Sung-Il Kim

Arabidopsis HIGH PLOIDY2 Sumoylates and Stabilizes Flowering Locus C through Its E3 Ligase Activity

Flowering Locus C (FLC), a floral repressor, plays an important role in flowering. The mechanisms regulating FLC gene expression and protein function have been studied extensively; however, post-translational regulation of FLC remains unclear. Here, we identified Arabidopsis HIGH PLOIDY2 (HPY2) as an E3 SUMO ligase for FLC. In vitro and vivo pull-down assays showed that FLC physically interacts with HPY2. In vitro assays showed that the stimulation of FLC sumoylation by HPY2 was dependent on SUMO-activating enzyme E1 and -conjugating enzyme E2, indicating that HPY2 was an E3 SUMO ligase for FLC. In transgenic plants, inducible HPY2 overexpression increased the concentration of FLC, indicating that HPY2 stabilized FLC through direct sumoylation. Flowering time in hpy2-2 mutants was shorter than in wild-type plants under long- and short-day conditions, with a greater effect under short-day conditions, and FLC was downregulated in hpy2-2 mutants. These data indicate that HPY2 regulates FLC function and stability at both the transcriptional and post-translational levels through its E3 SUMO ligase activity.

Arabidopsis CMT3 activity is positively regulated by AtSIZ1-mediated sumoylation

The activities of mammalian DNA and histone methyltransferases are regulated by post-translational modifications such as phosphorylation and sumoylation; however, it is unclear how the activities of these enzymes are regulated at the post-translational level in plants. Here, we demonstrate that the DNA methylation activity of Arabidopsis CHROMOMETHYLASE 3 (CMT3) is positively regulated by the E3 SUMO ligase AtSIZ1. The methylation level of the Arabidopsis genome, including transposons, was significantly lower in the siz1-2 mutant than in wild-type plants. CMT3 was sumoylated by the E3 ligase activity of AtSIZ1 through a direct interaction, and the DNA methyltransferase activity of CMT3 was enhanced by this modification. In addition, the methylation levels of a large number of genes, including the nitrate reductase gene NIA2, were lower in siz1-2 and cmt3 plants than in wild-type plants. Furthermore, the CHG methylation activity of CMT3 was specific for NIA2and not NIA1 (the other nitrate reductase gene in Arabidopsis), indicating that CMT3 selectively regulates the CHG methylation levels of target genes. Taken together, our results indicate that the sumoylation of CMT3 is critical for its role in the control of gene expression and that AtSIZ1 positively controls the epigenetic repression of CMT3-mediated gene expression.

Novel preprocessing technique to improve harmonic distortion in airborne parametric array

A novel modified preprocessing technique is proposed to reduce harmonic distortion in an airborne parametric array, which is designed to reproduce highly directed audible sound. This technique is based on the idea that the harmonic distortion is not fully canceled around 10 kHz because of the mismatch of phase and amplitude, even though previous simple preprocessing is activated. A digital filter is designed to compensate for this phase and amplitude mismatch. This linearization technique is verified by an experiment with an airborne parametric array for which the carrier frequency was 40 kHz. The results show that the second harmonic is reduced 11 dB and total harmonic distortion (THD) is improved 20% around 10 kHz compared to previous preprocessing. The proposed modified preprocessing is effective and good results render this technique suitable for the reproduction of high quality audible sound with high directivity.

The E3 SUMO ligase AtSIZ1 functions in seed germination in Arabidopsis

Seed germination is an important stage in the lifecycle of a plant because it determines subsequent vegetative growth and reproduction. Here, we show that the E3 SUMO ligase AtSIZ1 regulates seed dormancy and germination. The germination rates of the siz1 mutants were less than 50%, even after a short period of ripening. However, their germination rates increased to wild-type levels after cold stratification or long periods of ripening. In addition, exogenous gibberellin (GA) application improved the germination rates of the siz1 mutants to the wild-type level. In transgenic plants, suppression of AtSIZ1 caused rapid post-translational decay of SLEEPY1 (SLY1), a positive regulator of GA signaling, during germination, and inducible AtSIZ1 overexpression led to increased SLY1 levels. In addition, overexpressing wild-type SLY1 in transgenic sly1 mutants increased their germination ratios to wild-type levels, whereas the germination ratio of transgenic sly1 mutants overexpressing mSLY1 was similar to that of sly1. The germination ratios of siz1 mutant seeds in immature developing siliques were much lower than those of the wild-type. Moreover, SLY1 and DELAY OF GERMINATION 1 (DOG1) transcript levels were reduced in the siz1 mutants, whereas the transcript levels of DELLA and ABSCISIC ACID INSENSITIVE 3 (ABI3) were higher than those of the wild-type. Taken together, these results indicate that the reduced germination of the siz1 mutants results from impaired GA signaling due to low SLY1 levels and activity, as well as hyperdormancy due to high levels of expression of dormancy-related genes including DOG1.

Characterization of channel oil reservoirs with an aquifer using EnKF, DCT, and PFR:

Reservoir characterization is necessary for making reliable models to have future reservoir performances. Since an aquifer typically has positive influences on oil production, its characterization has rarely been regarded as a critical issue. However, in channel oil reservoirs, an aquifer amplifies uncertainty of permeability estimations and has its own uncertainty due to limited information without any direct measurement. Although there have been some researches on channel oil reservoirs using discrete cosine transformation, we cannot characterize reliably an aquifer using discrete cosine transformation alone. Thus, we need additional schemes to manage increased uncertainty by an aquifer and to estimate the aquifer itself. In this study, ensemble Kalman filter with the combination of preservation of facies ratio and discrete cosine transformation is proposed for channel reservoirs with an aquifer. By the proposed method, we confirm that discrete cosine transformation and preservation of facies ratio contribute to preservation of overall channel properties and fine-tuning of the channel in the ensemble Kalman filter algorithm, respectively. Consequently, the proposed method gives us stable characterization performances on oil and water productions, permeability distribution, and aquifer strengths for a reasonable decision.

Niclosamide inhibits leaf blight caused by Xanthomonas oryzae in rice

Rice leaf blight, which is caused by the bacterial pathogen Xanthomonas oryzae pv. oryzae (Xoo), results in huge losses in grain yield. Here, we show that Xoo-induced rice leaf blight is effectively controlled by niclosamide, an oral antihelminthic drug and molluscicide, which also functions as an anti-tumor agent. Niclosamide directly inhibited the growth of the three Xoo strains PXO99, 10208 and K3a. Niclosamide moved long distances from the site of local application to distant rice tissues. Niclosamide also increased the levels of salicylate and induced the expression of defense-related genes such as OsPR1 and OsWRKY45, which suppressed Xoo-induced leaf wilting. Niclosamide had no detrimental effects on vegetative/reproductive growth and yield. These combined results indicate that niclosamide can be used to block bacterial leaf blight in rice with no negative side effects.

Ammonium Inhibits Chromomethylase 3-Mediated Methylation of the Arabidopsis Nitrate Reductase Gene NIA2.

Gene methylation is an important mechanism regulating gene expression and genome stability. Our previous work showed that methylation of the nitrate reductase (NR) gene NIA2 was dependent on chromomethylase 3 (CMT3). Here, we show that CMT3-mediated NIA2 methylation is regulated by ammonium in Arabidopsis thaliana. CHG sequences (where H can be A, T, or C) were methylated in NIA2 but not in NIA1, and ammonium [(NH4)2SO4] treatment completely blocked CHG methylation in NIA2. By contrast, ammonium had no effect on CMT3 methylation, indicating that ammonium negatively regulates CMT3-mediated NIA2 methylation without affecting CMT3 methylation. Ammonium upregulated NIA2 mRNA expression, which was consistent with the repression of NIA2 methylation by ammonium. Ammonium treatment also reduced the overall genome methylation level of wild-type Arabidopsis. Moreover, CMT3 bound to specific promoter and intragenic regions of NIA2. These combined results indicate that ammonium inhibits CMT3-mediated methylation of NIA2 and that of other target genes, and CMT3 selectively binds to target DNA sequences for methylation.

Preferred diffusion paths for copper electromigration by in situ transmission electron microscopy

Ionic transport in the reverse direction of an electric field is caused by momentum transfer from free electrons to metal ions, i.e., electromigration (EM), which is a critical factor leading to copper (Cu) interconnect failure in integrated circuits under extreme operating conditions. We investigated Cu self-diffusion paths under electrical bias using in situ transmission electron microscopy (TEM). An electric current was applied to multigrain Cu lines in the TEM instrument for durations of up to the order of 104s to trace EM-induced Cu movement around voids and hillocks. Combining this approach with scanning nanobeam diffraction, we observed that high-angle grain boundaries exposed to the free surface are the most favored paths for Cu EM, rather than a specific orientation within the grain. On hillocks of accumulated Cu atoms, we directly observed grain growth, accompanied by the formation of Σ7 high-mobile and Σ3 twin coincidence site lattice boundaries for effective growth. This study provides insight into the EM mechanism to improve the reliability of metal interconnect design.

Ascorbate Peroxidase OsAPx1 is Involved in Seed Development in Rice

Ascorbate peroxidases (APXs) are enzymes that detoxify peroxides such as hydrogen peroxide using ascorbate. They are distributed as isoenzymes in distinct cellular compartments, such as the cytosol, mitochondria and peroxisomes, where they play essential roles in scavenging reactive oxygen species (ROS) and protecting cells against the toxic effects of these species in higher plants, algae, euglena and other organisms. APXs also respond to environmental stresses, such as salinity and drought, and rice ascorbate peroxidase 1 (OsAPx1) participates in salinity tolerance. However, it is still unclear how OsAPx1 is involved in growth and development before and after flowering. Here, we show that OsAPx1 plays an important function in seed development, including fertilization. Proteomic analysis and quantitative RT-PCR showed that protein and mRNA levels of OsAPx1 were much higher in immature seeds than in mature seeds. Plant height and grain size in an Osapx1 mutant were almost the same as those in wild-type plants. However, about 58% of the seeds were aborted in the Osapx1 mutant, although the mutant was capable of normal flowering. Our results suggest that rice ascorbate peroxidase functions both as a regulator of seed development and as a scavenger of ROS.