• BMB Reports
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• v.40 no.6
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• pp.911-920
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• 2007

Tuberculosis, caused by Mycobacterium tuberculosis, continues to be one of the leading infectious diseases to humans. It is urgent to discover novel drug targets for the development of antitubercular agents. The 2-C-methyl-Derythritol-4-phosphate (MEP) pathway for isoprenoid biosynthesis has been considered as an attractive target for the discovery of novel antibiotics for its essentiality in bacteria and absence in mammals. MEP cytidyltransferase (IspD), the third-step enzyme of the pathway, catalyzes MEP and CTP to form 4-diphosphocytidyl-2-C-methylerythritol (CDP-ME) and PPi. In the work, ispD gene from M. tuberculosis H37Rv (MtIspD) was cloned and expressed. With N-terminal fusion of a histidine-tagged sequence, MtIspD could be purified to homogeneity by one-step nickel affinity chromatography. MtIspD exists as a homodimer with an apparent molecular mass of 52 kDa. Enzyme property analysis revealed that MtIspD has high specificity for pyrimidine bases and narrow divalent cation requirements, with maximal activity found in the presence of CTP and $Mg^{2+}$. The turnover number of MtIspD is $3.4 s^{-1}$. The Km for MEP and CTP are 43 and $92{\mu}M$, respectively. Furthermore, MtIspD shows thermal instable above $50^{\circ}C$. Circular dichroism spectra revealed that the alteration of tertiary conformation is closely related with sharp loss of enzyme activity at higher temperature. This study is expected to help better understand the features of IspD and provide useful information for the development of novel antibiotics to treat M. tuberculosis.

• Parasites, Hosts and Diseases
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• v.54 no.4
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• pp.385-391
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• 2016

The discovery and understanding of antigenic proteins are essential for development of a vaccine against malaria. In Plasmodium falciparum, Pf92 have been characterized as a merozoite surface protein, and this protein is expressed at the late schizont stage, but no study of Pv92, the orthologue of Pf92 in P. vivax, has been reported. Thus, the protein structure of Pv92 was analyzed, and the gene sequence was aligned with that of other Plasmodium spp. using bioinformatics tools. The recombinant Pv92 protein was expressed and purified using bacterial expression system and used for immunization of mice to gain the polyclonal antibody and for evaluation of antigenicity by protein array. Also, the antibody against Pv92 was used for subcellular analysis by immunofluorescence assay. The Pv92 protein has a signal peptide and a sexual stage s48/45 domain, and the cysteine residues at the N-terminal of Pv92 were completely conserved. The N-terminal of Pv92 was successfully expressed as soluble form using a bacterial expression system. The antibody raised against Pv92 recognized the parasites and completely merged with PvMSP1-19, indicating that Pv92 was localized on the merozoite surface. Evaluation of the human humoral immune response to Pv92 indicated moderate antigenicity, with 65% sensitivity and 95% specificity by protein array. Taken together, the merozoite surface localization and antigenicity of Pv92 implicate that it might be involved in attachment and invasion of a merozoite to a new host cell or immune evasion during invasion process.

• Proceedings of the Korean Society of Crop Science Conference
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• 2017.06a
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• pp.7-7
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• 2017

Unfavorable weather and soil conditions reduce rice yield and land and water productivity, aggravating existing encounters of poverty and food insecurity. These conditions are foreseen to worsen with climate change and with the unceasing irrational human practices that progressively debilitate productivity despite global appeals for more food. Our understanding of plant responses to abiotic stresses is advancing and is complex, involving numerous critical processes - each controlled by several genetic factors. Knowledge of the physiological and molecular mechanisms involved in signaling, response and adaptation, and in some cases the genes involved, is advancing. Moreover, the genetic diversity being unveiled within cultivated rice and its wild relatives is providing ample resources for trait and gene discovery, and this is being scouted for rice improvement using modern genomics and molecular tools. Development of stress tolerant varieties is now being fast-tracked through the use of DNA markers and advanced breeding strategies. Large numbers of drought, submergence and salt tolerant varieties were commercialized over recent years in South and Southeast Asia and more recently in Africa. These varieties are making significant changes in less favorable areas, transforming lives of smallholder farmers - progress considered incredulous in the past. The stress tolerant varieties are providing assurance to farmers to invest in better management of their crops and the ability to adjust their cropping systems for even higher productivity and more income, sparking changes analogous to that of the first green revolution, which previously benefited only favorable irrigated and rainfed areas. New breeding tools using markers for multiple stresses made it possible to develop more resilient, higher yielding varieties to replace the aging and obsolete varieties still dominating these areas. Varieties with multiple stress tolerances are now becoming available, providing even better security for farmers and lessening their production risks even in areas affected by complex and overlapping stresses. The progress made in these less favorable areas triggered numerous favorable changes at the national and regional levels in several countries in Asia, including adjusting breeding and dissemination strategies to accelerate outreach and enabling changes at higher policy levels, creating a positive environment for faster progress. Exploiting the potential of these less productive areas for food production is inevitable, to meet the escalating global needs for more food and sustained production systems, at times when national resources are shrinking while demand for food is mounting. However, the success in these areas requires concerted efforts to make use of existing genetic resources for crop improvement and establishing effective evaluation networks, seed production systems, and seed delivery systems to ensure faster outreach and transformation.

• Asian Pacific Journal of Cancer Prevention
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• v.15 no.20
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• pp.8893-8900
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• 2014

Dysregulated expression of microRNAs (miRNAs) has been shown to be closely associated with tumor development, progression, and carcinogenesis. However, their clinical implications for gastric cancer remain elusive. To investigate the hypothesis that genome-wide alternations of miRNAs differentiate gastric cancer tissues from those matched adjacent non-tumor tissues (ANTTs), miRNA arrays were employed to examine miRNA expression profiles for the 5-pair discovery stage, and the quantitative real-time polymerase chain reaction (qRTPCR) was applied to validate candidate miRNAs for 48-pair validation stage. Furthermore, the relationship between altered miRNA and clinicopathological features and prognosis of gastric cancer was explored. Among a total of 1,146 miRNAs analyzed, 16 miRNAs were found to be significantly different expressed in tissues from gastric cancer compared to ANTTs (p<0.05). qRT-PCR further confirmed the variation in expression of miR-193b and miR-196a in the validation stage. Down-expression of miR-193b was significantly correlated with Lauren type, differentiation, UICC stage, invasion, and metastasis of gastric cancer (p<0.05), while over-expression of miR-196a was significantly associated with poor differentiation (p=0.022). Moreover, binary logistic regression analysis demonstrated that the UICC stage was a significant risk factor for down-expression of miR-193b (adjusted OR=8.69; 95%CI=1.06-56.91; p=0.043). Additionally, Kaplan-Meier survival curves indicated that patients with a high fold-change of down-regulated miR-193b had a significantly shorter survival time (n=19; median survival=29 months) compared to patients with a low fold-change of down-regulated miR-193b (n=29; median survival=54 months) (p=0.001). Overall survival time of patients with a low fold-change of up-regulated miR-196a (n=27; median survival=52 months) was significantly longer than that of patients with a high fold-change of up-regulated miR-196a (n=21; median survival=46 months) (p=0.003). Hence, miR-193b and miR-196a may be applied as novel and promising prognostic markers in gastric cancer.

• Journal of the Society of Cosmetic Scientists of Korea
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• v.43 no.2
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• pp.137-147
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• 2017

The human skin is an ecosystem that provides habitat to various microorganisms. These comprise the skin microbiome and provide numerous benefits in addition to maintaining a symbiotic relation with the host. Various metabolites generated by the skin microbiome exert beneficial effects such as strengthening the skin barrier, and anti-aging and anti-inflammatory functions. In this study, we isolated a novel bacterium, designated Sporichthyacae strain K-07, from the human skin. Analysis of 16S rRNA gene sequences showed that the newly found bacterium shares 93.4% homology with the genus Sporichthya, thus corroborating the discovery of a novel genus. We further analyzed the effect of the novel strain in vitro, by treating HaCaT cells with bacterial metabolite products. Treatment resulted in changes in the mRNA expression levels of filaggrin, claudin1, claudin4, SMase, CERS3, HAS3, aquaporin3, IL-6, TNF-${\alpha}$, TSLP, and TARC. Specifically, the levels of filaggrin, claudin1, claudin4, SMase, CERS3, HAS3, and aquaporin3 were higher in strain K-07 metabolite product-treated cells than in control cells. These results showed that metabolite products of the novel strain K-07 enhanced the skin barrier and exert anti-inflammatory effects. Therefore, these metabolite products could be potentially used for treatment of skin conditions.

• Journal of Microbiology and Biotechnology
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• v.28 no.6
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• pp.1007-1021
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• 2018

Cancer represents one of the most significant threats to human health on a global scale. Hence, the development of effective cancer prevention strategies, as well as the discovery of novel therapeutic agents against cancer, is urgently required. In light of this challenge, this research aimed to evaluate the effects of several potent bioactive peptides and proteins contained in crocodile white blood cell extract (cWBC) against LU-1, LNCaP, PC-3, MCF-7, and CaCo-2 cancer cell lines. The results demonstrate that 25, 50, 100, and $200{\mu}g/ml$ cWBC exhibits a strong cytotoxic effect against all investigated cell lines ($IC_{50}$ $70.34-101.0{\mu}g/ml$), while showing no signs of cytotoxicity towards noncancerous Vero and HaCaT cells. Specifically, cWBC treatment caused a significant reduction in the cancerous cells' colony forming ability. A remarkable suppression of cancerous cell migration was observed after treatment with cWBC, indicating potent antimetastatic properties. The mechanism involved in the cancer cell cytotoxicity of cWBC may be related to apoptosis induction, as evidenced by typical apoptotic morphology features. Moreover, certain cWBC concentrations induced significant overproduction of ROS and significantly inhibited the $S-G_2/M$ transition in the cancer cell. The molecular mechanisms of cWBC in apoptosis induction were to decrease Bcl-2 and XIAP expression levels and increase the expression levels of caspase-3, caspase-8, and p53. These led to a decrease in the expression level of the cell cycle-associated gene cyclin-B1 and the arrest of cell population growth. Consequently, these findings demonstrate the prospect of the use of cWBC for cancer therapy.

• Weed & Turfgrass Science
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• v.4 no.2
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• pp.118-123
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• 2015

Metagenomics is a powerful tool to isolate novel biocatalyst and biomolecules directly from the environmental DNA libraries. Since the metagenomics approach bypasses cultivation of microorganisms, un-cultured microorganisms that are majority of exists can be the richest reservoir for natural products discovery. To discover novel herbicidal substances from soil metagenome, we established three easy, simple and effective high throughput screening methods such as cucumber cotyledon leaf disc assay, microalgae assay and seed germination assay. Employing the methods, we isolated two active single clones (9-G1 and 9-G12) expressing herbicidal activity which whitened leaf discs, inhibited growth of microalgae and inhibited root growth of germinated Arabidopsis seeds. Spraying butanol fraction of the isolated active clones' culture broth led to growth retardation or desiccation of Digitalia sanguinalis (L) Scop. in vivo. These results represent that the screening methods established in this study are useful to screen herbicidal substances from metagenome libraries. Further identifying molecular structure of the herbicidal active substances and analyzing gene clusters encoding synthesis systems for the active substances are in progress.

• Journal of Genetic Medicine
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• v.4 no.1
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• pp.22-37
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• 2007

The autosomal dominant spinocerebellar ataxias (SCAs) are a group of neurodegenerative diseases, clinically and genetically heterogeneous, characterized by degeneration of spinocerebellar pathways with variable involvement of other neural systems. At present, 27 distinct genetic forms of SCAs are known: SCA1-8, SCA10-21, SCA23, SCA25-28, DRPLA (dentatorubral-pallidoluysian atrophy), and 16q-liked ADCA (autosomal dominant cerebellar ataxia). Epidemiological data about the prevalence of SCAs are restricted to a few studies of isolated geographical regions, and most do not reflect the real occurrence of the disease. In general a prevalence of about 0.3-2 cases per 100,000 people is assumed. As SCA are highly heterogeneous, the prevalence of specific subtypes varies between different ethnic and continental populations. Most recent data suggest that SCA3 is the commonest subtype worldwide; SCA1, SCA2, SCA6, SCA7, and SCA8 have a prevalence of over 2%, and the remaining SCAs are thought to be rare (prevalence <1%). In this review, we highlight and discuss the SCA7. The hallmark of SCA7 is the association of hereditary ataxia and visual loss caused by pigmentary macular degeneration. Visual failure is progressive, bilateral and symmetrical, and leads irreversibly to blindness. This association represents a distinct disease entity classified as autosomal dominant cerebellar ataxia (ADCA) type II by Harding. The disease affectsprimarily the cerebellum and the retina by the moderate to severe neuronal loss and gliosis, but also many other central nervous system structures as the disease progresses. SCA7 is caused by expansion of an unstable trinucleotide CAG repeat in the ATXN7 gene encoding a polyglutamine (polyQ) tract in the corresponding protein, ataxin-7. Normal ATXN7 alleles contain 4-35 CAG repeats, whereas pathological alleles contain from 36->450 CAG repeats. Immunoblott analysis demonstrated that ataxin-7 is widely expressed but that expression levels vary among tissues. Instability of expanded repeats is more pronounced in SCA7 than in other SCA subtypes and can cause substantial lowering of age at onset in successive generations termed ‘anticipation’ so that children may become diseased even before their parents develop symptoms. The strong anticipation in SCA7 and the rarity of contractions should have led to its extinction within a few generations. There is no specific drug therapy for this neurodegenerative disorder. Currently, therapy remains purely symptomatic. Cellular models and SCA7 transgenic mice have been generated which constitute valuable resources for studying the disease mechanism. Understanding the pathogenetic mechanisms of neurodegeneration in SCAs should lead to the identification of potential therapeutic targets and ultimately facilitate drug discovery. Here we summarize the clinical, pathological, and genetic aspects of SCA7, and review the current understanding of the pathogenesis of this disorder. Further, we also review the potential therapeutic strategies that are currently being explored in polyglutamine diseases.

• Plant Breeding and Biotechnology
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• v.6 no.4
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• pp.391-403
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• 2018

Genome resequencing by next-generation sequencing technology can reveal numerous single nucleotide polymorphisms (SNPs) within a closely-related cultivar group, which would enable the development of sufficient SNP markers for mapping and the identification of useful genes present in the cultivar group. We analyzed genome sequence data from 13 Korean japonica rice varieties and discovered 740,566 SNPs. The SNPs were distributed at 100-kbp intervals throughout the rice genome, although the SNP density was uneven among the chromosomes. Of the 740,566 SNPs, 1,014 SNP sites were selected on the basis of polymorphism information content (PIC) value higher than 0.4 per 200-kbp interval, and 506 of these SNPs were converted to Kompetitive Allele-Specific PCR (KASP) markers. The 506 KASP markers were tested for genotyping with the 13 sequenced Korean japonica rice varieties, and polymorphisms were detected in 400 KASP markers (79.1%) which would be suitable for genetic analysis and molecular breeding. Additionally, a genetic map comprising 205 KASP markers was successfully constructed with 188 $F_2$ progenies derived from a cross between the varieties, Junam and Nampyeong. In a phylogenetic analysis with 81 KASP markers, 13 Korean japonica varieties showed close genetic relationships and were divided into three groups. More KASP markers are being developed and these markers will be utilized in gene mapping, quantitative trait locus (QTL) analysis, marker-assisted selection and other strategies relevant to crop improvement.

• Journal of Life Science
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• v.28 no.12
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• pp.1529-1535
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• 2018

The number of antibiotic-resistant bacteria is increasing rapidly while the discovery rate of new antibiotics is in decline. A systematic study is therefore necessary to investigate which bacteria are resistant to medically important antibiotics and how high that resistance is. To that end, this study aimed to analyze which bacteria demonstrated resistance to ampicillin, one of the currently most-widely used medical antibiotics. Water samples were collected from the Changwon-Cheon that runs through Changwon City and from the pond in front of the dormitory building at Changwon University. Hundreds of ampicillin-resistant colonies were obtained and 22 morphologically distinct examples were chosen for further study. These bacteria were identified by amplifying their 16S rRNA genes and comparing those sequences with data in GenBank. The bacteria was identified as belonging to 10 families, 12 genera, and 17 species, and all were able to grow in the presence of $50{\mu}g/ml$ ampicillin while seven showed growth at ampicillin concentrations as high as 1.5 mg/ml.