In order to select a rice population with useful trait such as arsenic tolerance for crop improvement, we have developed 3000 M7 Targeting Induced Local Lesions IN Genomes (TILLING) lines by gamma ray (GR) irradiation treatment to a rice variety (cv. Donganbyeo). A total of 2 M7 lines exhibited the arsenic (AsV) tolerant phenotype (hereafter, named Arsenic Tolerant TILLING line 1 and 2, and designed as ATT1 and 2), in which the shoots and roots length of ATT lines were significantly longer than those of wild type (WT) during As(V) treatment. To survey the DNA polymorphism of these plants, we conducted the Whole genome resequencing with 10x coverage in ATT lines. By comparative analysis among ATT lines, we have identified the common DNA polymorphism such as 11,817 SNPs (49.83% in ATT1 and 48.35% in ATT2) and 30,618 InDels (86.72% in ATT1 and 86.23% in ATT2). Also, these mutants were showed the close relationships more than WT. To further study the changed amino acids of genes, we commonly identified the 758 genes for non-synonymous SNPs and 249 genes for changed codon InDels. These genes were mainly exhibited the enriched GO functions such as catalytic activity, nucleic acid binding and transferring phosphorus-containing groups. To determine the genes associated with arsenic-related mechanism in DNA polymorphism of ATT lines, we have retrieved the two structurally altered genes (Os11g47870 and Os03g19900) for metalloid As(V) detoxification toward induced genes in response to arsenic treatments by public microarray datasets. We suggest that As(V) tolerant phenotypes of ATT lines are certainly affected by structurally altered genes associated with phosphorus transferring and As(V) detoxification during GR treatment

The metalloid arsenic (As) and the hevy metal cadmium (Cd) are ubiquitously found at low concentrations in the earth, while high concentrations of the both elements in soil and crop are severe dangerous to human health. We have tried to retrieve RING E3 ligase gene, which is believed to regulate substrate proteins in As or Cd uptake via ubiquitin 26S proteasome pathway, related to inhibit metal ion transport system. A total of 48 rice RING E3 ligases were randomly selected and then conducted semi-quantitative RT-PCR for their expression patterns as exposed to As and Cd treatments. We discovered one gene, Oryza sativa heavy metal induced RING E3 ligase 1 (OsHIR1) that was significantly up-regulated against both treatments. A total of 31 positive interaction clones with OsHIR1 were screened depending on their strong α-galactosidase activity via yeast-two hybrid screen. Bimolecular fluorescence complementation analysis evidenced that the OsHIR1 protein was clearly interacted with each of six partner protein including aquaporin tonoplast intrinsic protein 4;1 (OsTIP4;1) in the plasma membrane. Protein degradation assay showed that OsHIR1 strongly degraded the protein level of OsTIP4;1 via ubiquitin 26S proteasome system. Heterogeneous overexpression of OsHIR1 in Arabidopsis showed As- and Cd-insensitive phenotype. In addition, the transgenic plant showed low levels of As and Cd accumulation than the control plant in leaf and root. Here, we report the novel finding that OsHIR1 E3 ligase positively regulates OsTIP4;1 related to As and Cd uptake.

Low temperature is a major factor restrict to growth and limiting productivity of rice crops. We used a cDNA microarray approach to monitor the expression profile of rice (Oryza sativa) under chilling stress and identified 20 chilling inducible genes in previously study. Ten such genes encoding bHLH, metal transporter and, zinc finger protein with unknown functions showed a significant change in expression under various abiotic stresses. Among them, OsCHI1 (Os07g15460), OsCHI2 (Os02g43660), and OsCHI3 (Os01g61160), were selected for further study. They have structural features such as metal-binding signature sequences in their protein sequences, and OsCHI genes were expressed in root of rice seedling and induced in chilling and salt or drought. Expression of OsCHI1, OsCHI3 and OsCHI2 were targeted to membrane and ER when transiently expressed in tobacco cell, respectively. The Arabidopsis (Arabidopsis thaliana) transgenic plants overexpressing showed increased tolerance to salt and drought stress in the seed germination and root elongation than that of wild type. This comprehensive study provides insight into the biological function of OsCHIs, which may be useful in understanding how rice plants adapt to unfavorable environmental conditions.

We used a microarray dataset that is deposited in the public database to evaluate plant responses to heat stress and selected two genes, OsSHSP1 (Os03g16030) and OsSHSP2 (Os01g04380), that are highly expressed under heat stress in rice. OsSHSP1 and OsSHSP2 gene transcripts were highly induced in response to salt and drought. In addition, OsSHSP1 and OsSHSP2 gene transcripts were induced under ABA and SA. Subcellular localization of proteins of 35S::OsSHSP1 were associated with the cytosol, whereas those of and 35S::OsSHSP2 were associated with the cytosol and nucleus. Heterogeneous overexpression of both genes exhibited higher germination rates than those of wild-type plants under the salt treatment, but not under heat or drought stress. The network of both genes harboring 9 sHSPs as well as at least 13 other chaperone genes might support the idea of a role for sHSPs in the chaperone network. Our findings might provide clues to shed light on the molecular functions of OsSHSP1 and OsSHSP2 in response to abiotic stresses, especially heat stress.

In order to better understand the biological systems that are affected in response to cosmic ray, we conducted the weighted gene co-expression network analysis with module detection method. By using the Pearson’s correlation coefficient value, we were evaluated the complex gene-gene functional interactions between 680 CR-response probes from integrated microarray datasets, which included large-scale transcriptional profiling of 918 microarray samples. These probes were divided into 6 distinct modules that contained 20 enriched function such as oxidoreductase activity, response to stimulus and stress, and hydrolase activity. Especially, module 1 and 2 commonly showed the enriched annotation categories such as oxidoreductase activity, including the enriched cis-regulatory elements known as ROS specific regulator. These results suggest in module1 and 2 that ROS-mediated irradiation response pathway are affected by CR. We found the 243 irradiation-dependent probes, which were exhibited the similarities of differentially expressed patterns in various irradiation microarray datasets, and RT-PCR for confirmations of several irradiation-dependent genes were exhibited the similar expressed patterns in rice by CR, gamma ray and Ion beam treatments. Interestingly, these genes were differentially expressed by non-gravity. Moreover, we were identified the co-regulations between several irradiation-dependent genes and functional interacted genes in the CR-responsive network by various GA treatments such as different conditions of dose and treatment time. These results of network-based analysis might provide a clue to understanding the complex biological system of CR.

Rice is one of the most important food crops in the world, and has been used as model monocots for genetic studies, because of its relatively small genome size. We have previously reported the different functions of several RING (Really Interesting New Gene) proteins to respond the various abiotic stresses. In order to study a regulation of RING proteins in rice under ionizing irradiation such as gamma ray (GA), we have identified the expression patterns of these genes by RT-PCR. We found Gamma-ray induced RING finger protein (OsGRP) gene, which were associated with cytosol by subcellular localization analysis. in vitro ubiquitination assay revealed that OsGRP possess E3 ligase activity. Also, we demonstrate that C196A point mutation in the RING finger domain of OsGRP can have a critical effect to the breakdown of structural integrity in RING constructs. To identify the interaction partners for OsGRP in protein-protein interactions, we found the seven genes interacted with OsGRP by Yeast Two Hybrid method. To examine the GA-influence of interaction partners by RT-PCR, two genes were specifically down-regulated in rice during GA treatment. These interaction partners were identified the reliable interactions and subcellular localizations via BiFC method. Interestingly, five genes associated with plastid, while two down-regulated genes associated with cytosol and plastid. These results of OsGRP based on genetic approach might provide a clue to understanding the GA responsive mechanism in rice.

Astronomical Observations at Chungbuk National University Observatory (CBNUO) with an 1 m telescope have begun since April 2008, and Near-Earth Space Survey observations also have been started since November 2010, with a 0.6 m wide field telescope developed by Korea Astronomy and Space Science Institute. To improve observational efficiency, we developed a weather monitoring system enabling automatic monitoring for the weather conditions and checking the status of the observational circumstances, such as dome status. We hope this weather monitoring system can be helpful to more than 100 Korean domestic observatories, including public outreach facilities. In this paper, we present the statistic analysis of the weather conditions collected at CBNUO for 3 years (2009- 2011) and comparisons were made for clear nights between using only humidity data and both humidity and cloud data.

The application of next generation sequencing technologies allows us to discover the high levels of DNA polymorphism throughout a genome, e.g., single nucleotide polymorphisms (SNPs), and insertions and deletions (InDels). We performed whole-genome resequencing of a Korean rice cultivar (cv. Donganbyeo) and then obtained the sequences of covered 366,042,872 bp (96.63%) with average mapped read depth of 34.17 on 382,788,128 bp of the Japanese cultivar genome (cv. Nipponbare). We characterized the polymorphisms of 173,711 SNPs, 295,334 insertions and 40,642 deletions based on the comparison of both genomes. About 11.5% and 17.8% of the annotated total SNPs were presented in the regions of 1kb upstreams and genes, respectively. The annotated InDels in gene regions were similar with 15.5% insertion (4,588) and 15.9% (5,100) deletions, but not in 1kb upstream regions with 9.0% insertion (2,662) and 14.3% deletions (5,100). In addition, the Korea rice genome sequences were mapped on individual chromosome, resulted that SNPs were shown with different frequencies from each chromosome. The InDels distributions on individual chromosomes exhibited similar pattern as compared to those of SNPs. Some gene families such as NB-ARC (NB-LRR), F-box, RLK (serine/threonine protein kinase) and Zinc-finger (RING) for SNPs occurred the similar pattern with those of Arabidopsis. These results might be useful for better understanding the genome structure and genetic diversity of the Korean rice cultivars.

Plants are known to have homeostatic cellular mechanisms to control the concentration of heavy metal inside the cell. We tried to retrieve rice RING finger protein genes, which are believed to regulate substrates via ubiqitinations, related to metal ions detoxification mechanisms. A total of 48 rice RING finger proteins were randomly selected and then examined for their expression patterns as exposed to cadmium and arsenic treatments. We discovered a RING finger protein gene that was significant up-regulated against both treatments and then named Oryza sativa heavy metal induced 1 (OsHMI1). We tested subsequently OsHMI1 expression patterns against to salinity, dehydration, cold, heat stress and phytohormones treatments. In addition, we evaluated its subcellular localization and determined E3 ligase activity. The interaction partner proteins were screened via yeast-two hybridization. These results might shed further light on the understanding of homeostatic cellular mechanisms to control heavy metal detoxification via protein degradation in plants.

In order to select superior tree from Korea, five major phenolic compounds including (-)-epicatechin(EC), chlorogenic acid (ChA), hyperoside (HP), isoquercitrin (IQ), and procyanidin B2 (PC-B2) in hawthorn fruit were evaluated. We also compared these hawthorn fruits of five clones with Chinese hawthorn cultivars. HPLC with a diode-array detector was used to determine the contents of the individual compounds. Hawthorn fruits of five clones (selected from different area of Korea), and four Chinese hawthorn cultivars grown in the Korea Forest Research Institute (Suwon) were utilized. With their high functional components, Jungsun is the clone including the highest contents of EC (11.26 mg/g) and PC-B2 (24.46 mg/g). The clone of Chuncheon 15 had highest HP (0.53 mg/g) and IQ (0.41 mg/g). From the results, the clone of Jungsun and Chuncheon 15 can be evaluated to be selected breeding material for cultivar development.

TILLING (Targeting Induced local Lesions IN Genomes) is known to be an excellent methodology for reverse genetics approach. About 15,000 M3 TILLING lines have been developed after gamma-ray irradiation to the rice seeds of Donganbye. In order to assess genetic diversity of the TILLING population. we have employed a multiple dominant marker technique, such as AFLP. A total of 96 (0.64%) lines including Dongganbye were randomly selected and their genetic diversity was assessed on the basis of AFLP marker polymorphism by using 5 primer combinations. An average of 100.4 loci with a range of 97 to 106 were detected by using the primer combinations, resulting in 173 (34.6%) polymorphic loci among 96 lines. A broad range of similarities with 80% to 96% was evidenced between Donganbye and each of 96 TILLING lines, reflecting genetic diversity of the TILLING population. About 30 polymorphic loci have been cloned and their sequences have been blasted against rice whole genome sequences. The sequences evidenced highly significant matches to each of genes including exons and introns, upstream sequences and downstream of genes, and intergeneic sequences. Therefore, the TILLING rice population would be valuable genetic sources for rice functional genomics.

In this study, we estimated the equivalent roughness using an estimation model, which considered grain distribution on the bed and the protrusion height of the grains. We also reviewed the appropriateness of the estimated equivalent roughness at the Goksung and Gurey station in the Seomjin River. To review the appropriateness of this model, we presented the water level-discharge relation curve applying the equivalent roughness to the flow model and compared and reviewed it to observed data. Also, we compared and reviewed the observed data by estimating the Manning coefficient , the Chezy coefficient , and the Darcy-Weisbach friction coefficient by the equivalent roughness. The calculation results of the RMSE showed within 5% error range in comparison with observed value. Therefore the estimated equivalent roughness values by the model could be proved appropriate.

Flow resistance in a natural stream is caused by complex factors, such as the grains on the bed, vegetation, and bed-form, reach profile. Flow resistance in a generally stable gravel bed stream is due to protrudent grains from bed. Therefore, the flow resistance can be calculated by equivalent roughness in gravel bed stream, but estimation of equivalent roughness is difficult because nonuniform size and irregular arrangement of distributed grain on natural stream bed. In previous study, equivalent roughness is empirically estimated using characteristic grain size. However, application of empirical equation have uncertainty in stream that stream bed characteristic differs. In this study, we developed a model using an analytical method considering grain diameter distribution characteristics of grains on the bed and also taking into account flow resistance acting on each grain. Also, the model consider the protrusion height of grain.