• The Plant Pathology Journal
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• v.31 no.1
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• pp.72-77
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• 2015

Spot blotch caused by the hemibiotrophic pathogen Cochliobolus sativus has been the major yield-reducing factor for barley production during the last decade. Monitoring transcriptional reorganization triggered in response to this fungus is an essential first step for the functional analysis of genes involved in the process. To characterize the defense responses initiated by barley resistant and susceptible cultivars, a survey of transcript abundance at early time points of C. sativus inoculation was conducted. A notable number of transcripts exhibiting significant differential accumulations in the resistant and susceptible cultivars were detected compared to the non-inoculated controls. At the p-value of 0.0001, transcripts were divided into three general categories; defense, regulatory and unknown function, and the resistant cultivar had the greatest number of common transcripts at different time points. Quantities of differentially accumulated gene transcripts in both cultivars were identified at 24 h post infection, the approximate time when the pathogen changes trophic lifestyles. The unique and common accumulated transcripts might be of considerable interest for enhancing effective resistance to C. sativus.

• Proceedings of the Korean Society of Plant Pathology Conference
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• 1995.06b
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• pp.55-75
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• 1995

Induction of HMG-Co A reductase (HMGR) is essential for the biosynthesis of sesquiterpenoid phytoalexins and steroid derivatives in Solanaceous plants following wounding and pathogen infection. To better understand this complex step in stress-responsive isoprenoid synthesis, three classes of cDNAs for HMGR (hmg1, hmg2, and hmg3) were isolated from a potato tuber library. The potato cDNAs had extensive homology in open reading frames but had low homology in the 3'-untranslated regions. RNA gel blot analysis using gene-specific probes revealed that hmg1 is induced by wounding but wound induction is strongly suppressed by arachidonic acid or by inoculation with Phytophthora infestants. In contrast, hmg2 and hmg3 are slightly induced by wounding and strongly enhanced by arachidonic acid or inoculation. The induction and suppression of HMGR genes parallel the suppression of steroid and stimulation of sesquiterpenoid accumulations observed in earlier investigations. Treatment of the tuber disks with a low concentration of methyl-jasmonate doubled the wound induced accumulation of hmg1 transcripts and steroid-glycoalkaloid accumulation, but did not affect the abundance of transcripts for hmg2 or hmg3 nor induce phytoalexins. High concentration of methyl-jasmonate suppressed hmg1 mRNA and steroid-glycoalkaloid accumulation, induced hmg3 mRNA, and did not elicit phytoalexins. Lipoxygenase inhibitors suppressed the accumulation of of hmg1 transcripts and steroid-glycoalkaloids, which were restored by exogeneous methyl-jasmonate. Methyl-jasmonate applied together with arachidonic acid enhanced the elicitor induced accumulation of sesquiterpenes and sustained steroid-glycoalkaloid levels with transcript levels for the various HMGR mRNAs equal to or greater than wound-only treatment. These results domonstrate that the consequences of wound- and pathogen-responses of plants are different at the levels of gene expression and associated secondary metabolism.

• Proceedings of the Botanical Society of Korea Conference
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• 1999.07a
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• pp.63-67
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• 1999

We have isolated more than a dozen cDNA clones corresponding to genes that were expressed in Arabidopsis leaves when they were kept in the dark. The nucleotide sequence analysis showed that some of the clones encoded proteins with significant homology to $\beta$-glucosidase (din2), branched-chain $\alpha$-keto acid dehydrogenase subunit E1$\beta$(din3), and another subunit E2 (din4), yeast RAD23 (din5), asparagine synthetase (din6), pre-mRNA splicing factor SRp35 (din7), phosphomannose isomerase (din9), seed imbibition protein (din10), and 2-oxoacid-dependent oxidase (din11). Accumulation of transcripts from din3,4,6 and 10 occurred rapidly after the plants were transferred to darkness. Transcripts from din2,9, and 11 could be detected only after 24 h of dark treatment. Inhibition of photo-synthesis by DCMU strongly induced the accumulation of transcripts from those genes, and application of sucrose to detached leaves suppressed the accumulation both in the dark and by DCMU. These observations indicate that expression of the genes is caused by sugar starvation resulted from the cessation of photosynthesis. We further showed that din2-encoded protein also accumulated in senescing leaves. Given these results, possible roles of din genes in leaves in the dark and senescing leaves are discussed.

• Journal of Life Science
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• v.11 no.1
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• pp.52-56
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• 2001

The present study intends to characterize the DNA damage-inducible responses in eukaryotic cells. The fission yeast, S. pombe, which displays efficient DNA repair systems, was used in this study as a model system for higher eukaryotes. To study UV-inducible responses in S. pombe, five UV-inducible cDNA clones were isolated from S. pombe by using subtration hybridization method. To investigate the expression of isolated genes, the cellular levels of the transcripts of these genes were determined by Northern blot analysis after UV-irradiation. The transcripts of isolated gene (UV130) increased rapidly and reached maximum accumulation after UV-irradiation. Compared to the message levels of control, the levels of maximal increase were approximately 5 fold to UV-irradiation. In order to investigation whether the increase of UV130 transcripts was a specific results of UV-irradiation, UV130 transcript levels were examined after treating the cells to Methylmethane sulfonate (MMS). The transcripts of UV130 were not induced by treatment of 0.25% MMS. These results implied that the effects of damaging agents are complex and different regulatory pathways exist for the induction of these genes. To characterize the structure of UV130 gene, nucleotide sequences were analyzed. The nucleotide sequence of 1,340 nucleotide excluding poly(A) tail contains one open reading frame, which encodes a protein of 270 amino acids. The predicted amino acid sequences of UV130 do not exhibit any significant similarity to ther known sequences in the database.

• The Plant Pathology Journal
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• v.28 no.2
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• pp.197-201
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• 2012

Potyviruses express their RNA genomes through the production of polyproteins that are processed in host cells by three virus-encoded proteases. Soybean plants produce large amounts of protease inhibitors during seed development and in response to wounding that could affect the activities of these proteases. The in vitro activities of two of the proteases of Soybean mosaic virus (SMV) and Tobacco vein mottling virus (TVMV) were compared in the rabbit reticulocyte lysate in vitro translation system using synthetic RNA transcripts. Transcripts produced from SMV and TVMV cDNAs that included the P1 and helper component-protease (HC-Pro) coding regions directed synthesis of protein products that were only partially processed. Unprocessed poly-proteins were not detected from transcripts that included all of the P1, HC-Pro, P3 and portions of the cylindrical inclusion protein coding regions of either virus. Addition of soybean trypsin inhibitor to in vitro translation reactions increased the accumulation of the unprocessed polyprotein from TVMV transcripts, but did not alter the patterns of proteins produced from SMV. These experiments suggest that SMV-and TVMV-encoded proteases are differentially sensitive to protease inhibitors.

• Proceedings of the Korean Society of Crop Science Conference
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• 2017.06a
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• pp.140-140
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• 2017

Nutritious and functional foods from crop have received great attention in recent years. Colored-grain wheat contains high phenolic compound and a large number of flavonoid. The anthocyanin and polyphenolic synthesis and accumulation is generally stimulated in response to biotic or abiotic stresses. Here, we analyzed genome wide transcripts in seedling of colored-grain wheat response to ABA and PEG treatment. About 900 and 1500 transcripts (p-value < 0.05) from ABA and PEG treatment were aligned to IWGSC1+popseq DB which is composed of over 110,000 transcripts including 100,934 coding genes. NR protein sequences of Poaceae from NCBI and protein sequence of transcription factors originated from 83 species in plant transcription factor database v3.0 were used for annotation of putative transcripts. Gene ontology analysis were conducted and KEGG mapping was performed to show expression pattern of biosynthesis genes related in flavonoid, isoflavonoid, flavons and anthocyanin biopathway. DroughtDB (http://pgsb.helmholtz-muenchen.de/droughtdb/) was used for detection of DEGs to explain that physiological and molecular drought avoidance by drought tolerance mechanisms. Drought response pathway, such as ABA signaling, water and ion channels, detoxification signaling, enzymes of osmolyte biosynthesis, phospholipid metabolism, signal transduction, and transcription factors related DEGs were selected to explain response mechanism under water deficit condition. Anthocyanin, phenol compound, and DPPH radical scavenging activity were measured and antioxidant activity enzyme assays were conducted to show biochemical adaptation under water deficit condition. Several MYB and bHLH transcription factors were up-regulated in both ABA and PEG treated condition, which means highly expressed MYB and bHLH transcription factors enhanced the expression of genes related in the biosynthesis pathways of flavonoids, such as anthocyanin and dihydroflavonols in colored wheat seedlings. Subsequently, the accumulation of total anthocyanin and phenol contents were observed in colored wheat seedlings, and antioxidant capacity was promoted by upregulation of genes involved in maintaining redox state and activation of antioxidant scavengers, such as CAT, APX, POD, and SOD in colored wheat seedlings under water deficit condition. This work may provide valuable and basic information for further investigation of the molecular responses of colored-grain wheat to water deficit stress and for further gene-based studies.

• The Plant Pathology Journal
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• v.19 no.4
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• pp.210-216
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• 2003

This study examined the existence of genetically diverse population of Cucumber mosaic virus (CMV), known as quasispecies, from lily, Nicotiana benthamiana and from purified virions. Based on the conserved sequences of CMV lily isolates in intergenic region (IR) on RNA3, the genetic variation of IR from three different sources was investigated by a specific restriction endonuclease hydrolysis of amplified reverse transcription-polymerase chain reaction (RT-PCR) products using virus-specific primers, and was compared with IR sequences. The IR nucleotide sequences of CMV lily isolates were highly conserved, however, quasispecies was detected from all three sources in low level, containing sub-populations of RNA3. These subpopulations of RNA3 were inoculated onto zucchini squash by in vitro transcripts from corresponding full-length cDNA clones together with Eny RNA1 and 2 transcripts. The systemic symptom of zucchini plants infected by these quasispecies was chlorotic spotting, which was milder than severe mosaic and stunt symptom caused by Eny-CMV. The severity of symptom was correlated with RNA accumulation of viruses. These results suggest that the genome of CMV lily isolates consists of quasispecies populations.

• Genomics & Informatics
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• v.16 no.4
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• pp.36.1-36.3
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• 2018

Next generation sequencing (NGS), a high-throughput DNA sequencing technology, is widely used for molecular biological studies. In NGS, RNA-sequencing (RNA-Seq), which is a short-read massively parallel sequencing, is a major quantitative transcriptome tool for different transcriptome studies. To utilize the RNA-Seq data, various quantification and analysis methods have been developed to solve specific research goals, including identification of differentially expressed genes and detection of novel transcripts. Because of the accumulation of RNA-Seq data in the public databases, there is a demand for integrative analysis. However, the available RNA-Seq data are stored in different formats such as read count, transcripts per million, and fragments per kilobase million. This hinders the integrative analysis of the RNA-Seq data. To solve this problem, we have developed a web-based application using Shiny, COEX-seq (Convert a Variety of Measurements of Gene Expression in RNA-Seq) that easily converts data in a variety of measurement formats of gene expression used in most bioinformatic tools for RNA-Seq. It provides a workflow that includes loading data set, selecting measurement formats of gene expression, and identifying gene names. COEX-seq is freely available for academic purposes and can be run on Windows, Mac OS, and Linux operating systems. Source code, sample data sets, and supplementary documentation are available as well.

• Journal of Life Science
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• v.16 no.1
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• pp.126-130
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• 2006

The present study intends to characterize the DNA damage-inducible responses in yeast. The fission yeast, Schizosaccharomyces pombe was used in this study as a model system for higher eukaryotes. To study UV-inducible responses in S. pombe, five UV-inducible cDNA clones were isolated from S. pombe by using subtration hybridization method. To investigate the expression of isolated genes, UVI-155, the cellular levels of the transcripts were determined by Northern blot analysis after UV-irradiation. The transcripts of isolated gene (UVI-155) increased rapidly and reached maximum accumulation after UV-irradiation. Compared to the message levels of control, the levels of maximal increase were approximately 5 fold to UV-irradiation. In order to investigation whether the increase of UVI-l55 trascripts was a specific results of UV-irradiation, UVI-155 transcript levels were examined after treating the cells to mthylmethane sulfonate (MMS). The transcripts of UVI-155 were not induced by treatment of $0.25\%$ MMS. These results implied that the effects of damaging agents are complex and different regulatory pathways exist for the induction of these genes. To characterize the UVI-155 gene, gene deletion experiments were analyzed. The deleted strain was not well grown. This result indicated that the UVI-155 gene is essential for cell viability.

• The Journal of Korean Medicine
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• v.24 no.2
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• pp.166-178
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• 2003

Objectives : Nitric oxide (NO) plays an important role in normal and pathophysiological cells as a messenger molecule, neurotransmitter, microbiological agent, or dilator of blood vessels and arteriosclerosis, respectively. This study was undertaken to understand the mechanism of NO production and effect of Hyeolbuchukeo-tang (Xiefuzhuyu-tang) on NO production in cultured vascular smooth muscle cell (VSMC). Methods and Results : VSMC was isolated from aorta and cultured. Cultured primary cells were identified as VSMC with anti--smooth muscle actin antibody. A large amount of NO was produced in cultured VSMC treated with $IFN-{\gamma}$ plus TNF in a time- and dose-dependent manner. $TNF-{\alpha}$ was a more efficient stimulator than $IFN-{\gamma}$ in NO production of cultured VSMC. iNOS protein wasdetected within 3 hrs and it increased up to 12 hrs in a time-dependent manner. However, accumulated NO in cytokine-treated VSMC was not detected within 3 hrs. NO production in cytokine-treated VSMC showed the dose- and time-dependent manner, and increased up to 48 hrs. The activated VSMC produced a large amount of NO (about 60 uM). Hyeolbuchukeo-tang (Xiefuzhuyu-tang) alone did not induceNO production, but it potentiated the effect of $TNF-{\alpha}$ on NO production and increased NO production by about 20%. Hyeolbuchukeo-tang (Xiefuzhuyu-tang) did not affect the transcriptional activity of iNOS gene, but increased the accumulation of iNOS. These results indicate that Hyeolbuchukeo-tang (Xiefuzhuyu-tang) could modulate the translational level of iNOS. PKC did not modulate NO production, but calcium ionophore A23187 decreased NO production. However, Hyeolbuchukeo-tang (Xiefuzhuyu-tang) elevated the decreased NO production in A23187-treated VSMC by modulating the stability of iNOS transcripts. Half-life of the synthesized transcripts appeared to have about 6 hrs. PDTC, an $NF-{\kappa}B$ inhibitor, blocked the accumulation of iNOS mRNA, indicating that $NF-{\kappa}B$ served as an important modulator in the transcriptional regulation of iNOS. As Hyeolbuchukeo-tang (Xiefuzhuyu-tang) potentiated the effect of the $TNF-{\alpha}$ on NO production but had no additional effect on PDTC-modulated NO production, it is suggested that Hyeolbuchukeo-tang (Xiefuzhuyu-tang) enhances the $TNF-{\alpha}-mediated$ NO production of VSMC by modulating the iNOS activity and the stability of iNOS transcripts in activated VSMC having the elevated intracellular calcium ion. Conclusions : This study suggests that Hyeolbuchukeo-tang (Xiefuzhuyu-tang) has a potential capacity for preventing and treating diseases of the circulation system, including arteriosclerosis.