Interface sulfur passivation using H₂S annealing for atomic-layer-deposited Al₂O₃ films on an ultrathin-body In_0.53Ga_0.47As-on-insulator

Jin, H.S.,Cho, Y.J.,Lee, S.M.,Kim, D.H.,Kim, D.W.,Lee, D.,Park, J.B.,Won, J.Y.,Lee, M.J.,Cho, S.H.,Hwang, C.S.,Park, T.J. New York] ; North-Holland 2014 APPLIED SURFACE SCIENCE - Vol.315 No.-

Atomic-layer-deposited Al<SUB>2</SUB>O<SUB>3</SUB> films were grown on ultrathin-body In<SUB>0.53</SUB>Ga<SUB>0.47</SUB>As substrates for III-V compound-semiconductor-based devices. Interface sulfur (S) passivation was performed with wet processing using ammonium sulfide ((NH<SUB>4</SUB>)<SUB>2</SUB>S) solution, and dry processing using post-deposition annealing (PDA) under a H<SUB>2</SUB>S atmosphere. The PDA under the H<SUB>2</SUB>S atmosphere resulted in a lower S concentration at the interface and a thicker interfacial layer than the case with (NH<SUB>4</SUB>)<SUB>2</SUB>S wet-treatment. The electrical properties of the device, including the interface property estimated through frequency dispersion in capacitance, were better for (NH<SUB>4</SUB>)<SUB>2</SUB>S wet-treatment than the PDA under a H<SUB>2</SUB>S atmosphere. They might be improved, however, by optimizing the process conditions of PDA. The PDA under a H<SUB>2</SUB>S atmosphere following (NH<SUB>4</SUB>)<SUB>2</SUB>S wet-treatment resulted in an increased S concentration at the interface, which improved the electrical properties of the devices.

Complete chloroplast genome sequences of Solanum commersonii and its application to chloroplast genotype in somatic hybrids with Solanum tuberosum

Cho, K. S.,Cheon, K. S.,Hong, S. Y.,Cho, J. H.,Im, J. S.,Mekapogu, M.,Yu, Y. S.,Park, T. H. Springer International 2016 Plant cell reports Vol. No.

<P>Chloroplast genome of Solanum commersonii and S olanum tuberosum were completely sequenced, and Indel markers were successfully applied to distinguish chlorotypes demonstrating the chloroplast genome was randomly distributed during protoplast fusion. Somatic hybridization has been widely employed for the introgression of resistance to several diseases from wild Solanum species to overcome sexual barriers in potato breeding. Solanum commersonii is a major resource used as a parent line in somatic hybridization to improve bacterial wilt resistance in interspecies transfer to cultivated potato (S. tuberosum). Here, we sequenced the complete chloroplast genomes of Lz3.2 (S. commersonii) and S. tuberosum (PT56), which were used to develop fusion products, then compared them with those of five members of the Solanaceae family, S. tuberosum, Capsicum annum, S. lycopersicum, S. bulbocastanum and S. nigrum and Coffea arabica as an out-group. We then developed Indel markers for application in chloroplast genotyping. The complete chloroplast genome of Lz3.2 is composed of 155,525 bp, which is larger than the PT56 genome with 155,296 bp. Gene content, order and orientation of the S. commersonii chloroplast genome were highly conserved with those of other Solanaceae species, and the phylogenetic tree revealed that S. commersonii is located within the same node of S. tuberosum. However, sequence alignment revealed nine Indels between S. commersonii and S. tuberosum in their chloroplast genomes, allowing two Indel markers to be developed. The markers could distinguish the two species and were successfully applied to chloroplast genotyping (chlorotype) in somatic hybrids and their progenies. The results obtained in this study confirmed the random distribution of the chloroplast genome during protoplast fusion and its maternal inheritance and can be applied to select proper plastid genotypes in potato breeding program.</P>

VP2 capsid domain of the H-1 parvovirus determines susceptibility of human cancer cells to H-1 viral infection

Cho, I-R,Kaowinn, S,Song, J,Kim, S,Koh, S S,Kang, H-Y,Ha, N-C,Lee, K H,Jun, H-S,Chung, Y-H Nature America, Inc. 2015 Cancer gene therapy Vol.22 No.5

Although H-1 parvovirus is used as an antitumor agent, not much is known about the relationship between its specific tropism and oncolytic activity. We hypothesize that VP2, a major capsid protein of H-1 virus, determines H-1-specific tropism. To assess this, we constructed chimeric H-1 viruses expressing Kilham rat virus (KRV) capsid proteins, in their complete or partial forms. Chimeric H-1 viruses (CH1, CH2 and CH3) containing the whole KRV VP2 domain could not induce cytolysis in HeLa, A549 and Panc-1 cells. However, the other chimeric H-1 viruses (CH4 and CH5) expressing a partial KRV VP2 domain induced cytolysis. Additionally, the significant cytopathic effect caused by CH4 and CH5 infection in HeLa cells resulted from preferential viral amplification via DNA replication, RNA transcription and protein synthesis. Modeling of VP2 capsid protein showed that two variable regions (VRs) (VR0 and VR2) of H-1 VP2 protein protrude outward, because of the insertion of extra amino-acid residues, as compared with those of KRV VP2 protein. This might explain the precedence of H-1 VP2 protein over KRV in determining oncolytic activity in human cancer cells. Taking these results together, we propose that the VP2 protein of oncolytic H-1 parvovirus determines its specific tropism in human cancer cells.

Predicting temporal shifts in the spring occurrence of overwintered Scotinophara lurida (Hemiptera: Pentatomidae) and rice phenology in Korea with climate change

Lee, H.,Kang, W. S.,Ahn, M. I.,Cho, K.,Lee, J. H. Springer Science + Business Media 2016 International journal of biometeorology Vol.60 No.1

<P>Climate change could shift the phenology of insects and plants and alter their linkage in space and time. We examined the synchrony of rice and its insect pest, Scotinophara lurida (Burmeister), under the representative concentration pathways (RCP) 8.5 climate change scenario by comparing the mean spring immigration time of overwintered S. lurida with the mean rice transplanting times in Korea. The immigration time of S. lurida was estimated using an overwintered adult flight model. The rice transplanting time of three cultivars (early, medium, and medium-late maturing) was estimated by forecasting the optimal cultivation period using leaf appearance and final leaf number models. A temperature increase significantly advanced the 99 % immigration time of S. lurida from Julian day 192.1 in the 2000s to 178.4 in the 2050s and 163.1 in the 2090s. In contrast, rice transplanting time was significantly delayed in the early-maturing cultivar from day 141.2 in the 2000s to 166.7 in the 2050s and 190.6 in the 2090s, in the medium-maturing cultivar from day 130.6 in the 2000s to 156.6 in the 2050s and 184.7 in the 2090s, and in the medium-late maturing cultivar from day 128.5 in 2000s to 152.9 in the 2050s and 182.3 in the 2090s. These simulation results predict a significant future phenological asynchrony between S. lurida and rice in Korea.</P>

Site-specific mutagenesis of yeast 2-Cys peroxiredoxin improves heat or oxidative stress tolerance by enhancing its chaperone or peroxidase function

Hong, S. H.,Lee, S. S.,Chung, J. M.,Jung, H. s.,Singh, S.,Mondal, S.,Jang, H. H.,Cho, J. Y.,Bae, H. J.,Chung, B. Y. Springer Science + Business Media 2017 Protoplasma Vol.254 No.1

<P>Yeast peroxiredoxin II (yPrxII) is an antioxidant enzyme that plays a protective role against the damage caused by reactive oxygen species (ROS) in Saccharomyces cerevisiae. This enzyme consists of 196 amino acids containing 2-Cys Prx with highly conserved two active cysteine residues at positions 48 and 171. The yPrxII has dual enzymatic functions as a peroxidase and molecular chaperone. To understand the effect of additional cysteine residues on dual functions of yPrxII, S79C-yPrxII and S109C-yPrxII, the substitution of Ser with Cys residue at 79 and 109 positions, respectively, was generated. S109C-yPrxII and S79C-yPrxII showed 3.7- and 2.7-fold higher chaperone and peroxidase activity, respectively, than the wild type (WT). The improvement in enzyme activity was found to be closely associated with structural changes in proteins. S109C-yPrxII had increased beta-sheet in its secondary structure and formed high-molecular-weight (HMW) as well as low-molecular-weight (LMW) complexes, but S79C-yPrxII formed only LMW complexes. HMW complexes predominantly exhibited a chaperone function, and LMW complexes showed a peroxidase function. In addition, transgenic yeast cells over-expressing Cys-substituted yPrxII showed greater tolerance against heat and oxidative stress compared to WT-yPrxII.</P>

Effect of bedrock stiffness and thickness of weathered rock on response spectrum in Korea

Manandhar, S.,Cho, H. I.,Kim, D. S. Springer Science + Business Media 2016 KSCE JOURNAL OF CIVIL ENGINEERING Vol.20 No.7

<P>The Standard Penetration Test (SPT) is increasingly used to generate shear wave velocity (V (S) ) profile of a site for seismic hazard assessment. However, it is difficult to perform site investigation using the SPT for weathered rock and bedrock even at shallow depths in most cases. Consequently, the stiffness of bedrock (V (Sb) ) is assumed to be 760 m/s, and only partial thickness of weathered rock is used for site response assessment in Korea. The increase in V (Sb) and thickness of weathered rock (H (w) ) may affect the overall seismic response of a site, even though the site response is mostly governed by the upper soil layers. In this study, the effect of V (Sb) and H (w) on response spectrum in Korea was investigated by performing equivalent-linear site response analyses on three representative sites each of S (C) and S (D) soil categories as defined in the Korean seismic code based on the average shear wave velocity of top 30 m of a site (V-S30). The S (C) and S (D) categories are defined similar to that in the International Building Code (IBC). Further, the effect of increase in V-Sb and H-w on the selection of design response spectrum based on seismic codes was also investigated. An increase in V (Sb) resulted in an increase in spectral amplification, while the effect of increase in H-w was not substantial for the representative sites considered in this study. This means that the V (S) of bedrock needs to be assessed properly. On the other hand, it is possible to get a reliable seismic response even if the H-w cannot be determined accurately. The incorporation of V (Sb) in V (S30) for shallow bedrock sites (bedrock depth < 30 m) fails to consider the effect of increase in seismic amplification at large V (Sb) . Hence, it is preferable to consider the effect of V (Sb) separately on the design response spectrum. In addition, the effect on soil non-linearity due to variation in the V (Sb) and H (w) was found to be insignificant.</P>

Effects of HA and NA glycosylation pattern changes on the transmission of avian influenza A(H7N9) virus in guinea pigs

Park, S.,Lee, I.,Kim, J.I.,Bae, J.Y.,Yoo, K.,Kim, J.,Nam, M.,Park, M.,Yun, S.H.,Cho, W.I.,Kim, Y.S.,Ko, Y.Y.,Park, M.S. Academic Press 2016 Biochemical and biophysical research communication Vol.479 No.2

Avian influenza H7N9 virus has posed a concern of potential human-to-human transmission by resulting in seasonal virus-like human infection cases. To address the issue of sustained human infection with the H7N9 virus, here we investigated the effects of hemagglutinin (HA) and neuraminidase (NA) N-linked glycosylation (NLG) patterns on influenza virus transmission in a guinea pig model. Based on the NLG signatures identified in the HA and NA genetic sequences of H7N9 viruses, we generated NLG mutant viruses using either HA or NA gene of a H7N9 virus, A/Anhui/0½013, by reverse genetics on the 2009 pandemic H1N1 virus backbone. For the H7 HA NLG mutant viruses, NLG pattern changes appeared to reduce viral transmissibility in guinea pigs. Intriguingly, however, the NLG changes in the N9 NA protein, such as a removal from residue 42 or 66 or an addition at residue 266, increased transmissibility of the mutant viruses by more than 33%, 50%, and 16%, respectively, compared with a parental N9 virus. Given the effects of HA-NA NLG changes with regard to viral transmission, we then generated the HA-NA NLG mutant viruses harboring the H7 HA of double NLG addition and the N9 NA of various NLG patterns. As seen in the HA NLG mutants above, the double NLG-added H7 HA decreased viral transmissibility. However, when the NA NLG changes occurred by a removal of residue 66 and an addition at 266 were additionally accompanied, the HA-NA NLG mutant virus recovered the transmissibility of its parental virus. These demonstrate the effects of specific HA-NA NLG changes on the H7N9 virus transmission by highlighting the importance of a HA-NA functional balance.

PHF2 histone demethylase acts as a tumor suppressor in association with p53 in cancer

Lee, K-H,Park, J-W,Sung, H-S,Choi, Y-J,Kim, W H,Lee, H S,Chung, H-J,Shin, H-W,Cho, C-H,Kim, T-Y,Li, S-H,Youn, H-D,Kim, S J,Chun, Y-S Macmillan Publishers Limited 2015 Oncogene Vol.34 No.22

Plant homeodomain finger 2 (PHF2) has a role in epigenetic regulation of gene expression by demethylating H3K9-Me2. Several genome-wide studies have demonstrated that the chromosomal region including the PHF2 gene is often deleted in some cancers including colorectal cancer, and this finding encouraged us to investigate the tumor suppressive role of PHF2. As p53 is a critical tumor suppressor in colon cancer, we tested the possibility that PHF2 is an epigenetic regulator of p53. PHF2 was associated with p53, and thereby, promoted p53-driven gene expression in cancer cells under genotoxic stress. PHF2 converted the chromatin that is favorable for transcription by demethylating the repressive H3K9-Me2 mark. In an HCT116 xenograft model, PHF2 was found to be required for the anticancer effects of oxaliplatin and doxorubicin. In PHF2-deficient xenografts, p53 expression was profoundly induced by both drugs, but its downstream product p21 was not, suggesting that p53 cannot be activated in the absence of PHF2. To find clinical evidence about the role of PHF2, we analyzed the expressions of PHF2, p53 and p21 in human colon cancer tissues and adjacent normal tissues from patients. PHF2 was downregulated in cancer tissues and PHF2 correlated with p21 in cancers expressing functional p53. Colon and stomach cancer tissue arrays showed a positive correlation between PHF2 and p21 expressions. Informatics analyses using the Oncomine database also supported our notion that PHF2 is downregulated in colon and stomach cancers. On the basis of these findings, we propose that PHF2 acts as a tumor suppressor in association with p53 in cancer development and ensures p53-mediated cell death in response to chemotherapy.

Coumarins reduce biofilm formation and the virulence of Escherichia coli O157:H7

Lee, J.H.,Kim, Y.G.,Cho, H.S.,Ryu, S.Y.,Cho, M.H.,Lee, J. G. Fischer 2014 Phytomedicine Vol.21 No.8

E. coli O157:H7 is the most common cause of hemorrhagic colitis, and no effective therapy exists for E. coli O157:H7 infection. Biofilm formation is closely related to E. coli O157:H7 infection and constitutes a mechanism of antimicrobial resistance. Hence, the antibiofilm or antivirulence approach provides an alternative to antibiotic strategies. Coumarin and its derivatives have a broad range of biological effects, and in this study, the antibiofilm activities of nine coumarins were investigated against E. coli O157:H7. Coumarin or umbelliferone at 50μg/ml was found to inhibit biofilm E. coli O157:H7 formation by more than 80% without affecting bacterial growth. Transcriptional analysis showed that coumarins repressed curli genes and motility genes in E. coli O157:H7, and these findings were in-line with observed reductions in fimbriae production, swarming motility, and biofilm formation. In addition, esculetin repressed Shiga-like toxin gene stx2 in E. coli O157:H7 and attenuated its virulence in vivo in the nematode Caenorhabditis elegans. These findings show that coumarins have potential use in antivirulence strategies against persistent E. coli O157:H7 infection.

Supplementation of oil-based inactivated H9N2 vaccine with M2e antigen enhances resistance against heterologous H9N2 avian influenza virus infection

Park, J.K.,Lee, D.H.,Cho, C.H.,Yuk, S.S.,To, E.O.,Kwon, J.H.,Noh, J.Y.,Kim, B.Y.,Choi, S.W.,Shim, B.S.,Song, M.K.,Lee, J.B.,Park, S.Y.,Choi, I.S.,Song, C.S. Elsevier Scientific Pub. Co 2014 Veterinary microbiology Vol.169 No.3

Avian influenza virus (AIV) subtype H9N2 has been evolving rapidly and vaccine escape variants have been reported to cause circulation of infections and economic losses. In the present study, we developed and evaluated ectodomain of the AIV matrix 2 (M2e) protein as a supplementing antigen for oil-based inactivated H9N2 vaccine to increase resistance against vaccine escape variants. AIV H9N2 M2e antigen was expressed in Escherichia coli and supplemented to inactivated H9N2 oil emulsion vaccine. Specific pathogen-free chickens received a single injection of inactivated H9N2 oil emulsion vaccines with or without M2e supplementation. At three weeks post vaccination, hemagglutination inhibition tests and enzyme-linked immunosorbent assays were performed to determine serological immune responses. Challenge study using a vaccine escape H9N2 variant was performed to evaluate the efficacy of M2e supplementation. M2e antigen supplemented in oil emulsion vaccine was highly immunogenic, and a single M2e-supplemented vaccination reduced challenge virus replication and shedding more effectively than non-supplemented vaccination.