DNA looping-mediated repression by histone-like protein H-NS: specific requirement of Esigma70 as a cofactor for looping.

Shin, Minsang,Song, Miryoung,Rhee, Joon Haeng,Hong, Yeongjin,Kim, You-Jin,Seok, Yeong-Jae,Ha, Kwon-Soo,Jung, Se-Hui,Choy, Hyon E Cold Spring Harbor Laboratory in association with 2005 Genes & development Vol.19 No.19

<P>Transcription initiation by RNA polymerase (RNP) carrying the house-keeping sigma subunit, sigma70 (Esigma70), is repressed by H-NS at a number of promoters including hdeABp in Escherichia coli, while initiation with RNP carrying the stationary phase sigma, sigma38 (Esigma38), is not. We investigated the molecular mechanism of selective repression by H-NS to identify the differences in transcription initiation by the two forms of RNPs, which show indistinguishable promoter selectivities in vitro. Using hdeABp as a model promoter, we observed with purified components that H-NS, acting at a sequence centered at -118, selectively repressed transcription by Esigma70. This selective repression is attributed to the differences in the interactions between hdeABp and the two forms of RNPs, since no other factor is required for the repression. We observed that the two forms of RNPs could form an open initiation complex (RP(O)) at hdeABp, but that Esigma70 failed to initiate transcription in the presence of H-NS. Interestingly, KMnO4 assays and high-resolution atomic force microscopy (AFM) revealed that hdeABp DNA wrapped around Esigma70 more tightly than around Esigma38, resulting in the potential crossing over of the DNA arms that project out of Esigma70 . RP(O) but not out of Esigma38 . RP(O). Based on these observations, we postulated that H-NS bound at -118 laterally extends by the cooperative recruitment of H-NS molecules to the promoter-downstream sequence joined by wrapping of the DNA around Esigma70 . RP(O), resulting in effective sealing of the DNA loop and trapping of Esigma70. Such a ternary complex of H-NS . Esigma70 hdeABp was demonstrated by AFM. In this case, therefore, Esigma70 acts as a cofactor for DNA looping. Expression of this class of genes by Esigma38 in the stationary phase is not due to its promoter specificity but to the architecture of the promoter . Esigma38 complex.</P>

축류식 사이클론의 성능 향상에 관한 연구

신민상(Minsang Shin),짱슈어(Shuo Zhang),유시연(Yoo Si Yeon),신원규(Weon Gyu Shin) 대한기계학회 2018 대한기계학회 춘추학술대회 Vol.2018 No.12

High-frequency characterization for SAW interdigital transducers

Shin Junggeun,Yoo Hansoo,Seong Minsang,Lee Donghun,Eo Yungseon 한국물리학회 2022 THE JOURNAL OF THE KOREAN PHYSICAL SOCIETY Vol.81 No.10

A new technique to accurately determine transmission line (TL) network parameters of surface acoustic wave (SAW) interdigital transducers (IDTs) is presented. Various test IDTs and radio frequency (RF) flters for experimental characterizations are designed and fabricated on a LiTaO3 piezoelectric material. S-parameters for test devices were measured in the broad frequency bands of 50 MHz to 6 GHz. Then decoupling the acoustic waves from electromagnetic waves with an electromechanical coupling coefcient (k2), accurate TL circuit model parameters for SAW devices are determined. The acoustic wave model parameters are determined in an iterative manner by combining the measured S-parameters with a physical model. We show that SAW-based RF flters that operate at the frequency higher than 1 GHz can be very accurately designed using the proposed technique.

The mechanism underlying Ler-mediated alleviation of gene repression by H-NS

Academic Press 2017 Biochemical and biophysical research communication Vol. No.

<P><B>Abstract</B></P> <P>Secretion of effector proteins in Enteropathogeneic <I>Escherichia coli</I> (EPEC) and Enterohemorrhagic <I>Escherichia coli</I> (EHEC) is mediated by a specialized type III secretion system, components of which are encoded in the LEE operons 1 to 5. H-NS, a global repressor in <I>E</I>. <I>coli</I>, silences the expression of LEE operons. Ler, a master regulator in LEE operons, shares 24% amnio acid identity and 44% amino acid similarity to H-NS. Interestingly, rather than a gene silencer, its main role has been characterized as an antagonizing protein that relieves H-NS-mediated transcriptional silencing. In the previous study we reported molecular mechanism for the repression of <I>LEE5</I> promoter in EPEC and EHEC by H-NS as a protein interaction between upstream DNA-bound H-NS and the αCTD of promoter-bound RNA polymerase. The mechanism underlying Ler-mediated alleviation of the genes repression by H-NS is largely unknown. We examined regulatory effect of these proteins on <I>LEE</I>5p activity using various in vitro tools. Our results revealed that binding affinity of Ler to the <I>LEE5</I>p DNA is about 40 folds greater than that of H-NS as determined by surface plasmon resonance. We verified that Ler binding removed H-NS bound to the same stretch of DNA on <I>LEE5</I> promoter resulting in a derepression.</P> <P><B>Highlights</B></P> <P> <UL> <LI> H-NS specifically represses <I>LEE5</I> promoter activity and Ler alleviates the repression by H-NS. </LI> <LI> Binding affinity of Ler to the <I>LEE5</I> promoter DNA is about 40 folds greater than that of H-NS. </LI> <LI> Ler binding can remove H-NS bound to the same sites on <I>LEE5</I> promoter region. </LI> </UL> </P>

Analysis of evolution of movies using massive movie-tag meme network data

Shin Seungkyu,Namgoong Minsang,Park Juyong 한국물리학회 2022 THE JOURNAL OF THE KOREAN PHYSICAL SOCIETY Vol.80 No.6

Cultural creations such as movies can be said to be the products of the times, influenced by successful predecessors and in turn influencing those that come afterwards. In this work we use network science and computational social science-inspired methods to analyze a large-scale data set of movies focusing on how they have changed and evolved over time using a comprehensive movie-meme association data to construct the network of movies that form the timeline of the history of cinema via the evolution of genres, and the rise and fall of prominent sub-genres. We also identify the impactful movies that were harbingers to popular memes that dominate a given period of time and from which certain genres form and grow. Finally, we measure how the impact of movies correlates with the experts’ and the public’s assessment to understand the conditions for success and further development. We believe this work showcases how network science can be used to understand the evolution of important components of society.

나셀 라이다 측정 데이터 특성 분석 및 신뢰성 검증

신동헌(Shin Dongheon),고경남(Ko Kyungnam),강민상(Kang Minsang) 한국태양에너지학회 2017 한국태양에너지학회 논문집 Vol.37 No.5

A study on Nacelle Lidar (Light detection and ranging) measurement error and the data reliability verification was carried out at Haengwon wind farm on Jeju Island. For measurement data error processing, the characteristics of Nacelle Lidar measurements were analyzed by dividing into three parts, which are weather conditions (temperature, humidity, atmosphere, amount of precipitation), mechanical movement (rotation of wind turbine blades, tilt variation of Nacelle Lidar) and Nacelle Lidar data availability. After processing the measurement error, the reliability of Nacelle Lidar data was assessed by comparing with wind data by an anemometer on a met mast, which is located at a distance of 200m from the wind turbine with Nacelle Lidar. As a result, various weather conditions and mechanical movement did not disturb reliable data measurement. Nacelle Lidar data with availability of 95% or more could be used for checking Nacelle Lidar wind data reliability. The reliability of Nacelle Lidar data was very high with regression coefficient of 98% and coefficient of determination of 97%.

DNA looping-dependent autorepression of <i>LEE1</i> P1 promoters by Ler in enteropathogenic <i>Escherichia coli</i> (EPEC)

Bhat, Abhayprasad,Shin, Minsang,Jeong, Jae-Ho,Kim, Hyun-Ju,Lim, Hyung-Ju,Rhee, Joon Haeng,Paik, Soon-Young,Takeyasu, Kunio,Tobe, Toru,Yen, Hilo,Lee, Gwangrog,Choy, Hyon E. National Academy of Sciences 2014 PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF Vol.111 No.25

<P>Ler, a homolog of H-NS in enteropathogenic <I>Escherichia coli</I> (EPEC), plays a critical role in the expression of virulence genes encoded by the pathogenic island, locus of <I>e</I>nterocyte <I>e</I>ffacement (LEE). Although Ler acts as an antisilencer of multiple <I>LEE</I> operons by alleviating H-NS–mediated silencing, it represses its own expression from two <I>LEE1</I> P1 promoters, P1A and P1B, that are separated by 10 bp. Various in vitro biochemical methods were used in this study to elucidate the mechanism underlying transcription repression by Ler. Ler acts through two AATT motifs, centered at position −111.5 on the coding strand and at +65.5 on the noncoding strand, by simultaneously repressing P1A and P1B through DNA-looping. DNA-looping was visualized using atomic force microscopy. It is intriguing that an antisilencing protein represses transcription, not by steric exclusion of RNA polymerase, but by DNA-looping. We propose that the DNA-looping prevents further processing of open promoter complex (<I>RP</I><SUB><I>O</I></SUB>) at these promoters during transcription initiation.</P>

Molecular insights into DNA interference by CRISPR-associated nuclease-helicase Cas3

Gong, Bei,Shin, Minsang,Sun, Jiali,Jung, Che-Hun,Bolt, Edward L.,van der Oost, John,Kim, Jeong-Sun National Academy of Sciences 2014 PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF Vol.111 No.46

<P><B>Significance</B></P><P>Bacteria can repel invader DNA and RNA molecules by using an adaptive immunity mechanism called clustered regularly interspaced short palindromic repeats (CRISPRs)-Cas. CRISPR loci in a host genome are a repository of DNA fragments obtained from previous encounters with an invader, which can be transcribed and activated into short RNA molecules (crRNA) with sequences complementary to invader DNA or RNA. In some CRISPR-Cas systems, crRNA is assembled into a targeting complex called “Cascade” that seeks invader DNA to form an R-loop that triggers recruitment of a nuclease-helicase, Cas3, to destroy invader DNA. In this study, we show atomic resolution structures of a full-length Cas3, revealing how Cas3 coordinates binding, ATP-dependent translocation, and nuclease digestion of invader DNA.</P><P>Mobile genetic elements in bacteria are neutralized by a system based on clustered regularly interspaced short palindromic repeats (CRISPRs) and CRISPR-associated (Cas) proteins. Type I CRISPR-Cas systems use a “Cascade” ribonucleoprotein complex to guide RNA specifically to complementary sequence in invader double-stranded DNA (dsDNA), a process called “interference.” After target recognition by Cascade, formation of an R-loop triggers recruitment of a Cas3 nuclease-helicase, completing the interference process by destroying the invader dsDNA. To elucidate the molecular mechanism of CRISPR interference, we analyzed crystal structures of Cas3 from the bacterium <I>Thermobaculum terrenum</I>, with and without a bound ATP analog. The structures reveal a histidine-aspartate (HD)-type nuclease domain fused to superfamily-2 (SF2) helicase domains and a distinct C-terminal domain. Binding of ATP analog at the interface of the SF2 helicase RecA-like domains rearranges a motif V with implications for the enzyme mechanism. The HD-nucleolytic site contains two metal ions that are positioned at the end of a proposed nucleic acid-binding tunnel running through the SF2 helicase structure. This structural alignment suggests a mechanism for 3′ to 5′ nucleolytic processing of the displaced strand of invader DNA that is coordinated with ATP-dependent 3′ to 5′ translocation of Cas3 along DNA. In agreement with biochemical studies, the presented Cas3 structures reveal important mechanistic details on the neutralization of genetic invaders by type I CRISPR-Cas systems.</P>

복합재난을 고려한 원자력시설 사고대비 방재계획 수립방안

신지훈(Jihoon Shin),박윤원(Younwon Park),김승현(Seunghyeon Kim),차민호(Minho Cha),유민상(Minsang Ryu) 한국방재안전학회 2023 한국방재안전학회 논문집 Vol.16 No.4

By the social advancement, radiological disaster prevention planning is getting important considering complex disasters as in the Fukushima radiological disaster occurred by a chain of natural disasters. However, it has yet to be suggested the specific prevention plans for the complex disasters in the field of national radiological disaster prevention. This study aims to analyze the types of complex disasters in order to select the ones that are relatively more likely to occur in the domestic environment. It is also to analyze the impact on the radiological disaster prevention by searching damage spread of the classified natural disasters. We provides the necessary criterial for establishing disaster prevention plans through the scenarios for radiological emergency responses based on complex disasters. it is thought that these criteria can help prepare for the worst case scenario and implement effective resident protection. 현대사회가 고도화되고, 후쿠시마 원전사고 역시 자연재난의 연쇄적인 영향으로 인해 발생함에 따라 복합재난을 고려한 방재계획의 중요성이 나날이 커지고 있다. 그러나 현재 국내의 방사능방재 분야에서 복합재난을 고려한 구체적인 방재계획은 제시되지 않고 있다. 따라서, 본 연구에서는 복합재난의 유형을 분석하여 국내 환경에서 비교적 발생 가능성이 높은 유형을 선정하고, 자연재난 유형별 피해확산이 방사능방재에 미치는 영향을 분석하고자 한다. 복합재난을 고려한 방사능방재 시나리오를 통해 방재계획 수립에 필요한 기준들을 제시하였고, 이러한 기준은 최악의 상황 대비에 활용한다. 이는 실효적인 주민보호조치를 결정하고 이행하는 데에 도움을 줄 수 있을 것으로 판단된다.

Preparation of ultrathin TiO₂ coating on boron particles by thermal chemical vapor deposition and their oxidation-resistance performance

Sung, Jinyeong,Shin, Minsang,Deshmukh, P.R.,Hyun, Hyung Soo,Sohn, Youngku,Shin, Weon Gyu Elsevier 2018 JOURNAL OF ALLOYS AND COMPOUNDS Vol.767 No.-

<P><B>Abstract</B></P> <P>In the present study, we have demonstrated an easy approach for the ultrathin TiO<SUB>2</SUB> coating on boron particles by simple chemical vapor deposition (CVD) method. Boron particles dispersed in ethanol and titanium tetra isopropoxide (TTIP) were delivered in the tube furnace held at 450 °C through the atomizer and bubbler, respectively where the formation of TiO<SUB>2</SUB> coated boron particles arises. The obtained TiO<SUB>2</SUB> coated boron particles were characterized with different characterization techniques, such as, transmission electron microscopy (TEM), X-ray diffraction (XRD), energy dispersive X-ray spectroscopy (EDX), X-ray photoelectron spectroscopy (XPS), Raman spectroscopy and thermogravimetric analysis (TGA). TEM analysis shows that the boron particles are utterly covered by a thin layer TiO<SUB>2</SUB> particles and the thickness of TiO<SUB>2</SUB> layer on the surface of boron particles varies with respect to the bubbler flow rate. Moreover, TiO<SUB>2</SUB> coated boron particles represents the core-shell like structure. Amorphous nature of boron is observed from the XRD. Further, XPS and EDX analysis shows the presence of B, Ti and O elements in the obtained samples. TGA analysis demonstrate the enhanced oxidation-resistance performance of TiO<SUB>2</SUB> coated boron particles as compared to pristine boron particles, which is due to the effective protection of the boron by thin TiO<SUB>2</SUB> coating against oxidation in oxygen environment.</P> <P><B>Highlights</B></P> <P> <UL> <LI> Preparation of ultrathin TiO<SUB>2</SUB> coating on irregular shaped boron particles by thermal CVD method. </LI> <LI> Thickness of TiO<SUB>2</SUB> coating tuned by bubbler flow rate was confirmed from TEM study. </LI> <LI> TEM analysis resemble core-shell like structure of TiO<SUB>2</SUB> coated boron particle. </LI> <LI> Enhancement in oxidation-resistance performance of boron particles by means of TiO<SUB>2</SUB> coating. </LI> </UL> </P> <P><B>Graphical abstract</B></P> <P>[DISPLAY OMISSION]</P>