• BMB Reports
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• v.46 no.1
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• pp.41-46
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• 2013

Identifying genes indispensable for an organism's life and their characteristics is one of the central questions in current biological research, and hence it would be helpful to develop computational approaches towards the prediction of essential genes. The performance of a predictor is usually measured by the area under the receiver operating characteristic curve (AUC). We propose a novel method by implementing genetic algorithms to maximize the partial AUC that is restricted to a specific interval of lower false positive rate (FPR), the region relevant to follow-up experimental validation. Our predictor uses various features based on sequence information, protein-protein interaction network topology, and gene expression profiles. A feature selection wrapper was developed to alleviate the over-fitting problem and to weigh each feature's relevance to prediction. We evaluated our method using the proteome of budding yeast. Our implementation of genetic algorithms maximizing the partial AUC below 0.05 or 0.10 of FPR outperformed other popular classification methods.

• Korean Journal of Microbiology
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• v.38 no.1
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• pp.19-25
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• 2002

Colletotrichum species are important fungal pathogen that cause great damages on various host plant species worldwide. In Korea, Colletotrichum species cause massive economic losses on apple, peach, grape, and essecially, sweet persimon productions. In the past, Identification of the pathogen and the studies on the genetic relationships among the pathogenic isolates were mainly based on morphology, cultural characteristics, and the difference in pathogenicity. However, in recent years, these traditional methods have been replaced with molecular methods to solve the difficulty of classification on pathogens. Therefore, in this study, RAPD and PCR-RFLP methods were employed for the studies of genetic relationship among the different isolates of Colletotrichum species that cause damages on sweet persimon. As a results of genetic relationship analysis, Colletotrichum species tested were divided into two big groups or five small groups.

• Journal of Life Science
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• v.25 no.12
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• pp.1347-1353
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• 2015

The fleshy shrimp, Fenneropenaeus chinensis, is the family of Penaeidae and one of the most economically important marine culture species in Korea. However, its genetic characteristics have never been studied. In this study, a total of 240 wild F. chinensis individuals were collected from four locations as follows: Narodo (NRD, n = 60), Beopseongpo (BSP, n = 60), Chaesukpo (CSP, n = 60), and Cheonsuman (CSM, n = 60). Genetic variability and the relationships among four wild F. chinensis populations were analyzed using 13 newly developed microsatellite loci. Relatively high levels of genetic variability (mean allelic richness = 16.87; mean heterozygosity = 0.845) were found among localities. Among the 52 population loci, 13 showed significant deviation from the Hardy–Weinberg equilibrium. Neighbor-joining, principal coordinate, and molecular variance analyses revealed the presence of three subpopulations (NRD, CSM, BSP and CSP), which was consistent with clustering based on genetic distance. The mean observed heterozygosity values of the NRD, CSM, BSP, and CSP populations were 0.724, 0.821, 0.814, and 0.785 over all loci, respectively. These genetic variability and differentiation results of the four wild populations can be applied for future genetic improvement using selective breeding and to design suitable management guidelines for Korean F. chinensis culture.

• Molecules and Cells
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• v.25 no.2
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• pp.301-304
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• 2008

Microsatellites, short tandem repeats, are useful markers for genetic analysis because of their high frequency of occurrence over the genome, high information content due to variable repeat lengths, and ease of typing. To establish a panel of microsatellite markers useful for genetic studies of the Korean population, the allele frequencies and heterozygosities of 207 microsatellite markers in 119 unrelated Korean, Indian and Pakistani individuals were compared. The average heterozygosity of the Korean population was 0.71, similar to that of the Indian and Pakistani populations. More than 80% of the markers showed heterozygosity of over 0.6 and were valuable as genetic markers for genome-wide screening for disease susceptibility loci in these populations. To identify the allelic distributions of the multilocus genetic data from these microsatellite markers, the population structures were assessed by clustering. These markers supported, with the most probability, three clustering groups corresponding to the three geographical populations. When we assumed only two hypothetical clusters (K), the Korean population was separate from the others, suggesting a relatively deep divergence of the Korean population. The present 207 microsatellite markers appear to reflect the historical and geographical origins of the different populations as well as displaying a similar degree of variation to that seen in previously published genetic data. Thus, these markers will be useful as a reference for human genetic studies on Asians.

• Journal of Interdisciplinary Genomics
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• v.2 no.2
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• pp.13-17
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• 2020

Infantile nystagmus syndrome (INS) is a genetically heterogeneous disorder. To date, more than 100 genes have been reported to cause INS and there is significant overlap in phenotypic characteristics. The most common form of X-linked INS is attributed to FRMD7 at Xq26. Recent advances in molecular genetics have facilitated the identification of pathogenic variants of FRMD7 and the investigation for underlying mechanisms of FRMD7-associated INS. This review summarizes genetic and clinical features of FRMD7-associated INS, and introduces updates on the pathogenesis of FRMD7 mutation.

• BMB Reports
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• v.36 no.5
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• pp.488-492
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• 2003

Neurofilament-L (NF-L) is a major element of neuronal cytoskeletons and known to be important for neuronal survival in vivo. Since oxidative stress might play a critical role in the pathogenesis of neurodegenerative diseases, we investigated the role of copper and peroxide in the modification of NF-L. When disassembled NF-L was incubated with copper ion and hydrogen peroxide, then the aggregation of protein was proportional to copper and hydrogen peroxide concentrations. Dityrosine crosslink formation was obtained in copper-mediated NF-L aggregates. The copper-mediated modification of NF-L was significantly inhibited by thiol antioxidants, N-acetylcysteine, glutathione, and thiourea. A thioflavin-T binding assay was performed to determine whether the copper/$H_2O_2$ system-induced in vitro aggregation of NF-L displays amyloid-like characteristics. The aggregate of NF-L displayed thioflavin T reactivity, which was reminiscent of amyloid. This study suggests that copper-mediated NF-L modification might be closely related to oxidative reactions which may play a critical role in neurodegenerative diseases.

• ALGAE
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• v.28 no.1
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• pp.53-62
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• 2013

Actinotrichia is a calcified galaxauracean red algal genus with temperate and tropical distributions in the Indian and Pacific Oceans. Morphological characteristics, along with rbcL and cox1 sequences, were analyzed from specimens collected in the western Pacific and the Indian Oceans. Both rbcL and cox1 data confirmed the occurrence of A. fragilis, A. robusta, and Actinotrichia sp. in this region. The presence of A. fragilis was verified in tropical Indo-Pacific and temperate northeast Asian waters and was characterized by high genetic diversity. Although A. robusta commonly occurs in the East China Sea, we confirmed its presence on rocks and crustose algae in the subtidal zone of three islands in the Andaman Sea. Actinotrichia sp. was similar to A. calcea in morphology and distribution, but with sufficiently different sequences, thus, additional sampling over the range will enable a more realistic evaluation of its taxonomic status.

• Annals of Clinical Neurophysiology
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• v.22 no.1
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• pp.29-32
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• 2020

Sarcoglycanopathies are a rare group of autosomal recessive limb-girdle muscular dystrophies (LGMDs) caused by genetic variants in α-, β-, γ-, or δ-sarcoglycan that maintain membrane integrity and contribute to molecular signal processing. High-throughput nucleotide sequencing was performed in patients with slowly progressive proximal muscle weakness from early childhood with respiratory involvement, which detected a novel homozygous nonsense variant (c.601C>T;p.Gln201Ter) in SGCB. This report informs about the clinical characteristics of LGMD2E (type-2E LGMD) in Korea and provides genetic confirmation of the disease.

• Mycobiology
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• v.38 no.2
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• pp.122-127
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• 2010

Different strains of mold were screened for the production of high quality Korean traditional rice wine with anti-hypertension and good acceptability. We isolated 867 nuruk mold strains and selected 24 for further study based on measurement of amylase activity. Among them, mold No. 17 showed high ethanol production upon fermentation with Saccharomyces cerevisiae as well as anti-hypertensive properties. The No. 17 strain was therefore selected as the functional mold and later identified as Rhizopus stolonifer based on molecular biological characteristics. Optimal fermentation conditions for the brewing of anti-hypertensive traditional rice wine comprised the addition of R. stolonifer No. 17 koji at a concentration of 35 sp/g and a fermentation period of 10 days at $25^{\circ}C$ using S. cerevisiae.

• Korean Journal of Poultry Science
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• v.27 no.2
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• pp.91-98
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• 2000

Phylogenetic tree constructed from the nucleotide sequences of the S1 gene showed that the 15 Korean strains of infectious bronchitis virus(IBV) examined were classified into 2 genetically distinct groups, except one respiratory strain, RB86, which was clustered with Massachusetts group. All the 5 respiratory strains belonged to Korean group I and the rest 9 nephropathogenic strains belonged to Korean group II according to the analysis, based on S1 gene sequences. Like previous classifications corresponded with the geographic origin, Korean stains were discriminated from geographically distinct reference strains of IBV. The nephropathogenic strains within Korean group IIsharing 96% homology were continuously isolated since 1990, and seemed to be genetically stable. Whereas the respiratory strains within Korean group Ⅰ sharing 88% homology were sporadically isolate since 1986m and seemed to be genetically unstable. Because we found putative accumulated point mutation as well as recombination events in Korean group Ⅰ, we discussed why genetic variations have often occurred in respiratory strains rather than nephropathognic strains.