Microbacterium rhizosphaerae sp. nov., isolated from a Ginseng field, South Korea

Cho, S. J.,Lee, S. S. Springer Science + Business Media 2017 Antonie van Leeuwenhoek Vol.110 No.1

<P>A novel Gram-stain positive, aerobic, short rod-shaped, non-motile bacterium, designated strain CHO1(T), was isolated from rhizosphere soil from a ginseng agriculture field. Strain CHO1(T) was observed to form yellow colonies on R2A agar medium. The cell wall peptidoglycan was found to contain alanine, glycine, glutamic acid, d-ornithine and serine. The cell wall sugars were identified as galactose, mannose, rhamnose and ribose. Strain CHO1(T) was found to contain MK-11, MK-12, MK-13 as the predominant menaquinones and anteiso-C-15:0, iso-C-16:0, and anteiso-C-17:0 as the major fatty acids. Diphosphatidylglycerol, phosphatidylglycerol, phosphoglycolipid, an unidentified phospholipid and three unidentified glycolipids were found to be present in strain CHO1(T). Based on 16S rRNA gene sequence analysis, strain CHO1(T) was found to be closely related to Microbacterium mangrovi DSM 28240(T) (97.81 % similarity), Microbacterium immunditiarum JCM 14034(T) (97.45 %), Microbacterium oryzae JCM 16837(T) (97.33 %) and Microbacterium ulmi KCTC 19363(T) (97.10 %) and to other species of the genus Microbacterium. The DNA G+C content of CHO1(T) was determined to be 70.1 mol %. The DNA-DNA hybridization values of CHO1(T) with M. mangrovi DSM 28240(T), M. immunditiarum JCM 14034(T), M. oryzae JCM 16837(T) and M. ulmi KCTC 19363(T) were 46.7 +/- 2, 32.4 +/- 2, 32.0 +/- 2 and 29.2 +/- 2 %, respectively. On the basis of genotypic, phenotypic and phylogenetic properties, it is concluded that strain CHO1(T) represents a novel species within the genus Microbacterium, for which the name Microbacterium rhizosphaerae sp. nov. is proposed. The type strain of M. rhizosphaerae is CHO1(T) (= KEMB 7306-513(T) = JCM 31396(T)).</P>

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>

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>

Production of soluble truncated spike protein of porcine epidemic diarrhea virus from inclusion bodies of Escherichia coli through refolding

Piao, D.C.,Lee, Y.S.,Bok, J.D.,Cho, C.S.,Hong, Z.S.,Kang, S.K.,Choi, Y.J. Academic Press 2016 Protein expression and purification Vol.126 No.-

The emergence of highly pathogenic variant porcine epidemic diarrhea virus (PEDV) strains, from 2013 to 2014, in North American and Asian countries have greatly threatened global swine industry. Therefore, development of effective vaccines against PEDV variant strains is urgently needed. Recently, it has been reported that the N-terminal domain (NTD) of S1 domain of PEDV spike protein is responsible for binding to the 5-N-acetylneuraminic acid (Neu5Ac), a possible sugar co-receptor. Therefore, the NTD of S1 domain could be an attractive target for the development of subunit vaccines. In this study, the NTD spanning amino acid residues 25-229 (S25-229) of S1 domain of PEDV variant strain was expressed in Escherichia coli BL21 (DE3) in the form of inclusion bodies (IBs). S25-229 IBs were solubilized in 20 mM sodium acetate (pH 4.5) buffer containing 8 M urea and 1 mM dithiothreitol with 95% yield. Solubilized S25-229 IBs were refolded by 10-fold flash dilution and purified by one-step cation exchange chromatography with >95% purity and 20% yield. The CD spectrum of S25-229 showed the characteristic pattern of alpha helical structure. In an indirect ELISA, purified S25-229 showed strong reactivity with mouse anti-PEDV sera. In addition, immunization of mice with 20 μg of purified S25-229 elicited highly potent serum IgG titers. Finally, mouse antisera against S25-229 showed immune reactivity with native PEDV S protein in an immunofluorescence assay. These results suggest that purified S25-229 may have potential to be used as a subunit vaccine against PEDV variant strains.

세관 양광주 방전에서 플라즈마 확산의 완전 해

김동준,정종문,김정현,황하청,정재윤,조윤희,임현교,구제환,최은하,조광섭,Jin, D.J.,Jeong, J.M.,Kim, J.H.,Hwang, H.C.,Chung, J.Y.,Cho, Y.H.,Lim, H.K.,Koo, J.H.,Choi, E.H.,Cho, G.S. 한국진공학회 2010 Applied Science and Convergence Technology Vol.19 No.1

관경이 수 mm인 세관 램프 내부에서 플라즈마의 확산을 조사하기 위하여 이극성(ambipolar) 확산방정식을 해하였다. 반경 방향의 확산에 의한 유리관 벽에서의 플라즈마 소멸 특성시간은 $\tau_r\;=\;(r_0/2.4)^2/D_a$로 주어진다. 반경 $r_0{\sim}1\;mm$이고 이극성 확산계수 $D_a{\sim}0.01\;m^2/s$ 이면, $\tau_r{\sim}17\;{\mu}s$이다. 이는 램프의 교류전원 구동에서 플라즈마를 유지하기 위한 구동 최소 주파수 ~30 kHz에 해당한다. 고전압이 인가되는 전극부에 발생한 고밀도의 플라즈마가 양광주로 확산되는 특성시간은 $\tau_z{\sim}0.1\;s$이다. 고밀도 플라즈마 경계에서의 시간에 대한 확산속도는 $t{\sim}10^{-6}\;s$일 때 $u_D{\sim}10^2\;m/s$이고, $t{\sim}10^{-3}\;s$이면 그 속도는 $u_D{\sim}1\;m/s$로 느려진다. 따라서 램프 길이 ~1 m에 대하여 전극부에서 생성된 고밀도 플라즈마가 양광주 전체로 확산되는 시간은 수 초가 걸린다. The ambipolar diffusion equation has been solved in a fine-tube lamp of a few mm in diameter. In the diffusion of radial direction, the plasma diffuses and vanishes away at the glass wall by recombination with the characteristic time of plasma loss is given by $\tau_r\;=\;(r_0/2.4)^2/D_a$. With the radius $r_0{\sim}1\;mm$ and the ambipolar diffusion coefficient $D_a{\sim}0.01\;m^2/s$, the vanishing time is calculated $\tau_r{\sim}10\;{\mu}s$ which corresponds to the least value of frequency 30 kHz for the sustaining the plasma in the operation of high voltage AC-power. In the diffusion of longitudinal z-direction, a high density plasma generated at the area of a high voltage electrode, diffuses into the positive column with the characteristic time $\tau_z{\sim}0.1\;s$. The plasma diffusion velocity at the boundary of high density plasma is $u_D{\sim}10^2\;m/s$ at the time $t{\sim}10^{-6}$ s and the diffusion velocity becomes slow as $u_D{\sim}1\;m/s$ at $t{\sim}10^{-3}\;s$. Therefore, for the long lamp of 1 m, it takes about several seconds for the high density plasma at the area of electrode to diffuse through the whole positive column space.

燐酸 및 加里肥料가 葉煙草의 收量 및 니코틴의 含量에 미치는 影響

趙成鎭,金才正,裵孝元 충북대학교 엽연초연구소 1971 煙草硏究 Vol.1 No.-

This experiment was Carried out to determine the effect of different levels of phosphate and potash fertilizers applied on yields and quality of leaf tobacco. It was done at all varying levels of phosphate and potassium fertilizers. S0 (non-fertilizer Plot) ; N:P:K=0:0:0(kg/10a) S1 (1/2amount Plot) ; N:P:K=10:7.5:10(〃) S2 (Standard Plot) ; N:P:K=10: 15:20(〃) S3 (1.5 times Plot) ; N:P:K=10:22.5:30(〃) S4 (2.0 times Plot) ; N:P:K=10:30:70 (kg/10a) Urea was applied as nitrogen, triple super phosphate as phosphate, potassium sulfate as potash source. The total amount of fertilizers was applied as basal dressing per one plant. This experiment was carried out by using randomized block design with 3 replication. The results obtained in terms of yields and quality are summarized as follows. 1.By increasing the amounts of phosphate and qotassium fertilizers, growing status of the largest leaf length, the largest leaf width and stem size of tobacco increased in the order of S4> S3> S2> S1> S0. 2.By increasing the amount of phosphate and potassium fertilizers, yield was increased in theorder of S4> S3> S2> S1> S0. This increase showed generally high significance among various levels of treatments. 3.The regressive equation was derived from the relationship between treatment levels and tobacco leaf yield. The most desirable treatment level for the maximum yield was estimated as the 2.87 times as much as the treatment level of phospate and potasium fertilizers of standardlot. 4.By increased application of phosphate and potash fertilizers, the contents of P2O5 K2 and K2O in the tobacco leaf became greater while the content of nicotine was decreased. Thus, a negative correlation between fertilizer application and nicotine content has been observed.

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>

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>

Prediction of stone-free status and complication rates after tubeless percutaneous nephrolithotomy: a comparative and retrospective study using three stone-scoring systems and preoperative parameters

Choi, S. W.,Bae, W. J.,Ha, U. S.,Hong, S. H.,Lee, J. Y.,Kim, S. W.,Cho, H. J. Springer Science + Business Media 2017 World journal of urology Vol.35 No.3

<P>To investigate the factors predictive of surgical outcomes of tubeless percutaneous nephrolithotomy (TPCNL) and to compare the predictability and accuracy of the Guy's stone score, S.T.O.N.E. nephrolithometry, and CROES nomogram. We reviewed retrospectively the surgical outcomes recorded consecutively and imaging data of preoperative computed tomography scans of 141 patients who had undergone TPCNL from June 2012 to October 2015. Guy's, S.T.O.N.E., and CROES stone-scoring systems (SSSs) and other prognostic factors were assessed using univariate and multivariate statistical analyses. The initial stone-free and complication rates after TPCNL were 78.7 (111/141) and 17.0 % (24/141). On univariate analysis, all three scoring systems were identified as significant factors in terms of stone-free rate (SFR). The multivariate logistic regression analysis showed that the Guy's stone score and stone burden 385 mm(2) had significant correlations with stone-free status [odds ratios (OR) = 3.220, p = 0.001 and OR = 6.451, p = 0.002, respectively]. Guy's stone score (OR = 1.879, p = 0.013) was an independent risk factor for the development of complications. The area under the receiver operating characteristic (ROC) curves for the Guy's, S.T.O.N.E., and CROES SSSs and stone burden showed good results (0.821, 0.816, 0.820, and 0.800, respectively). Pairwise comparison of ROC curves showed that there was no significant difference between each final score and stone burden. Of the three scoring systems, Guy's stone score was the only significant predictive factor for SFR and complication rates after TPCNL in the multivariate logistic regression analysis. Stone burden was significantly associated with a postoperative stone-free status (SFS).</P>

디지털 세계에서의 압수수색

Orin S. Kerr,조기영(Cho, Gi Yeong) 전북대학교 법학연구소 2016 法學硏究 Vol.49 No.-

이 글은 미국 조지워싱턴대학교 로스쿨의 Orin S. Kerr 교수의 논문인 『디지털 세계에서의 압수수색』을 번역한 것이다. Kerr 교수의 위 논문은 디지털 증거의 압수수색과 관련한 형사소송법적 쟁점을 포괄적으로 검토한 미국내 최초의 논문으로 평가할 수 있다. 이 논문을 통해 디지털 증거의 맥락에서 압수수색의 의미 및 압수수색의 합리성에 관한 미국 판례 및 학설의 현황을 종합적으로 이해하는 것도 우리 형사소송법의 운용에도 기여하는 바가 있을 것이라는 판단이 위 논문을 번역하게 된 이유이다. Orin S. Kerr 교수는 미국내 저명한 형사소송법 학자이며 컴퓨터 형법 전문가이다. 2001년 조지워싱턴대학교 로스쿨에 근무한 이후 Kerr 교수가 발표한 논문은 다른 논문에서는 2,000번 이상, 법원의 판결에서는 200번 이상 인용된 바 있다. Kerr 교수는 미국 법무부에서 컴퓨터 범죄와 재산권 부문 공판 변호사로 근무하였으며, 미국 연방대법원 대법관 Anthony M. Kennedy의 로클럭으로 근무하기도 하였다. Kerr 교수는 50편 이상의 논문을 저술하였으며, 우리나라에도 잘 알려져 있는 형사소송법 연구서(LaFave, Wayne, et al., Criminal Procedure. 4th ed. St. Paul, MN: West, 2015, 제3판은 2009년 출간됨)와 케이스 북(Kamisar, Yale, et. al., Modern Criminal Procedure: Cases, Comments, and Questions. 14th ed. St. Paul, MN: West Academic Pub., 2015)의 최근 공저자이기도 하다. 이 논문에서 Kerr 교수는 컴퓨터라는 새로운 환경에 미국수정헌법 제4조가 어떻게 적용될 수 있는지를 검토하고 있다. Kerr 교수는 먼저 전통적인 주거 수색과 컴퓨터 수색의 4가지 차이점을 상세하게 분석한 후 디지털 증거에 대한 압수수색의 단계를 디지털 증거의 수집과 분석 2단계로 나누어 종래 미국의 판례와 학설들을 검토하며 자신의 논지를 전개하고 있다. Kerr 교수는 디지털 증거의 수집 단계에서 컴퓨터의 정보에 접근하는 것은 프라이버시에 대한 합리적 기대를 침해하는 것으로서 미국수정헌법 제4조의 수색에 해당하며, 수색이 일어나는 시기는 정보 또는 데이터가 경찰관에 노출되는 시점(노출기준설)을 기준으로 하여야 한다고 주장한다. 따라서 컴퓨터에서 정보를 검색하기 위해서는 영장을 발부받거나 영장주의의 예외가 인정될 수 있어야 한다는 것이다. 동 교수는 또한 수사기관에 의한 비트스트림 복제는 소유자의 재산권을 침해한다는 점에서 압수수색으로 보아야 하며, 복제본에 대한 수색은 원본에 대한 수색과 마찬가지로 취급하여야 한다고 주장한다. 디지털 증거 분석 단계에서는, 미국 판례가 상당히 넓게 인정하고 있는 ‘명백한 발견의 예외’는 일반영장 또는 탐색적 영장에 의한 압수수색을 저지하기 위해서 디지털 증거의 압수수색에는 적용을 제한하거나 배제해야 한다는 것이 이 논문의 주요 주장이다. This paper is a translation of the above mentioned article of Professor Orin. S. Kerr of George Washington University, School of Law. I think that Kerr’s article has offered a comprehensive look at the meaning of searches, seizures, and reasonableness in the context of digital evidence for the first time in the academic world of the USA, and that is the reason why I translated this article into Korean. I think that this article will be a useful academic source for the comparative study of the USA to the issue of digital evidence. Orin S. Kerr is a nationally recognized scholar of criminal procedure and computer crime law. Since he joined the faculty in 2001, his publications have been cited in over 2,000 articles and more than 200 judicial opinions. Professor Kerr is a former trial attorney in the Computer Crime and Intellectual Property Section at the U.S. Department of Justice. He clerked for Justice Anthony M. Kennedy of the United States Supreme Court. Professor Kerr has argued cases in the United States Supreme Court and three federal circuits. He has testified six times before Congressional committees. In 2013, Chief Justice Roberts appointed Professor Kerr to serve on the Advisory Committee for the Federal Rules of Criminal Procedure. Chief Justice Roberts appointed Professor Kerr again in 2015 to serve on the Judicial Conference’s committee to review the Criminal Justice Act. Professor Kerr has written more than 50 articles, he has authored and co-authored popular casebook (with Kamisar, Yale, et. al., Modern Criminal Procedure: Cases, Comments, and Questions. 14th ed. St. Paul, MN: West Academic Pub., 2015) and co-authored the leading criminal procedure treatise (with LaFave, Wayne, et al., Criminal Procedure. 4th ed. St. Paul, MN: West, 2015, Third edition published in 2009). In this article Professor Kerr try to develop a normative framework for applying the Fourth Amendment of the United States Constitution to searches of computer hard drives and other electronic storage devices. In advance he explores four basic differences between the dynamics of traditional home searches and the new computer searches that trigger a need to rethink how the Fourth Amendment applies. In the data acquisition stage of computer searches, according to Professor Kerr, a Fourth Amendment “search” occurs whenever data is exposed to human observation, such as through a computer monitor. Under this standard, retrieving evidence from a computer ordinarily should require a warrant or an applicable exception to the warrant requirement. He also argue that court should regulate generating a bitstream copy as a search or seizure based on its interference with the owner’s property right and apply the same rules that regulate searches of originals to searches of copies. In the data acquisition stage of computer searches, Professor Kerr’s main theme is that it needs to tighten or even eliminate the plain view exception for digital evidence to limit the invasiveness of searches to avoid creating the digital equivalent of general searches.