• Journal of Plant Biotechnology
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• v.44 no.2
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• pp.125-134
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• 2017

Enhanced disease susceptibility1 (EDS1) is a regulator of basal defense responses required for resistance mediated by TIR-NBS-LRR containing R proteins. We identified three transcripts of EDS1-like genes encompassing diverse/separate expression patterns, based on the transcriptome analysis by Next Generation Sequencing (NGS) of V. flexuosa inoculated with Elsinoe ampelina. These genes were designated VfEDL1 (Vitis flexuosa Enhanced Disease Susceptibility1-like1), VfEDL2 and VfEDL3, and contained 2464, 1719 and 1599 bp, with 1791, 1227 and 1599 bp open reading frames (ORFs), encoding proteins of 596, 408 and 532 amino acids, respectively. The predicted amino acid sequences of all three genes showed the L-family lipase-like domain (class 3 lipase domain), and exhibited a potential lipase catalytic triad, aspartic acid, histidine and serine in the conserved G-X-S-X-G. All three VfEDL genes were upregulated at 1 hpi against the bacterial and fungal pathogens Rizhobiumvitis and E. ampelina, respectively, except VfEDL1, which was downregulated against E. ampelina at all time points. Against E. ampelina, VfEDL2 and VfEDL3 showed downregulated expression at later time points. When evaluated against R. vitis, VfEDL1 showed downregulated expression at all time points after 1 hpi, while VfEDL3 showed upregulation up to 24 hpi. Based on the expression response, all three genes may be involved in plant resistant responses against R. vitis, and VfEDL2 and VfEDL3 show additional resistant responses against E. ampelina infection.

• Parasites, Hosts and Diseases
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• v.58 no.3
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• pp.287-299
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• 2020

Cystic echinococcosis (CE) is a zoonotic infection caused by Echinococcus granulosus larvae. It seriously affects the development of animal husbandry and endangers human health. Due to a poor understanding of the cystic fluid formation pathway, there is currently a lack of innovative methods for the prevention and treatment of CE. In this study, the protoscoleces (PSCs) in the encystation process were analyzed by high-throughput RNA sequencing. A total of 32,401 transcripts and 14,903 cDNAs revealed numbers of new genes and transcripts, stage-specific genes, and differently expressed genes. Genes encoding proteins involved in signaling pathways, such as putative G-protein coupled receptor, tyrosine kinases, and serine/threonine protein kinase, were predominantly up-regulated during the encystation process. Antioxidant enzymes included cytochrome c oxidase, thioredoxin glutathione, and glutathione peroxidase were a high expression level. Intriguingly, KEGG enrichment suggested that differentially up-regulated genes involved in the vasopressin-regulated water reabsorption metabolic pathway may play important roles in the transport of proteins, carbohydrates, and other substances. These results provide valuable information on the mechanism of cystic fluid production during the encystation process, and provide a basis for further studies on the molecular mechanisms of growth and development of PSCs.

• Journal of Plant Biotechnology
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• v.42 no.4
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• pp.298-311
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• 2015

Grape is one of the important fruit crops around the world, and exposed to disease and pests, and internal or environmental stresses in the vineyards. Breeding and cultivation of new varieties of high quality-grapes resistant to diseases and pests and tolerant to stresses are the most important steps in the grape production. However, conventional breeding has laborious and time-consuming procedures in maintaining and selecting seedlings in the fields. Development of molecular breeding technology through understanding of molecular mechanism of useful traits can be used as an alternative strategy to improve the efficiency of grape breeding program by cross hybridization in grape development programs. The completion of the grape genome sequencing project provided the way to discover the novel genes and to analyze their functions. Comparative genomics, transcriptomic analysis, and the genome-wide identification and analysis of useful genes as well as development of molecular marker for valuable traits could provide novel insights into fruit quality and the responses to diseases and stresses, and can be used as important information in molecular breeding programs for grape development.

• International Journal of Industrial Entomology and Biomaterials
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• v.31 no.1
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• pp.14-19
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• 2015

In a previous report, we identified several candidate antimicrobial peptides through de novo RNA sequencing of the centipede Scolopendra subspinipes mutilans. Here, we identify and characterize one of these peptides, Scolopendrasin I. We identified the centipede antimicrobial peptide Cecropin from the centipede transcriptome using an SVM algorithm, and subsequently analyzed the amino acid sequence for predicted secondary structure using a GOR algorithm. We identified an alpha helical region of Cecropin and named it Scolopendrasin I. We then assessed antimicrobial and hemolytic activity of Scolopendrasin I. Scolopendrasin I showed antimicrobial activity against various microbes, including antibiotic-resistant Gram-negative bacteria, in a radial diffusion assay. Scolopendrasin I had potent antibacterial activity against acne-associated microbes in a colony count assay and showed no hemolytic activity in a hemolysis assay. In addition, we confirmed that Scolopendrasin I bound to the surface of bacteria via a specific interaction with lipoteichoic acid and lipopolysaccharide, two components of bacterial cell membranes. In conclusion, the results presented here provide evidence that this is an efficient strategy for antimicrobial peptide candidate identification and that Scolopendrasin I has potential for successful antibiotic development.

• Asian-Australasian Journal of Animal Sciences
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• v.30 no.1
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• pp.20-33
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• 2017

Objective: Superstimulatory treatment of one-month-old lambs can achieve synchronous development of numerous growing follicles. However, these growing follicles cannot complete maturation and ovulation. Oocyte maturation and competence are acquired during follicular development, in which granulosa cells play an essential role. Methods: In this study, we applied RNA sequencing to analyze and compare gene expression between prepubertal and adult superstimulated follicle granulosa cells in sheep. Results: There were more than 300 genes that significantly differed in expression. Among these differently expressed genes, many extracellular matrix genes (EGF containing Fibulin Like Extracellular Matrix Protein 1, pentraxin 3, adrenomedullin, and osteopontin) were significantly down-regulated in the superstimulated follicles. Ingenuity pathway and gene ontology analyses revealed that processes of axonal guidance, cell proliferation and DNA replication were expressed at higher levels in the prepubertal follicles. Epidermal growth factor, T-Box protein 2 and beta-estradiol upstream regulator were predicted to be active in prepubertal follicles. By comparison, tumor protein P53 and let-7 were most active in adult follicles. Conclusion: These results may contribute to a better understanding of the mechanisms governing the development of granulosa cells in the growing follicle in prepubertal sheep.

• Journal of Microbiology and Biotechnology
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• v.24 no.9
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• pp.1170-1177
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• 2014

Mycobacterium gilvum PYR-GCK is a bacterial strain under study for its bioremediation use on heavy hydrocarbon pollutants in the environment. During the course of our study, mammalian cell entry (mce) genes, known to facilitate pathogenicity in M. tuberculosis, were highly expressed during a comparative and substrate-related cultural global transcriptomic study. RNA sequencing of the global transcriptome of the test strain in two different substrates, pyrene and glucose, showed high expression of the mce genes based on the differential results. After validating the expression of these genes with quantitative real-time PCR, we arrived at the conclusion that the genes were expressed based on the pyrene substrate (a phytosterol compound), and sterol metabolism is said to activate the expression of the mce genes in some actinomycetes bacteria, M. gilvum PYR-GCK in this case. This study is believed to be important based on the fact that some mycobacterial strains are undergoing a continuous research as a result of their use in practical bioremediation of anthropogenic exposure of toxic organic wastes in the environment.

• Journal of Microbiology and Biotechnology
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• v.23 no.9
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• pp.1293-1303
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• 2013

Antibiotic resistance of soilborne Acinetobacter species has been poorly explored. In this study, norfloxacin resistance of a soil bacterium, Acinetobacter oleivorans DR1, was investigated. The frequencies of mutant appearance of all tested non-pathogenic Acinetobacter strains were lower than those of pathogenic strains under minimum inhibitory concentration (MIC). When the quinolone-resistance-determining region of the gyrA gene was examined, only one mutant (His78Asn) out of 10 resistant variants had a mutation. Whole transcriptome analysis using a RNA-Seq demonstrated that genes involved in SOS response and DNA repair were significantly up-regulated by norfloxacin. Determining the MICs of survival cells after norfloxacin treatment confirmed some of those cells were indeed persister cells. Ten colonies, randomly selected from among those that survived in the presence of norfloxacin, did not exhibit increased MIC. Thus, both the low mutation frequency of the target gene and SOS response under norfloxacin suggested that persister formation might contribute to the resistance of DR1 against norfloxacin. The persister frequency increased without a change in MIC when stationary phase cells, low growth rates conditions, and growth-deficient dnaJ mutant were used. Taken together, our comprehensive approach, which included mutational analysis of the target gene, persister formation assays, and RNA sequencing, indicated that DR1 survival when exposed to norfloxacin is related not only to target gene mutation but also to persister formation, possibly through up-regulation of the SOS response and DNA repair genes.

• Proceedings of the Korean Society of Crop Science Conference
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• 2017.06a
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• pp.57-57
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• 2017

Chrysanthemum is one of the most important floral crop in Korea produced about 7 billion dollars (1 billion for pot and 6 billion for cutting) in 2013. However, it is difficult to breed and to do genetic study because 1) it is highly self-incompatible, 2) it is outcrossing crop having heterozygotes, and 3) commercial cultvars are hexaploid (2n = 6x = 54). Although low-density genetic map and QTL study were reported, it is not enough to apply for the marker assisted selection and other genetic studies. Therefore, we are trying to make high-density genetic mapping using GBS with about 100 $F_1s$ of C. boreale that is oHohhfd diploid (2n = 2x = 18, about 2.8Gb) instead of commercial culitvars. Since Chrysanthemum is outcrossing, two-way pseudo-testcross model would be used to construct genetic map. Also, genotype-by-sequencing (GBS) would be utilized to generate sufficient number of markers and to maximize genomic representation in a cost effective manner. Those completed sequences would be analyzed with TASSEL-GBS pipeline. In order to reduce sequence error, only first 64 sequences, which have almost zero percent error, would be incorporated in the pipeline for the analysis. In addition, to reduce errors that is common in heterozygotes crops caused by low coverage, two rare cutters (NsiI and MseI) were used to increase sequence depth. Maskov algorithm would also used to deal with missing data. Further, sparsely placed markers on the physical map would be used as anchors to overcome problems caused by low coverage. For this purpose, were generated from transcriptome of Chrysanthemum using MISA program. Among those, 10 simple sequence repeat (SSR) markers, which are evenly distributed along each chromosome and polymorphic between two parents, would be selected.

• BMB Reports
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• v.43 no.9
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• pp.635-641
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• 2010

Piwi proteins and Piwi-interacting RNAs (piRNAs) have been implicated in transposon control in germline from Drosophila to mammals. To examine the profile of small RNA expression in human cancer cells and explore difference in small RNA transcriptome, small RNA libraries prepared from wildtype, HILI overexpressed and HILI knockdowned Hela cells were sequenced using Solexa technology. piRNAs and other repeat-associated small RNAs were observed in Hela cells. By using in situ hybridization, piR-49322 was localized in the nucleolus and around the periphery of nuclear membrane in Hela cells. Following the overexpression of HILI, the retrotransposon elements LINE1 was significantly repressed, while LINE1-associated small RNAs decreased in abundance. The present study demonstrated that HILI along with piRNAs plays a role in LINE1 suppression in Hela cancer cell line.

• The Plant Pathology Journal
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• v.29 no.3
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• pp.223-233
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• 2013

Rice stripe virus (RSV) is one of the most destructive viruses of rice, and greatly reduces rice production in China, Japan, and Korea, where mostly japonica cultivars of rice are grown. RSV is transmitted by the small brown plant-hopper (SBPH) in a persistent and circulative-propagative manner. Several methods have been developed for detection of RSV, which is composed of four single-stranded RNAs that encode seven proteins. Genome sequence data and comparative phylogenetic analysis have been used to identify the origin and diversity of RSV isolates. Several rice varieties resistant to RSV have been selected and QTL analysis and fine mapping have been intensively performed to map RSV resistance loci or genes. RSV genes have been used to generate several genetically modified transgenic rice plants with RSV resistance. Recently, genome-wide transcriptome analyses and deep sequencing have been used to identify mRNAs and small RNAs involved in RSV infection; several rice host factors that interact with RSV proteins have also been identified. In this article, we review the current statues of RSV research and propose integrated approaches for the study of interactions among RSV, rice, and the SBPH.