Publications by authors named "Jung Eun Hwang"

24 Publications

  • Page 1 of 1

Effects of Different Growth Media on In Vitro Seedling Development of an Endangered Orchid Species .

Plants (Basel) 2021 Jun 11;10(6). Epub 2021 Jun 11.

Division of Restoration Research, Research Center for Endangered Species, National Institute of Ecology, Yeongyang 36531, Korea.

is becoming endangered, and even extinct, due to habitat destruction and illegal collection, and the development of an optimized artificial propagation system is necessary for its conservation and reintroduction. Thus, the effects of plant growth medium strength (Murashige and Skoog (MS) and Hyponex media) and the addition of activated charcoal (AC) and organic supplements on seedling growth of were investigated through in vitro seed culture. The results showed that seedling growth was higher in half-strength (1/2) media than in full-strength media. After the addition of AC, the highest leaf area (2.14 cm) was recorded in the seedlings grown in 1/2 Hyponex medium, and after the addition of organic supplements, root development increased regardless of the media type. Among the sixteen suitable media tested at later seedling growth stages, 1/2 MS medium with the addition of 0.6 g·L AC, 30 g·L banana homogenate and 10 g·L apple homogenate was generally effective in fresh weight (6.13 g) and root length (9.59 cm). We demonstrated which organic supplements are preferred for in vitro growth of seedlings developed from protocorms by asymbiotic seed culture, which can be used for mass production and conservation of this rare epiphytic orchid.
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http://dx.doi.org/10.3390/plants10061193DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8230817PMC
June 2021

Overexpression of rice jacalin-related mannose-binding lectin (OsJAC1) enhances resistance to ionizing radiation in Arabidopsis.

BMC Plant Biol 2019 Dec 18;19(1):561. Epub 2019 Dec 18.

Advanced Radiation Technology Institute, Korea Atomic Energy Research Institute, 29 Geumgu-gil, Jeongeup-si, Jeollabuk-do, 56212, Republic of Korea.

Background: Jacalin-related lectins in plants are important in defense signaling and regulate growth, development, and response to abiotic stress. We characterized the function of a rice mannose-binding jacalin-related lectin (OsJAC1) in the response to DNA damage from gamma radiation.

Results: Time- and dose-dependent changes of OsJAC1 expression in rice were detected in response to gamma radiation. To identify OsJAC1 function, OsJAC1-overexpressing transgenic Arabidopsis plants were generated. Interestingly, OsJAC1 overexpression conferred hyper-resistance to gamma radiation in these plants. Using comparative transcriptome analysis, genes related to pathogen defense were identified among 22 differentially expressed genes in OsJAC1-overexpressing Arabidopsis lines following gamma irradiation. Furthermore, expression profiles of genes associated with the plant response to DNA damage were determined in these transgenic lines, revealing expression changes of important DNA damage checkpoint and perception regulatory components, namely MCMs, RPA, ATM, and MRE11.

Conclusions: OsJAC1 overexpression may confer hyper-resistance to gamma radiation via activation of DNA damage perception and DNA damage checkpoints in Arabidopsis, implicating OsJAC1 as a key player in DNA damage response in plants. This study is the first report of a role for mannose-binding jacalin-related lectin in DNA damage.
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http://dx.doi.org/10.1186/s12870-019-2056-8DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6921557PMC
December 2019

Overexpression of rice F-box protein OsFBX322 confers increased sensitivity to gamma irradiation in Arabidopsis.

Genet Mol Biol 2020 2;43(1):e20180273. Epub 2020 Mar 2.

Korea Atomic Energy Research Institute, Advanced Radiation Technology Institute, Jeongeup, Republic of Korea.

Ionizing radiation has a substantial effect on physiological and biochemical processes in plants via induction of transcriptional changes and diverse genetic alterations. Previous microarray analysis showed that rice OsFBX322, which encodes a rice F-box protein, was downregulated in response to three types of ionizing radiation: gamma irradiation, ion beams, and cosmic rays. In order to characterize the radiation-responsive genes in rice, OsFBX322 was selected for further analysis. OsFBX322 expression patterns in response to radiation were confirmed using quantitative RT-PCR. Transient expression of a GFP-OsFBX322 fusion protein in tobacco leaf epidermis indicated that OsFBX322 is localized to the nucleus. To determine the effect of OsFBX322 expression on radiation response, OsFBX322 was overexpressed in Arabidopsis. Transgenic overexpression lines were more sensitive to gamma irradiation than control plants. These results suggest that OsFBX322 plays a negative role in the defense response to radiation in plants. In addition, we obtained four co-expression genes of OsFBX322 by specific co-expression networks using the ARANCE. Quantitative RT-PCR showed that the four genes were also downregulated after exposure to the three types of radiation. These results imply that the co-expressed genes may serve as key regulators in the radiation response pathway in plants.
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http://dx.doi.org/10.1590/1678-4685-GMB-2018-0273DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7251472PMC
March 2020

Comparisons of item difficulty and passing scores by test equating in a basic medical education curriculum.

Korean J Med Educ 2019 Jun 30;31(2):147-157. Epub 2019 May 30.

Department of Pathology, College of Medicine, The Catholic University of Korea, Seoul, Korea.

Purpose: Test equating studies in medical education have been conducted only for high-stake exams or to compare two tests given in a single course. Based on item response theory, we equated computer-based test (CBT) results from the basic medical education curriculum at the College of Medicine, the Catholic University of Korea and evaluated the validity of using fixed passing scores.

Methods: We collected 232 CBTs (28,636 items) for 40 courses administered over a study period of 9 years. The final data used for test equating included 12 pairs of tests. After test equating, Wilcoxon rank-sum tests were utilized to identify changes in item difficulty between previous tests and subsequent tests. Then, we identified gaps between equated passing scores and actual passing scores in subsequent tests through an observed-score equating method.

Results: The results of Wilcoxon rank-sum tests indicated that there were no significant differences in item difficulty distribution by year for seven pairs. In the other five pairs, however, the items were significantly more difficult in subsequent years than in previous years. Concerning the gaps between equated passing scores and actual passing scores, equated passing scores in 10 pairs were found to be lower than actual passing scores. In the other two pairs, equated passing scores were higher than actual passing scores.

Conclusion: Our results suggest that the item difficulty distributions of tests taught in the same course during successive terms can differ significantly. It may therefore be problematic to use fixed passing scores without considering this possibility.
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http://dx.doi.org/10.3946/kjme.2019.126DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6589614PMC
June 2019

Functional Mechanisms Underlying the Antimicrobial Activity of the Trx-like Protein.

Int J Mol Sci 2019 Mar 20;20(6). Epub 2019 Mar 20.

National Institute of Ecology, 1210 Geumgang-ro, Maseo-myeon, Seocheon-gun 33657, Korea.

Plants are constantly subjected to a variety of environmental stresses and have evolved regulatory responses to overcome unfavorable conditions that might reduce or adversely change a plant's growth or development. Among these, the regulated production of reactive oxygen species (ROS) as a signaling molecule occurs during plant development and pathogen defense. This study demonstrates the possible antifungal activity of Tetratricopeptide Domain-containing thioredoxin (OsTDX) protein against various fungal pathogens. The transcription of OsTDX was induced by various environmental stresses known to elicit the generation of ROS in plant cells. OsTDX protein showed potent antifungal activity, with minimum inhibitory concentrations (MICs) against yeast and filamentous fungi ranging between 1.56 and 6.25 and 50 and 100 µg/mL, respectively. The uptake of SYTOX-Green into fungal cells and efflux of calcein from artificial fungus-like liposomes suggest that its killing mechanism involves membrane permeabilization and damage. In addition, irregular blebs and holes apparent on the surfaces of OsTDX-treated fungal cells indicate the membranolytic action of this protein. Our results suggest that the OsTDX protein represents a potentially useful lead for the development of pathogen-resistant plants.
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http://dx.doi.org/10.3390/ijms20061413DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6471494PMC
March 2019

A comprehensive analysis of the Korean fir (Abies koreana) genes expressed under heat stress using transcriptome analysis.

Sci Rep 2018 07 6;8(1):10233. Epub 2018 Jul 6.

Division of Ecological Conservation, Bureau of Ecological Research, National Institute of Ecology, Seocheon, Republic of Korea.

Korean fir (Abies koreana), a rare species endemic to South Korea, is sensitive to climate change. Here, we used next-generation massively parallel sequencing technology and de novo transcriptome assembly to gain a comprehensive overview of the Korean fir transcriptome under heat stress. Sequencing control and heat-treated samples of Korean fir, we obtained more than 194,872,650 clean reads from each sample. After de novo assembly and quantitative assessment, 42,056 unigenes were generated with an average length of 908 bp. In total, 6,401 differentially expressed genes were detected, of which 2,958 were up-regulated and 3,443 down-regulated, between the heat-treated and control samples. A gene ontology analysis of these unigenes revealed heat-stress-related terms, such as "response to stimulus". Further, in depth analysis revealed 204 transcription factors and 189 Hsps as differentially expressed. Finally, 12 regulated candidate genes associated with heat stress were examined using quantitative real-time PCR (qRT-PCR). In this study, we present the first comprehensive characterisation of Korean fir subjected to heat stress using transcriptome analysis. It provides an important resource for future studies of Korean fir with the objective of identifying heat stress tolerant lines.
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http://dx.doi.org/10.1038/s41598-018-28552-1DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6035224PMC
July 2018

Prevalence and predictors of tricyclic antidepressant use among elderly Koreans in primary-care and specialty clinics.

Int J Clin Pharmacol Ther 2018 May;56(5):224-230

Objectives: Tricyclic antidepressants (TCAs) are prescribed with caution in the elderly due to diverse side effects. We analyzed the patterns of TCA use in elderly patients in primary-care and specialty clinics and investigated factors influencing TCA prescriptions.

Materials And Methods: Elderly patients (≥ 65 years old) prescribed antidepressants in primary-care clinics in 2013 were included from the Health Insurance Review and Assessment Service-Aged Patient Sample (HIRA-APS). Prevalence of TCA prescriptions was assessed by insurance coverage status, clinical specialty, and region. Multiple logistic regression analysis was performed to compute odds ratios (ORs) and 95% confidence intervals (CIs) for factors associated with TCA prescriptions.

Results: TCAs and selective serotonin reuptake inhibitors (SSRIs) comprised 45.2% and 15.0% of all antidepressant prescriptions, respectively. TCAs comprised 61.5% and 20.7% of antidepressant prescriptions for pain and depression, respectively. Patients aged ≥ 85 years were less likely to be treated with TCAs (OR 0.81, 95% CI 0.79 - 0.84) than those aged 65 - 69 years. The odds for being prescribed TCAs were higher for patients residing in cities (OR 1.20, 95% CI 1.18 - 1.23), treated in nonpsychiatric clinics (OR 5.64, 95% CI 5.53 - 5.76), and those covered by Veteran's Health (OR 1.62, 95% CI 1.37 - 1.90) when compared to patients residing in the Seoul metropolitan area, treated in psychiatric clinics, or covered by National Health Insurance, respectively. The prescriptions of TCAs with pain diagnoses were much higher than prescriptions for depression (OR 1.87, 95% CI 1.82 - 1.93).

Conclusions: Compared with a 2005 report, the prevalence of TCA prescriptions in elderly patients in Korea has decreased substantially, but remains high. Various efforts should be considered to reduce TCA prescriptions in the elderly.
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http://dx.doi.org/10.5414/CP203157DOI Listing
May 2018

Individual class evaluation and effective teaching characteristics in integrated curricula.

BMC Med Educ 2017 Dec 12;17(1):252. Epub 2017 Dec 12.

Department of Pathology, College of Medicine, The Catholic University of Korea, Seoul, Republic of Korea.

Background: In an integrated curriculum, multiple instructors take part in a course in the form of team teaching. Accordingly, medical schools strive to manage each course run by numerous instructors. As part of the curriculum management, course evaluation is conducted, but a single, retrospective course evaluation does not comprehensively capture student perception of classes by different instructors. This study aimed to demonstrate the need for individual class evaluation, and further to identify teaching characteristics that instructors need to keep in mind when preparing classes.

Methods: From 2014 to 2015, students at one medical school left comments on evaluation forms after each class. Courses were also assessed after each course. Their comments were categorized by connotation (positive or negative) and by subject. Within each subject category, test scores were compared between positively and negatively mentioned classes. The Mann-Whitney U test was performed to test group differences in scores. The same method was applied to the course evaluation data.

Results: Test results for course evaluation showed group difference only in the practice/participation category. However, test results for individual class evaluation showed group differences in six categories: difficulty, main points, attitude, media/contents, interest, and materials. That is, the test scores of classes positively mentioned in six domains were significantly higher than those of negatively mentioned classes.

Conclusions: It was proved that individual class evaluation is needed to manage multi-instructor courses in integrated curricula of medical schools. Based on the students' extensive feedback, we identified teaching characteristics statistically related to academic achievement. School authorities can utilize these findings to encourage instructors to develop effective teaching characteristics in class preparation.
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http://dx.doi.org/10.1186/s12909-017-1097-7DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5728067PMC
December 2017

Molecular dissection of the response of the rice Systemic Acquired Resistance Deficient 1 (SARD1) gene to different types of ionizing radiation.

Int J Radiat Biol 2017 07 16;93(7):717-725. Epub 2017 Mar 16.

a Advanced Radiation Technology Institute, Korea Atomic Energy Research Institute , Jeongeup , Jeollabuk , Republic of Korea.

Purpose: Exposure to ionizing radiation induces plant defenses by regulating the expression of response genes. The systemic acquired resistance deficient 1 (SARD1) is a key gene in plant defense response. In this study, the function of Oryza sativa SARD1 (OsSARD1) was investigated after exposure of seeds/plants to ionizing radiation, jasmonic acid (JA) or salicylic acid (SA).

Materials And Methods: Rice seeds exposed to two types of ionizing radiations (gamma ray [GR] and ion beam [IB]) were analyzed by quantitative reverse transcription PCR (qRT-PCR) to identify the genes that are altered in response to ionizing radiation. Then, OsSARD1-overexpressing homozygous Arabidopsis plants were generated to assess the effects of OsSARD1 in the response to irradiation. The phenotypes of these transgenic plants, as well as control plants, were monitored after GR irradiation at doses of 200 and 300 Gray (Gy).

Results: The OsSARD1 transcript was strongly downregulated after exposure to GR and IB irradiation. Previous phylogenetic analysis showed that the Arabidopsis SARD1 (AtSARD1) protein is closely related to Arabidopsis calmodulin-binding protein 60g (AtCBP60g), which is known to be required for activation of SA biosynthesis. In this study, phylogenetic analysis showed that OsSARD1 was grouped with AtSARD1. The OsSARD1 gene was induced after exposure to SA and JA. The biological phenotype of OsSARD1-overexpressing Arabidopsis plants was examined. OsSARD1-overexpressing plants displayed resistance to GR; in comparison with wild-type plants, the height and weight of OsSARD1-overexpressing plants were significantly greater after GR irradiation. In addition, OsSARD1 protein was abundantly accumulated in the nucleus.

Conclusions: The results indicate that OsSARD1 plays an important role in the regulation of the defense responses to GR and IB irradiation and exhibits phytohormone induced expression.
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http://dx.doi.org/10.1080/09553002.2017.1297901DOI Listing
July 2017

Identification of gamma ray irradiation-induced mutations in membrane transport genes in a rice population by TILLING.

Genes Genet Syst 2017 Apr 1;91(5):245-256. Epub 2016 Sep 1.

Advanced Radiation Technology Institute, Korea Atomic Energy Research Institute (KAERI).

A high-salt environment represents environmental stress for most plants. Those that can grow and thrive in such an environment must have membrane transport systems that can respond effectively. Plant roots absorb Na from the soil, and the plant must maintain Na homeostasis to survive salt stress. A major mechanism by which salt-tolerant plants adapt to salt stress is through modulation of ion transport genes. We have subjected a population of rice plants to mutagenesis, and identified lines with both single-nucleotide polymorphisms (SNPs) in membrane transport genes and altered responses to salt stress. Primers labeled with FAM or HEX fluorescent dyes were designed for nine target genes encoding membrane transport proteins that are believed to regulate salt stress tolerance. A TILLING (Targeting Induced Local Lesions IN Genome) assay was performed on 2,961 M rice mutant lines using electrophoresis. After the TILLING assay, a total of 41 mutant lines containing SNPs in the target genes were identified and screened. The average number of mutations per gene was 1/492 kb in lines having SNPs, and the percentage of mutation sites per total sequence was 0.67. Among the 41 lines, nine had altered sequences in the exon region of the genes. Of these nine lines, seven were tolerant to salt stress after exposure to 170 mM NaCl for three weeks, while the other two lines were not more salt-tolerant than the control lines. Furthermore, five mutant lines containing SNPs in the coding region of OsAKT1, OsHKT6, OsNSCC2, OsHAK11 and OsSOS1 showed changed expression levels for each gene. We conclude that variation in membrane transport genes, such as expression levels and protein structures, may affect the rice plant's tolerance to salt stress. These mutations represent traits that may be selected for large rice mutant populations, permitting efficient acquisition of salt-tolerant lines.
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http://dx.doi.org/10.1266/ggs.15-00052DOI Listing
April 2017

Transcriptome analysis of reproductive-stage Arabidopsis plants exposed gamma-ray irradiation at various doses.

Int J Radiat Biol 2016 08 6;92(8):451-65. Epub 2016 May 6.

a Plant Genomics Laboratory, Department of Applied Plant Sciences , Kangwon National University , Chuncheon , Korea ;

Purpose: Gamma rays (GR) induce significant changes in the structure and expression of genes involved in the regulation of diverse biochemical and physiological processes. Arabidopsis plants exhibit different growth and development patterns in response to exposure to GR. The effects on gene expression of different radiation doses of GR (100 and 800 Gy) administered to Arabidopsis plants were examined at the reproductive stage.

Materials And Methods: We irradiated 26-day-old plants with three replications [developmental stages 5.1-6.0, according to Boyes et al. ( 2001 )] using a GR irradiator (60 Co, ca. 150 TBq capacity, Atomic Energy of Canada Limited, Ontario, Canada) at the Korea Atomic Energy Research Institute. Plants were treated with 100, 200, 300, 400, 800, 1200, 1600, or 2000 Gy, and the doses were made from varying the distance to the source.

Results: We conducted a high-throughput screening analysis and detected 883 GR-responsive genes that showed significant changes; these were involved in several putative metabolic pathways related to biotic stress. Additionally, five overrepresented cis-regulatory elements were identified in the 1-kb upstream regions of GR-responsive genes by using motif enrichment analysis. We also detected three GR-responsive genes associated with stamen development and confirmed their co-regulation with functionally interacting genes.

Conclusions: This finding suggests that a network-based analysis is a viable approach to identify significant GR-responsive genes associated with the reproductive stage of Arabidopsis. Our results provide further insights into the complex biological systems involved in the response to different doses of GR in plants.
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http://dx.doi.org/10.1080/09553002.2016.1178865DOI Listing
August 2016

Identification of altered metabolic pathways of γ-irradiated rice mutant via network-based transcriptome analysis.

Genetica 2015 Dec 11;143(6):635-44. Epub 2015 Sep 11.

Plant Genomics Lab, Department of Applied Plant Sciences, Kangwon National University, Chuncheon, 200-713, South Korea.

In order to develop rice mutants for crop improvement, we applied γ-irradiation mutagenesis and selected a rice seed color mutant (MT) in the M14 targeting-induced local lesions in genome lines. This mutant exhibited differences in germination rate, plant height, and root length in seedlings compared to the wild-type plants. We found 1645 different expressed probes of MT by microarray hybridization. To identify the modified metabolic pathways, we conducted integrated genomic analysis such as weighted correlation network analysis with a module detection method of differentially expressed genes (DEGs) in MT on the basis of large-scale microarray transcriptional profiling. These modules are largely divided into three subnetworks and mainly exhibit overrepresented gene ontology functions such as oxidation-related function, ion-binding, and kinase activity (phosphorylation), and the expressional coherences of module genes mainly exhibited in vegetative and maturation stages. Through a metabolic pathway analysis, we detected the significant DEGs involved in the major carbohydrate metabolism (starch degradation), protein degradation (aspartate protease), and signaling in sugars and nutrients. Furthermore, the accumulation of amino acids (asparagine and glutamic acid), sucrose, and starch in MT were affected by gamma rays. Our results provide an effective approach for identification of metabolic pathways associated with useful agronomic traits in mutation breeding.
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http://dx.doi.org/10.1007/s10709-015-9861-2DOI Listing
December 2015

Selection and molecular characterization of a lipoxygenase-free soybean mutant line induced by gamma irradiation.

Theor Appl Genet 2014 Nov 5;127(11):2405-13. Epub 2014 Sep 5.

Advanced Radiation Technology Institute, Korea Atomic Energy Research Institute, 1266 Sinjeong, Jeongeup, Jeonbuk, 580-185, Republic of Korea,

Key Message: A lipoxygenase-free soybean mutant line (H70) induced by gamma ray was selected and its detailed information about the lipoxygenase was analyzed by comparison of DNA sequence. Soybean seeds contain three lipoxygenase enzymes, which induce a beany or grassy flavor. The elimination of lipoxygenases can reduce the poor stability and off-flavors of soybean oil and protein products. In this study, we selected a soybean mutant (H70) in which the three lipoxygenases had been mutated using gamma rays. To obtain detailed information about the lipoxygenase, we investigated the sequences of the Lox1, Lox2 and Lox3 genes in H70 compared to the original cultivar, Hwanggum. Comparisons of the sequences of the Lox1 and Lox2 genes in H70 with those in a line with normal lipoxygenase (HG) showed that the mutations in these genes affected a highly conserved group of six histidine residues necessary for enzymatic activity. Lox1 in H70 contained a 74 bp deletion in exon 8, creating a stop codon that prematurely terminates translation. A single point mutation (T-A) in exon 8 of Lox2 changed histidine (H532, one of the iron-binding ligands essential for Lox2 activity) to glutamine. The mutation in the Lox3 gene in H70 was a single-point mutation in exon 6 (A-G), which changed the amino acid from histidine to arginine. This amino acid alteration in Lox3 was located in the N-terminal barrel, which might play a role in molecular recognition during catalysis and/or proteolysis. These results suggest that gene analysis based on DNA sequencing could be useful for elucidating the lipoxygenase content in soybean mutant lines. Additionally, the soybean mutant line selected in this study could be used to develop soybean cultivars with improved flavor.
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http://dx.doi.org/10.1007/s00122-014-2385-9DOI Listing
November 2014

Selection and molecular characterization of a high tocopherol accumulation rice mutant line induced by gamma irradiation.

Mol Biol Rep 2014 Nov 7;41(11):7671-81. Epub 2014 Aug 7.

Advanced Radiation Technology Institute, Korea Atomic Energy Research Institute, 1266 Sinjeong, Jeongeup, Jeonbuk, 580-185, Republic of Korea.

Tocopherols are micronutrients with antioxidant properties. They are synthesized by photosynthetic bacteria and plants, and play important roles in animal and human nutrition. In this study, we isolated a new rice mutant line with elevated tocopherol content (MRXII) from an in vitro mutagenized population induced by gamma irradiation. The mutant exhibited greater seed longevity than the control, indicating a crucial role for tocopherols in maintaining viability during quiescence, and displayed faster seedling growth during the early growth stage. To study the molecular mechanism underlying vitamin E biosynthesis, we examined the expression patterns of seven rice genes encoding vitamin E biosynthetic enzymes. Accumulation levels of the OsVTE2 transcript and OsVTE2 protein in the MRXII mutant were significantly higher than in the control. Sequence analysis revealed that the MRXII mutant harbored a point mutation in the OsVTE2 promoter region, which resulted in the generation of MYB transcription factor-binding cis-element. These results help identify the promoter regions that regulate OsVTE2 transcription, and offer insights into the regulation of tocopherol content.
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http://dx.doi.org/10.1007/s11033-014-3660-1DOI Listing
November 2014

Identification of rice genes associated with cosmic-ray response via co-expression gene network analysis.

Gene 2014 May 12;541(2):82-91. Epub 2014 Mar 12.

Plant Genomics Lab., Department of Applied Plant Sciences, Kangwon National University, Chuncheon 200-713, South Korea. Electronic address:

In order to better understand the biological systems that are affected in response to cosmic ray (CR), we conducted weighted gene co-expression network analysis using the module detection method. By using the Pearson's correlation coefficient (PCC) value, we evaluated complex gene-gene functional interactions between 680 CR-responsive probes from integrated microarray data sets, which included large-scale transcriptional profiling of 1000 microarray samples. These probes were divided into 6 distinct modules that contained 20 enriched gene ontology (GO) functions, such as oxidoreductase activity, hydrolase activity, and response to stimulus and stress. In particular, modules 1 and 2 commonly showed enriched annotation categories such as oxidoreductase activity, including enriched cis-regulatory elements known as ROS-specific regulators. These results suggest that the ROS-mediated irradiation response pathway is affected by CR in modules 1 and 2. We found 243 ionizing radiation (IR)-responsive probes that exhibited similarities in expression patterns in various irradiation microarray data sets. The expression patterns of 6 randomly selected IR-responsive genes were evaluated by quantitative reverse transcription polymerase chain reaction following treatment with CR, gamma rays (GR), and ion beam (IB); similar patterns were observed among these genes under these 3 treatments. Moreover, we constructed subnetworks of IR-responsive genes and evaluated the expression levels of their neighboring genes following GR treatment; similar patterns were observed among them. These results of network-based analyses might provide a clue to understanding the complex biological system related to the CR response in plants.
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http://dx.doi.org/10.1016/j.gene.2014.02.060DOI Listing
May 2014

Transcriptome profiling in response to different types of ionizing radiation and identification of multiple radio marker genes in rice.

Physiol Plant 2014 Apr 23;150(4):604-19. Epub 2013 Nov 23.

Advanced Radiation Technology Institute, Korea Atomic Energy Research Institute, 1266 Sinjeong, Jeongeup, Jeonbuk 580-185, Republic of Korea.

Ionizing radiation (IR) affects gene expression from plant genomes. To monitor the genome-wide transcriptional changes induced by three types of IR, we used the rice Affymetrix GeneChip microarray to identify genes that are up- or down-regulated by gamma rays (GAs), cosmic rays (CRs) and ion beams (IBs). The overall expression patterns in rice seedlings generated from seeds exposed to GAs and IBs were similar but differed for CRs exposure. Expression profiles of genes involved in metabolic pathways and cellular response were identified using MapMan analysis. This result revealed that IRs induced gene expression related to sucrose-starch metabolisms; sugar and starch accumulation was significantly increased in response to three types of IR in rice. In addition, we compared the genes commonly up- or down-regulated by exposure to three types of IR and identified 53 candidate radio marker genes (RMGs) that were differentially regulated by radiation exposure but not by other stresses. Among these genes, we selected six RMGs commonly applicable to different types of IR by specific coexpression networks using the algorithm for the reconstruction of accurate cellular networks (aracne) and confirmed the expression of these genes by reverse transcription-polymerase chain reaction (RT-PCR) analysis. Our results provided insight into the mechanisms of the responses to different types of IR and identified multiple marker genes to predict sensitivity to three types of IR.
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http://dx.doi.org/10.1111/ppl.12121DOI Listing
April 2014

DREB2C acts as a transcriptional activator of the thermo tolerance-related phytocystatin 4 (AtCYS4) gene.

Transgenic Res 2014 Feb 19;23(1):109-23. Epub 2013 Jul 19.

Division of Applied Life Science, Systems and Synthetic Agrobiotech Center and PMBBRC, Gyeongsang National University, Jinju, 660-701, Korea.

Phytocystatins are proteinaceous inhibitors of cysteine proteases. They have been implicated in the regulation of plant protein turnover and in defense against pathogens and insects. Here, we have characterized an Arabidopsis phytocystatin family gene, Arabidopsis thaliana phytocystatin 4 (AtCYS4). AtCYS4 was induced by heat stress. The heat shock tolerance of AtCYS4-overexpressing transgenic plants was greater than that of wild-type and cys4 knock-down plants, as measured by fresh weight and root length. Although no heat shock elements were identified in the 5'-flanking region of the AtCYS4 gene, canonical ABA-responsive elements (ABREs) and dehydration-responsive elements (DREs) were found. Transient promoter activity measurements showed that AtCYS4 expression was up-regulated in unstressed protoplasts by co-expression of DRE-binding factor 2s (DREB2s), especially by DREB2C, but not by bZIP transcription factors that bind to ABREs (ABFs, ABI5 and AREBs). DREB2C bound to and activated transcription from the two DREs on the AtCYS4 promoter although some preference was observed for the GCCGAC DRE element over the ACCGAC element. AtCYS4 transcript and protein levels were elevated in transgenic DREB2C overexpression lines with corresponding decline of endogenous cysteine peptidase activity. We propose that AtCYS4 functions in thermotolerance under the control of the DREB2C cascade.
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http://dx.doi.org/10.1007/s11248-013-9735-2DOI Listing
February 2014

The identification of candidate radio marker genes using a coexpression network analysis in gamma-irradiated rice.

Physiol Plant 2013 Dec 26;149(4):554-70. Epub 2013 Apr 26.

Advanced Radiation Technology Institute, Korea Atomic Energy Research Institute, Jeongeup, Jeonbuk, 580-185, Republic of Korea.

Plant physiological and biochemical processes are significantly affected by gamma irradiation stress. In addition, gamma-ray (GA) differentially affects gene expression across the whole genome. In this study, we identified radio marker genes (RMGs) responding only to GA stress compared with six abiotic stresses (chilling, cold, anoxia, heat, drought and salt) in rice. To analyze the expression patterns of differentially expressed genes (DEGs) in gamma-irradiated rice plants against six abiotic stresses, we conducted a hierarchical clustering analysis by using a complete linkage algorithm. The up- and downregulated DEGs were observed against six abiotic stresses in three and four clusters among a total of 31 clusters, respectively. The common gene ontology functions of upregulated DEGs in clusters 9 and 19 are associated with oxidative stress. In a Pearson's correlation coefficient analysis, GA stress showed highly negative correlation with salt stress. On the basis of specific data about the upregulated DEGs, we identified the 40 candidate RMGs that are induced by gamma irradiation. These candidate RMGs, except two genes, were more highly induced in rice roots than in other tissues. In addition, we obtained other 38 root-induced genes by using a coexpression network analysis of the specific upregulated candidate RMGs in an ARACNE algorithm. Among these genes, we selected 16 RMGs and 11 genes coexpressed with three RMGs to validate coexpression network results. RT-PCR assay confirmed that these genes were highly upregulated in GA treatment. All 76 genes (38 root-induced genes and 38 candidate RMGs) might be useful for the detection of GA sensitivity in rice roots.
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http://dx.doi.org/10.1111/ppl.12058DOI Listing
December 2013

A proximal promoter region of Arabidopsis DREB2C confers tissue-specific expression under heat stress.

J Integr Plant Biol 2012 Sep 30;54(9):640-51. Epub 2012 Aug 30.

Systems and Synthetic Agrobiotech Center and PMBBRC, Division of Applied Life Science, Gyeongsang National University, Jinju 660-701, Korea.

The dehydration-responsive element-binding factor 2C (DREB2C) is a member of the CBF/DREB subfamily of proteins, which contains a single APETALA2/Ethylene responsive element-binding factor (AP2/ERF) domain. To identify the expression pattern of the DREB2C gene, which contains multiple transcription cis-regulatory elements in its promoter, an approximately 1.4 kb upstream DREB2C sequence was fused to the β-glucuronidase reporter gene (GUS) and the recombinant p1244 construct was transformed into Arabidopsis thaliana (L.) Heynh. The promoter of the gene directed prominent GUS activity in the vasculature in diverse young dividing tissues. Upon applying heat stress (HS), GUS staining was also enhanced in the vasculature of the growing tissues. Analysis of a series of 5'-deletions of the DREB2C promoter revealed that a proximal upstream sequence sufficient for the tissue-specific spatial and temporal induction of GUS expression by HS is localized in the promoter region between -204 and -34 bps relative to the transcriptional start site. Furthermore, electrophoretic mobility shift assay (EMSA) demonstrated that nuclear protein binding activities specific to a -120 to -32 bp promoter fragment increased after HS. These results indicate that the TATA-proximal region and some latent trans-acting factors may cooperate in HS-induced activation of the Arabidopsis DREB2C promoter.
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http://dx.doi.org/10.1111/j.1744-7909.2012.01137.xDOI Listing
September 2012

Overexpression of Arabidopsis dehydration- responsive element-binding protein 2C confers tolerance to oxidative stress.

Mol Cells 2012 Feb;33(2):135-40

Systems and Synthetic Agrobiotech Center and PMBBRC, Gyeongsang National University, Jinju 660-701, Korea.

Dehydration-responsive element-binding proteins (DREBs)regulate plant responses to environmental stresses. In the current study, transcription of DREB2C, a class 2 Arabidopsis DREB, was induced by a superoxide anion propagator, methyl viologen (MV). The oxidative stress tolerance of DREB2C-overexpressing transgenic plants was significantly greater than that of wild-type plants, as measured by ion leakage and chlorophyll fluorescence under light conditions. The transcriptional activity of several ascorbate peroxidase (APX) genes as well as APX protein activity was induced in DREB2C overexpressors. Additionally, the level of H2O2 in the overexpressors was lower than in wt plants under similar oxidative stress conditions. An electrophoretic mobility shift assay and transient activator reporter assay showed that APX2 expression was regulated by heat shock factor A3 (HsfA3) and that HsfA3 is regulated at the transcriptional level by DREB2C. These results suggest that DREB2C plays an important role in promoting oxidative stress tolerance in Arabidopsis.
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http://dx.doi.org/10.1007/s10059-012-2188-2DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3887724PMC
February 2012

Arabidopsis DREB2C functions as a transcriptional activator of HsfA3 during the heat stress response.

Biochem Biophys Res Commun 2010 Oct 16;401(2):238-44. Epub 2010 Sep 16.

Division of Applied Life Science, Graduate School of Gyeongsang National University, Plant Molecular Biology and Biotechnology Research Center, Jinju 660-701, Republic of Korea.

The dehydration-responsive element binding protein (DREB) family is important in regulating plant responses to abiotic stresses. DREB2C is one of the Arabidopsis class 2 DREBs and is induced by heat stress (HS). Here, we present data concerning the interaction of DREB2C with heat shock factor A3 (HsfA3) in the HS signal transduction cascade. RT-PCR showed that HsfA3 is the most up-regulated gene among the 21 Arabidopsis Hsfs in transgenic plants over-expressing DREB2C. DREB2C and HsfA3 displayed similar transcription patterns in response to HS and DREB2C specifically transactivated the DRE-dependent transcription of HsfA3 in Arabidopsis mesophyll protoplasts. Yeast one-hybrid assays and invitro electrophoretic mobility shift assays further showed that DREB2C interacts with two DREs located in the HsfA3 promoter with a binding preference for the distal DRE2. Deletion mutants of DREB2C indicated that transactivation activity was located in the C-terminal region. In addition, dual activator-reporter assays showed that the induction of heat shock protein (Hsp) genes in transgenic plants could be attributed to the transcriptional activity of HsfA3. Taken together, these results indicate that DREB2C and HsfA3 are key players in regulating the heat tolerance of Arabidopsis.
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http://dx.doi.org/10.1016/j.bbrc.2010.09.038DOI Listing
October 2010

Distinct expression patterns of two Arabidopsis phytocystatin genes, AtCYS1 and AtCYS2, during development and abiotic stresses.

Plant Cell Rep 2010 Aug 5;29(8):905-15. Epub 2010 Jun 5.

Division of Applied Life Science (BK21 Program), Environmental Biotechnology National Core Research Center and PMBBRC, Graduate School of Gyeongsang National University, Jinju 660-701, Korea.

The phytocystatins of plants are members of the cystatin superfamily of proteins, which are potent inhibitors of cysteine proteases. The Arabidopsis genome encodes seven phytocystatin isoforms (AtCYSs) in two distantly related AtCYS gene clusters. We selected AtCYS1 and AtCYS2 as representatives for each cluster and then generated transgenic plants expressing the GUS reporter gene under the control of each gene promoter. These plants were used to examine AtCYS expression at various stages of plant development and in response to abiotic stresses. Histochemical analysis of AtCYS1 promoter- and AtCYS2 promoter-GUS transgenic plants revealed that these genes have similar but distinct spatial and temporal expression patterns during normal development. In particular, AtCYS1 was preferentially expressed in the vascular tissue of all organs, whereas AtCYS2 was expressed in trichomes and guard cells in young leaves, caps of roots, and in connecting regions of the immature anthers and filaments and the style and stigma in flowers. In addition, each AtCYS gene has a unique expression profile during abiotic stresses. High temperature and wounding stress enhanced the expression of both AtCYS1 and AtCYS2, but the temporal and spatial patterns of induction differed. From these data, we propose that these two AtCYS genes play important, but distinct, roles in plant development and stress responses.
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http://dx.doi.org/10.1007/s00299-010-0876-yDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2903682PMC
August 2010

Regulation of seed germination and seedling growth by an Arabidopsis phytocystatin isoform, AtCYS6.

Plant Cell Rep 2009 Nov 19;28(11):1623-32. Epub 2009 Aug 19.

Environmental Biotechnology National Core Research Center and PMBBRC, Graduate School of Gyeongsang National University, Jinju, Korea.

Phytocystatins are cysteine proteinase inhibitors in plants that are implicated in the endogenous regulation of protein turnover and defense mechanisms against insects and pathogens. A cDNA encoding a phytocystatin called AtCYS6 (Arabidopsis thaliana phytocystatin6) has been isolated. We show that AtCYS6 is highly expressed in dry seeds and seedlings and that it also accumulates in flowers. The persistence of AtCYS6 protein expression in seedlings was promoted by abscisic acid (ABA), a seed germination and post-germination inhibitory phytohormone. This finding was made in transgenic plants bearing an AtCYS6 promoter-beta-glucuronidase (GUS) reporter construct, where we found that expression from the AtCYS6 promoter persisted after ABA treatment but was reduced under control conditions and by gibberellin(4+7) (GA(4+7)) treatment during the germination and post-germinative periods. In addition, constitutive over-expression of AtCYS6 retarded germination and seedling growth, whereas these were enhanced in an AtCYS6 knock-out mutant (cys6-2). Additionally, cysteine proteinase activities stored in seeds were inhibited by AtCYS6 in transgenic Arabidopsis. From these data, we propose that AtCYS6 expression is enhanced by the germination inhibitory phytohormone ABA and that it participates in the control of germination rate and seedling growth by inhibiting the activity of stored cysteine proteinases.
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http://dx.doi.org/10.1007/s00299-009-0762-7DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2766501PMC
November 2009

Over-expression of the Arabidopsis DRE/CRT-binding transcription factor DREB2C enhances thermotolerance.

Biochem Biophys Res Commun 2007 Oct 10;362(2):431-6. Epub 2007 Aug 10.

Division of Applied Life Science (BK21), Environmental Biotechnology National Core Research Center and PMBBRC, Gyeongsang National University, Jinju 660-701, Republic of Korea.

The dehydration responsive element binding protein 2 (DREB2) subgroup belongs to the plant-specific APETALA2/ethylene-responsive element binding factor (AP2/ERF) family of transcription factors. We have characterized cDNA encoding Arabidopsis thaliana DREB2C, which is induced by mild heat stress. Both an electrophoretic mobility shift assay (EMSA) and a yeast one-hybrid assay revealed that DREB2C(145-528) was able to form a complex with the dehydration responsive element/C-repeat (DRE/CRT; A/GCCGAC) motif. A trans-activating ability test in yeast demonstrated that DREB2C could effectively function as a trans-activator. Constitutive expression of DREB2C under the control of the cauliflower mosaic virus (CaMV) 35S promoter led to enhanced thermotolerance in transgenic lines of Arabidopsis. Microarray and RT-PCR analyses of transgenic plants revealed that DREB2C regulates expression of several heat stress-inducible genes that contain DRE/CRT elements in their promoters. From these data, we deduced that DREB2C is a regulator of heat stress tolerance in Arabidopsis.
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http://dx.doi.org/10.1016/j.bbrc.2007.08.007DOI Listing
October 2007
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