• Proceedings of the Korean Society of Crop Science Conference
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• 2017.06a
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• pp.141-141
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• 2017

The ubiquitin-proteasome pathway is the major regulatory mechanism in a number of cellular processes for selective degradation of proteins and involves three steps: (1) ATP dependent activation of ubiquitin by E1 enzyme, (2) transfer of activated ubiquitin to E2 and (3) transfer of ubiquitin to the protein to be degraded by E3 complex. F-box proteins are subunit of SCF complex and involved in specificity for a target substrate to be degraded. F-box proteins regulate many important biological processes such as embryogenesis, floral development, plant growth and development, biotic and abiotic stress, hormonal responses and senescence. However, little is known about the F-box genes in wheat. The draft genome sequence of wheat (IWGSC Reference Sequence v1.0 assembly) used to analysis a genome-wide survey of the F-box gene family in wheat. The Hidden Markov Model (HMM) profiles of F-box (PF00646), F-box-like (PF12937), F-box-like 2 (PF13013), FBA (PF04300), FBA_1 (PF07734), FBA_2 (PF07735), FBA_3 (PF08268) and FBD (PF08387) domains were downloaded from Pfam database were searched against IWGSC Reference Sequence v1.0 assembly. RNA-seq paired-end libraries from different stages of wheat, such as stages of seedling, tillering, booting, day after flowering (DAF) 1, DAF 10, DAF 20, and DAF 30 were conducted and sequenced by Illumina HiSeq2000 for expression analysis of F-box protein genes. Basic analysis including Hisat, HTseq, DEseq, gene ontology analysis and KEGG mapping were conducted for differentially expressed gene analysis and their annotation mappings of DEGs from various stages. About 950 F-box domain proteins identified by Pfam were mapped to wheat reference genome sequence by blastX (e-value < 0.05). Among them, more than 140 putative F-box protein genes were selected by fold changes cut-offs of > 2, significance p-value < 0.01, and FDR<0.01. Expression profiling of selected F-box protein genes were shown by heatmap analysis, and average linkage and squared Euclidean distance of putative 144 F-box protein genes by expression patterns were calculated for clustering analysis. This work may provide valuable and basic information for further investigation of protein degradation mechanism by ubiquitin proteasome system using F-box proteins during wheat development stages.

• Proceedings of the Korean Society of Embryo Transfer Conference
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• 2002.11a
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• pp.98-98
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• 2002

Recruitment of primordial follicles(PMF) is crucial for female fertility. however, factors and mechanisms that regulate this process is poorly understood. The present study was conducted to obtain an inclusive view of the gene expression and to identify novel factors and their pathways of regulating PMF arrest and/or growth initiation. Ovaries from one-day neonatal(consists of oocyte and PMF) and five-day old(consists of PMF and primary follicles, PRIF) mice were collected, either total RNA or mRNA was isolated, and suppression subtractive hybridization(SSH) was used to isolate and clone genes that differentially expressed in day 1 and day 5 ovaries. Confirmation that some of these genes are differentially expressed in PMF and/or in PRIF was accomplished by using laser captured microdissection(LCM), RT-PCR. in situ hybridization(ISH) and/or immunohistochemistry(IHC). In toto, 357 clones were sequenced and analyzed by BLAST and RIKEN program. Sequences of 330 clones significantly matched database entries while 27 clones were novel. Forty-two and 47 different genes were identified as differentially expressed in day 1 and day 5 ovaries, respectively, while 7 genes were expressed in both stages of ovaries. Day 5-subtracted library included several genes known as markers far growing follicles, such as ZP2, MATER, and fetuin. Among the genes with assigned functions, 23.8% was associated with cell cycle/apoptosis regulation, 7.1% with cellular structure, 11.9% with metabolism, 26.2% with signal transduction, and 31.0% with gene/protein expression in day 1; while 10.6%, 17.0%, 23.5%, 25.5%, and 23.4% in day 5, respectively. Genes such as GDF-8, Lats2, Septin2, and Weel were the highly expressed genes in PMF, while HSP84, Laminin2, MATER, MTi7, PTP, and Wrn were highly expressed genes in PRIF. We have successfully discovered list of genes expressed in day 1 and day 5 ovaries and confirmed that some of them are differentially expressed in PMF and/or PRIF. Gene expression profile from the present study would provide insight for the future study on the mechanism(s) involved in primordial-primary follicular transition. This work was Supported by Korean Health 21 RND Project, Ministry of Health and Welfare, Korea (01-PJ10-PG6-01GN13-0002).

• Korean Journal of Clinical Laboratory Science
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• v.52 no.3
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• pp.229-236
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• 2020

Sixty-five molds isolated from clinical specimens were included in this study. All the isolates were molds that could be identified morphologically, strains that are difficult to identify because of morphological similarities, and strains that require species-level identification. PCR and direct sequencing were performed to target the internal transcribed spacer (ITS) region, the D1/D2 region, and the β-tubulin gene. Comparative sequence analysis using the GenBank database was performed using the basic local alignment search tool (BLAST) algorithm. The fungi identified morphologically to the genus level were 67%. Sequencing analysis was performed on 62 genera and species level of the 65 strains. Discrepancies were 14 (21.5%) of the 65 strains between the results of phenotypic and molecular identification. B. dermatitidis, T. marneffei, and G. argillacea were identified for the first time in Korea using the DNA sequencing method. Morphological identification is a very useful method in terms of the reporting time and costs in cases of frequently isolated and rapid growth, such as Aspergillus. When molecular methods are employed, the cost and clinical significance should be considered. On the other hand, the molecular identification of molds can provide fast and accurate results.

• Journal of Life Science
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• v.30 no.7
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• pp.625-629
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• 2020

The Ocean is a rich source of diverse living organisms include viruses. In this study, we examined the microbial communities in the sea adjacent to Jeju Island in two seasons by metatranscriptomics. We collected and extracted total RNA, and, using the next-generation sequencing HiSeq 2000 and de novo transcriptome assembly, we identified 652,984 and 163,759 transcripts from the March and December samples, respectively. The most abundant organisms in March were bacteria, while eukaryotes were dominant in the December sample. The bacterial communities differed between the two samples, suggesting seasonal change. To identify the viruses, we searched the transcripts against a viral reference database using MegaBLAST with the most identified being bacteriophages infecting the marine bacteria. However, we also revealed an abundance of transcripts associated with diverse herpesviruses in the two transcriptomes, indicating the presence or possible threat of infection of fish in the sea around Jeju Island. This data is valuable for the study of marine microbial communities and for identifying possible viral pathogens.

• Korean Journal of Food Science and Technology
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• v.34 no.2
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• pp.283-289
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• 2002

This study was performed to search for potential microorganism that has rapid fermenting and physiological function from anchovy sauce. We isolated three bacterial strains, JM-1, JM-2, and JM-3 with proteolytic and fibrinolytic activity from anchovy sauce. Among the 3 bacterial strains, JM-3 showed the strongest proteolytic and fibrinolytic activity. Bacterial strain JM-3 was gram-positive rod, motile and formed endospore. The 16S rRNA of bacterial strain JM-3 was amplified by PCR and then its sequence was determined by ABI 310 genetic analyzer. The 16S rRNA sequence of bacterial strain JM-3 was compared to BLAST DNA database and identified to Bacillus subtilis with 99% of homology. The optimum temperature, pH and NaCl concentration for growth of B. subtilis JM-3 were $40^{\circ}C$, 5.0 and 0%, respectively. The optimum temperature, pH and NaCl concentration for proteolytic and fibrinolytic enzyme production of B. subtilis JM-3 were same as optimum conditions for growth. At 20% of NaCl concentration which is common NaCl concentration of fish sauce, B. subtilis JM-3 showed about 60% of proteolytic and fibrinolytic activity of 0% NaCl concentration. From above results, we found that B. subtilis JM-3 will be able to used for starter of functional fish sauce.

• Korean Journal of Ichthyology
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• v.29 no.2
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• pp.139-145
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• 2017

The spontaneous color mutant, albino individuals of genus Misgurnus, are rarely discovered in Korea and there are difficult to identify morphological species due to lack melanin pigmentation. In this study, we developed a genetic identification method for the species of albino Misgurnus individuals based on phylogenetic analysis by using recombination activating gene 1 (rag1) and cytochrome b (cytb) region of mitochondrial DNA. As a result of molecular phylogenetic analysis, three clades were identified as Misgurnus mizolepis, M. anguillicaudatus and M. mohoity. The homology of the cytb sequences of M. mohoity was best match to that of M. mohoity sequences in GenBank database. As a result of species identification of 25 albino Misgurnus individuals based on the phylogenetic tree, the red-eye type was identified as 16 M. anguillicaudatus and one M. mizolepis. The remaining three individuals were identified as one M. mizolepis ♀${\times}$M. anguillicaudatus ♂, and two M. mohoity ♀${\times}$M. anguillicaudatus ♂, respectively. In addition, the five black-eye type individuals were identified as one M. anguillicaudatus, three M. mizolepis and one M. mohoity. Therefore, this genetic identification method will be an useful techniques for species or hybrid identification in genus Misgurnus.

• KDI Journal of Economic Policy
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• v.35 no.1
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• pp.63-101
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• 2013

'Venture firms' in Korea are the firms who are certified as 'venture', whose certification types are defined by a law ('Special Law for the Support of Venture Firms'), and therefore encompass not only the venture capital-financed companies, which are usually regarded as ventures in USA and European countries, but also other types of firms such as R&D-intensive firms and the firms with financial guarantee or loans through technology evaluation ('technology finance or loan firms'). This paper examines the differences in the Korean venture firms' growth between the venture certification types. For the empirical analysis, this paper uses the lists of venture-certified firms from 1998 to 2010 which are then linked with their financial data in Korea Enterprises Database (KED). According to the results of empirical analyses, the companies in the 'venture capital-financed firms' type show greater growth rate in sales and the number of regular employees 3 and 5 years after first venture certification than the firms in type of 'technology finance/loan firms'. Moreover, the newly certified companies in 'R&D-intensive firms' type are also showing faster growth than the 'technology finance/loan firms' since 2003 where the venture industry has undergone a consolidation phase after the blast of so-called 'IT venture bubble' in 2001~2002. These results imply that the so-called 'venture firms' in Korea are composed with heterogeneous firm groups with different characteristics and that the companies selected through market mechanism ('venture capital-financed firms') outperforms the companies selected on the basis of policy interests ('technology finance/loan firms') in terms of the growth in sales and employment. On the basis of these findings, this paper suggests that the current venture-support policy should consider the different policy demands of firms across the type of venture certification more actively and that should refocus the objective of policies on facilitating venture capital market rather than emphasizing the nominal increase in the number of venture-certified firms.

• Journal of Life Science
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• v.14 no.4
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• pp.650-656
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• 2004

Oryza grandiglumis (CCDD, 2n=48), one of the wild rice species, has been known to possess fungal-,bacterial-, and insect-resistance against sheath blight, rice blast, bacterial leaf blight and brown plant hopper (Nilaparvata lugens). To rapidly isolate differentially expressed genes responding to fungal and wounding stress, wounding and yeast extract were treated to O. grandiglumis for 24 hrs. Suppression subtractive hybridization (SSH) method was used to obtain differentially expressed genes from yeast extract and wounding treated plants. Seven hundreds and seventy six clones were obtained by subcloning PCR product, and colony array and screening were carried out using radio-isotope labeled cDNA probes prepared from the wounding and yeast extract treated plants. One hundred and fifteen colonies were confirmed as true positive ones. Average insert size of the clones were ranged from 400 bp to 700 bp and all the inserts were sequenced. To decide the identity of those clones, sequences were analyzed by sequence homology via GenBank database. The homology search result showed that 68 clones were matched to the genes with known function; 16 were related to primary metabolism, 5 to plant retrotransposons, 5 to defense related metallothionein-like genes. In addition to that, others were matched to various genes with known function in amino acid synthesis and processing, membrane transport, and signal transduction, so on. In northern blot analysis, induced expressions of ogwfi-161, ogwfi-646, ogwfi-663, and ogwfi-695 by wounding and yeast extract treatments were confirmed. The result indicates that SSH method is very efficient for rapid screening of differentially expressed genes.

• Journal of Life Science
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• v.17 no.2 s.82
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• pp.279-285
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• 2007

Detection of Mycoplasma DNA from the 30 cases of cancer tissues and the normal tissues surrounding the cancer tissues obtained from the patients with gastric cancer and the other 30 cases of cancer tissues and the normal tissues surrounding the cancer tissues obtained from the patients with colon cancer were evaluated by polymerase chain reaction(PCR). The PCR products were sequenced using an ABI 377 automatic DNA sequencer, and these sequences were confirmed by comparing sequences with the database of the National Center for Biotechnology Information BLAST network server. Mycoplasmas DNA were defected in 18 (60%) cases of normal tissues which were around gastric cancer and were 13 (43.3%) cases of gastric cancer tissues. Mycoplasmas DNA were detected in 15(50%) cases of normal tissues which were around colon cancer and 12 (40%) cases of colon cancer tissues. The M. faucium, M. subdolum, M. salivarium, M. auris, M. hyosynoviae, and M. conjunctivae were detected from the gastric cancer tissues. The M. faucium, M. subdolum,, M. salivarium, M. auris, M. hyosynoviae, M. bovigenitalium and M. pulmonis were detected from the normal tissues around gastric cancer. The M. faucium, M. subdolum, M. salivarium, M. auris, M. hyosynoviae, M. synoviae M. bovigenitalium, M. gallinarum, and M. moatsii were detected from the colon cancer. The M. faucium, M. subdolum, M. salivarium, M. auris, M. hyosynoviae, M. bovis, M. opalescens, M. bovigenitalium, M. gallinarum, and M. moatsii were detected from the normal tissues around the colon cancer. These results suggest that Mycoplasmas infection may not correlate with gastric cancer and colon cancer, because of the detection rate of Mycoplasmas DNA were not significantly differences between normal and cancer tissues from the patients.