 16 hrs after bombardment resulted in a statistically significant increase with 3.2-fold in transient expression frequency gusA. In five independent experiments, the average frequency of transformation showing GUS activities was $8.86\%$. A large number of morphologically normal, fertile transgenic rice plants were obtained. Integration of foreign gene into the genome of $R_0$ transgenic plants was confirmed by Southern blot analysis. GUS and HPT were detected in $R_1$ progeny and Mendelian segregation of these genes was observed in $R_1$ progeny.

• International Journal of Industrial Entomology and Biomaterials
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• v.1 no.2
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• pp.111-114
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• 2000

The female pupae of the silkworms Bombyx mori, were injected with recombinant Autographa californica nuclear polyhedrosis virus (AcNPV) expressing green fluorescent protein (GFP) by percutaneous inoculation. When the 4 day-old female pupae were injected with 1x10$^{7}$ or 2${\times}$10$^{7}$ plaque forming units (pfu) of the recombinant AcNPV, oviposited number and egg weight were significantly decreased. Furthermore, the shape of the eggs was obviously divides into normal and abnormal shapes. The percentage of the eggs with an abnormal shape was 7.8% and 57.1% at 1${\times}$10$^{7}$ and 2${\times}$10$^{7}$ pfu inoculation, respectively. PCR analysis of the genomic DNA extracted from the eggs revealed that gfp and AcNPV ecdysteroid UDP-glucosyltransferase genes were amplified from both types of eggs with normal and abnormal shapes. The results demonstrate that AcNPV DNA, and gfp gene cloned into the AcNPV genome, injected in pupal stage were transmitted to eggs and remained stable through at least next generation.

• The Plant Pathology Journal
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• v.22 no.3
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• pp.215-221
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• 2006

Gibberella zeae (anamorph: Fusarium graminearum) is an important pathogen of cereal crops. This fungus produces a broad range of secondary metabolites, including polyketides such as aurofusarin (a red pigment) and zearalenone (an estrogenic mycotoxin), which are important mycological characteristics of this species. A screen of G. zeae insertional mutants, generated using a restriction enzyme-mediated integration (REMI) procedure, led to the isolation of a mutant (Z43R606) that produced neither aurofusarin nor zearalenone yet showed normal female fertility and virulence on host plants. Outcrossing analysis confirmed that both the albino and zearalenone-deficient mutations are linked to the insertional vector in Z43R606. Molecular characterization of Z43R606 revealed a deletion of at least 220 kb of the genome at the vector insertion site, including the gene clusters required for the biosynthesis of aurofusarin and zearalenone, respectively. A re-creation of the insertional event of Z43R606 in the wild-type strain demonstrated that the 220-kb deletion is responsible for the phenotypic changes in Z43R606 and that a large region of genomic DNA can be efficiently deleted in G. zeae by double homologous recombination. The results showed that 52 putative genes located in the deleted genomic region are not essential for phenotypes other than the production of both aurofusarin and zearalenone. This is the first report of the molecular characterization of a large genomic deletion in G. zeae mediated by the REMI procedure.

• Journal of Animal Science and Technology
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• v.49 no.3
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• pp.295-302
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• 2007

Leptin, the product of the obese(ob) gene, is an adipocyte-derived hormone for the regulation of whole- body energy storage and energy usage. It has been reported that the homozygous mutations in the gene for leptin(LEP) induce obesity and reduce energy expenditure. In cattle, LEP has significant roles directly or indirectly related with phenotypes such as body weight and fat deposits, therefore SNPs of LEP have been considered important genetic marker to estimate carcass fat content in cattle. In this study, SNPs were screened in LEP(2,222 bp) between intron 1 to 3'-UTR from 24 independent Hanwoo(Korean cattle) by PCR and DNA sequencing. Total 25 SNPs were found and two nonsynonymous SNPs including T1163A(V19E) and G3256A(G132D) were newly detected only from Hanwoo. Among 20 SNPs previously reported in cattle, 16 SNPs were found in Hanwoo; however, the frequencies of some SNPs were significantly different between Hanwoo and western cattle breeds. The other 4 SNPs were not detected from Hanwoo. These Hanwoo specific SNP patterns in LEP will be used in development of molecular marker and application to genetic improvement of Hanwoo.

• The Plant Pathology Journal
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• v.21 no.2
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• pp.167-171
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• 2005

We isolated the Cucumber green mottle mosaic virus(CGMMV) particles from watermelon leaves and designated as CGMMV-HY1 as a watermelon isolate and attempted to characterize the pathogenic isolate responsible for such an epidemic in watermelon and also to monitor dominant viral isolates in greenhouse. The watermelon plants infected with CGMMV generally showed mottle mosaic, mosaic, growth stunting, necrosis and deformed fruit. The reactions of indicator plants to CGMMV-HY1 were the local lesions on Nicotiana tabacum cv. White Burley, Nicotiana tabacum cv. Samsun, and Chenopodium amaranticola, and the mosaic symptoms only on Cucumis sativus, but the CGMMV-HY1 did not infect Nicotiana sylvesytis, Datura stramonium, Chenopodium quinoa, and Petunia hybrida. Purified virus particles were rod-shaped and about 300 nm long. The coat protein (CP) of purified CGMMV-HY1 was single band with molecular weight of about 16.5 kDa which was confirmed by western blot analysis probed with monoclonal antibody of CGMMV-HY1. The genomic and subgenomic RNAs of 6.4 kb and 0.75 kb were revealed by the electrophoresis on 1.2% formaldehydedenatured agarose gel. Viral and complementary CGMMV-specific primer sets were designed for spanning the genome using previously reported CGMMV sequences. A 464bp of CP gene of CGMMV-HY1 was amplified by RT-PCR and cloned into PGEM-T easy vector. The nucleotide sequence of CP gene of CGMMV-HY1 shared 98%, 99%, and 100% identities with that of CGMMV strains W, KOM, and KW respectively. Based on these results, we identified CGMMV-HY1 as a CGMMV isolate of watermelon, a member of Tobamovirus.