Rice is a staple food for over one-half of the world population, especially in Asian countries. Recently, the growth and yield of crop plants was affected by various abiotic stresses, such as salt, drought, and high temperature due to change of climate environment. To study molecular functions of Oryza sativa nuclear-targeted RING Finger Proteins (OsNRFPs) in response to abiotic stresses, we selected 44 OsNRFPs genes, whose subcelluar localizations are predicted to the nucluear, on the basis of expression patterns of a microarray dataset. A total of 44 OsNRFPs were grouped into two types such as RING-HC and RING-H2 via phylogeneitc analysis of their RING domains structures. Subsequently, we surveyed the expression patterns of 44 genes in response to salt stress via qRT-PCR in roots. We found 10 salt stress-induced OsNRFPs and then examined their subcellular localizations. These genes were clearly localized to the nucleus (OsNRFPHC-10), cytoplasm (OsNRFPHC-17 and OsNRFPH2-16) and microtuble (OsNRFPHC-23, OsNRFPH2-17 and OsNRFPH2-05), respectively. These results might provide a key clue for understanding moleuclar functions of the OsNRFP genes associated with salt stress-related signaling pathway

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

Chrysanthemum white rust, caused by Puccinia horiana, is one of the most destructive fungal diseases in chrysanthemum cultivation worldwide. For increasing efficiency of resistant breeding, molecular markers linked to chrysanthemum white rust resistance gene were developed in pseudo F1 cross population between ‘Puma White’ as susceptible and ‘Dancer’ as resistant using bulked segregant analysis (BSA). Of 280 RAPD primers (Operon 10 mer), 18 primers found to be polymorphic. After screening of these primers in 20 individual lines, only OPI-13520 was selected as closely linked marker to white rust disease resistance. Based on correspondence between phenotypic resistant level and marker in 187 segregation population, the genetic distance between white rust resistance gene and OPI-13520 marker assumed to be 3.8 cM. For OPI-13520 marker conversion into sequence characterized amplified region (SCAR) marker, the amplified fragment of OPI-13520 was purified, cloned and sequenced. Based on the DNA sequence of OPI-13520, SCAR maker was generated and verified in 20 individual lines used in BSA-RAPD.The results showed SCAR marker could be used to identify white rust resistance in chrysanthemum.

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.

Plant growth under water-deficit conditions adversely affects many key processes. Efforts to understand drought stress-related defense mechanisms have revealed a host of plant genes using molecular approaches in rice. Here, we report the novel finding that OsCTR1 E3 ligase regulates both chloroplast-localized chloroplast protein 12 (OsCP12) and ribosomal protein 1 (OsRP1) in protein levels and subcellular localization. The results of a yeast-two hybrid assay, bimolecular fluorescence complementation assay, ubiquitination assay, subcellular localization, and a protein degradation assay support the hypothesis that OsCTR1 functions in trafficking inhibition and proteolysis of OsCP12 and OsRP1 via the ubiquitin 26S proteasome pathway. Heterogeneous overexpression of OsCTR1 in Arabidopsis showed ABA-hypersensitive phenotype in seed germination, seedling growth, and stomatal closure. The transgenic plants also exhibited improvement of water-deficit tolerance with an accumulation of hydrogen peroxide production. These results demonstrate that the OsCTR1 E3 ligase might positively regulate the cellular functions of OsCP12 and RP1 related to photosynthesis under drought stress conditions in rice.

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.

Abscission is an important developmental process used to shed organs such as leaves, flowers and fruits. Despite the detailed characterization of growth dynamics and hormonal balance during the early steps of fruit development, the molecular aspects remain unclear. Abscission of young fruit occurs by separation of cells in anatomically distinct regions between the pedicel and junction. Differences of gene expression between central pedicel and lateral pedicel were investigated by NGS. Partial cDNAs from 15 clones from both the central pedicel and lateral pedicel were selected for nucleotide sequence determination and homology searches, and 12 clones were subsequently selected for further analysis. In preliminary series of Real Time PCR analysis, 9 genes were confirmed as showing a higher expression level in lateral pedicel than in central pedicel. Many of these genes are expressed in a central or lateral pedicel in specific manner, and the expression profiles of the representative genes were confirmed. To clarify the mechanism of MdIAA14 transcription factor gene underlying abscission zone development, we are investigating the expression patterns between central and lateral pedicels in different apple cultivar using real-time PCR and constructing the vector for transformation into apple.

Inactivation of the gene (DFR-A) coding for dihydroflavonol 4-reductase (DFR) involved in the anthocyanin biosynthesis pathway results in a yellow bulb color in onion (Allium cepa L.) and three inactive alleles have previously been identified in onion. Additionally, three active and six inactive DFR-A alleles were newly identified from extensive analyses of diverse onion germplasm. Presently, a yellow mutant containing a 171-bp deletion in the promoter region was identified and designated DFR-APD. Critically reduced transcription of this mutant allele and perfect co-segregation with color phenotypes in segregating populations were observed. Another yellow mutant (DFR-A5’DEL) containing a 518-bp deletion covering exons 1 and 2, which played important roles in DFR function, was identified. Meanwhile, both 2-bp and 4-bp insertions in the coding region leading to creation of pre-mature stop codons were also identified and designated DFR-AGT and DFR-A2AT, respectively. A 1-bp substitution mutation (DFR-AK48N) changing a positively charged lysine residue into a neutral asparagine was identified. This lysine residue, a NADPH binding site, was strictly conserved in other species. In addition, insertion of a leucine residue around substrate binding sites and catalytic triad was identified in several yellow accessions and was designated DFR-ATTA. Phylogenetic analysis of DFR-A alleles showed that all inactive alleles were independently derived from four different active alleles. In addition, the close relatedness and diversity of DFR-A mutants implied that all these mutations might have occurred after domestication of onions and had probably been maintained by artificial selection.

A 72-year-old female patient was admitted to our hospital with a rapidly growing left eyelid mass. Other ocular findings were normal. Excision biopsy and a cytological study were performed. Histopathology of the excised tissue showed malignant cells in extracellular lumens and glands with prominent micronuclei and mitotic figures. The tissue was also strongly positive for cytokeratin. As a result, of these fingings primary eyelid hidradenocarcinoma was diagnosed. This case demonstrates that hidradenocarcinoma should be considered in the differential diagnosis of primary eyelid tumors.

Gene expressions of cytochrome P4501A (CYP1A), aryl hydrocarbon receptor (AhR) and vitellogenin (Vg) by endocrine disruptors, benzo[]pyrene (B[a]P) and tributyltin (TBT) were examined in cultured eel hepatocytes which were isolated from eels treated previously with B[a]P (10 mg/kg) or estradiol- (20 mg/kg) in vivo, and the relationship between CYP1A, AhR and Vg genes were studied. When the cultured eel hepatocytes were treated with B[a]P () the gene expressions of CYP1A and AhR were enhanced in a concentration-dependent manner. However, when treated with TBT () the gene expressions of CYP1A and AhR were suppressed at high concentrations (), while having no effects at low concentrations (). Gene expression of Vg was also suppressed by TBT in a concentration-dependent manner in cultured eel hepatocytes which was previously treated in vivo with estradiol-.

The concept of causality is among the primary human concept- ualizations and thus carries special significance in its linguistic represen- tation. This is well illustrated by numerous cognitive explorations with respect to ``force dynamics``. Since the human construal of caused events in real-world situations involves diversified classification of the causal force, the causal force takes on equally diverse linguistic representations. In Korean such dimensionality of causality is perceptually attributable to, and analytically retrievable from, the semantics of the source lexemes of the complex postpositions and connectives, where the so-called defective nouns participate as a nominal component of the formal constructs. The typology of causality along the physical dimension bears significance in that the members of each subcategory exhibit different behavior in terms of their syntagmatic cooccurrence, as a result of differing semantic constraints. This paper shows that there is a systematic correlation between the semantics of the source nominals and that of the grammaticalized forms; that the dimensional differences can account for the interchangeability and incom- patibility among complex postpositions and connectives; and that the grammaticalization process often involves subjectification of the language user, whereby only a particular aspect of an event is selected for emphasis.

Dandelion has been widely utilized for medicinal and edible purposes. This research was conducted to evaluate the effect of supplemental LED (light-emitting diode) light on germination, growth characteristics and anthocyanin content of dandelion (Taraxacum officinale) seedling using LED blue (460 nm), red (660 nm, R), blue + red (B:R=6:4) and fluorescent lamp light treatment. By LED illumination to T. officinale seed germination speed was delayed, and germination rate was the highest in the fluorescent light. The growth characteristics (plant height, number of leaves, root length and fresh weight) were greatly influenced by supplemental LED light compared with control treatment, and the growth promotion was the most effective in the red LED illumination. After 60 days of red and mixed LED light treatments, anthocyanin content of dandelion plants was significantly changed. The anthocyanin content was increased by 12~19 mg/100 g under the red LED and the mixed light conditions compared with the control and the blue LED. Results indicate that illumination with red and mix LEDs, compared with other light treatments, is beneficial for promotion of growth and anthocyanin content in dandelion.

Ionizing radiation is known to cause chromosomal alterations such as inversions and deletions and affects gene expression within the plant genome. To monitor the genome-wide transcriptome changes by ionizing radiation, we used rice Affimetrix GeneChip microarray to identify genes that are up- or down regulated by gamma-ray (200 Gy, 60Co source), cosmic-ray and ion beam (40 Gy, 220 MeV carbon ion). The overall expression patterns between gamma-ray and ion beam were similar but cosmic-ray was regulated differently. Combined results from all 3 radiations identified 27 up-regulated genes and 188 down regulated genes. These results mean the induction of similar mechanism changes in treatments of gamma ray and ion beam. However the different expression in treatment of cosmic-ray might be due to the other environmental conditions. Among the commonly up- or down- regulated genes, we chose highly up- or down- regulated several genes and confirmed its regulation in response to ionizing radiation exposure by RT-PCR analysis. Moreover, we showed that specific co-expression networks of candidate radio marker genes by ARACNE algorithm. Our results present profiles of gene expression related to different ionizing radiation and marker gene to predict sensitivity to ionizing radiation, such as GS (glutelin subunit) and FBX322.

Carotenoids are major secondary compounds in Citrus determining the color of fruit and nutritional values. Carotenoids are isoprenoic compounds, and function as color pigments in the flower and fruit to attract pollinators and seed-dispersing animal and chromophore for light harvest and photoprotectant during photosynthesis. In the aim of developing new cultivars with high value using molecular breeding technology, we had performed screening of flesh and peel specific genes by differentially expressed gene screening in Citrus unshiu fruits. From the screening, carotenoid isomerase (CRTISO)1, which converts pro-lycopene to all-trans-lycopene, was identified as peel-specifically expressed gene. In this study, the gene encoding the CRTISO1 was cloned, sequenced, and compared to the CRTISOs in other plant species. Comparison of the cds sequence to other plant species revealed 75% and 78% identity with CRTISO1 of Zea maize and CRTISO2 of Arabidopsis thaliana respectively. We also cloned CRTISO2 from C. unshiu which declines the expression while maturation (Kato et al., 2004), and the gene structure was analyzed. This is the first work reporting the full sequence and gene structure of CRTISOs in C. unshiu, and would give important information in understanding the carotenoid synthesis in the Citrus fruit.

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.