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Bacterial Logic Devices Reveal Unexpected Behavior of Frameshift Suppressor tRNAs

  • Sawyer, Eric M.;Barta, Cody;Clemente, Romina;Conn, Michel;Davis, Clif;Doyle, Catherine;Gearing, Mary;Ho-Shing, Olivia;Mooney, Alyndria;Morton, Jerrad;Punjabi, Shamita;Schnoor, Ashley;Sun, Siya;Suresh, Shashank;Szczepanik, Bryce;Taylor, D. Leland;Temmink, Annie;Vernon, William;Campbell, A. Malcolm;Heyer, Laurie J.;Poet, Jeffrey L.;Eckdahl, Todd T.
    • Interdisciplinary Bio Central
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    • v.4 no.3
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    • pp.10.1-10.12
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    • 2012
  • Introduction: We investigated frameshift suppressor tRNAs previously reported to use five-base anticodon-codon interactions in order to provide a collection of frameshift suppressor tRNAs to the synthetic biology community and to develop modular frameshift suppressor logic devices for use in synthetic biology applications. Results and Discussion: We adapted eleven previously described frameshift suppressor tRNAs to the BioBrick cloning format, and built three genetic logic circuits to detect frameshift suppression. The three circuits employed three different mechanisms: direct frameshift suppression of reporter gene mutations, frameshift suppression leading to positive feedback via quorum sensing, and enzymatic amplification of frameshift suppression signals. In the course of testing frameshift suppressor logic, we uncovered unexpected behavior in the frameshift suppressor tRNAs. The results led us to posit a four-base binding hypothesis for the frameshift suppressor tRNA interactions with mRNA as an alternative to the published five-base binding model. Conclusion and Prospects: The published five-base anticodon/codon rule explained only 17 of the 58 frameshift suppression experiments we conducted. Our deduced four-base binding rule successfully explained 56 out of our 58 frameshift suppression results. In the process of applying biological knowledge about frameshift suppressor tRNAs to the engineering application of frameshift suppressor logic, we discovered new biological knowledge. This knowledge leads to a redesign of the original engineering application and encourages new ones. Our study reinforces the concept that synthetic biology is often a winding path from science to engineering and back again; scientific investigations spark engineering applications, the implementation of which suggests new scientific investigations.

Economic Injury Level of Thrips tabaci (Thysanoptera: Thripidae) on Welsh onions (Allium fistulosum L. var) in the Early Transplanting Stage (파에서 정식초기 파총채벌레의 경제적피해수준 설정)

  • Kang, Taek-Jun;Cho, Myoung-Rae;Kim, Hyeong-Hwan;Jeon, Heung-Yong;Kim, Dong-Soon
    • Korean journal of applied entomology
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    • v.50 no.4
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    • pp.289-293
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    • 2011
  • This study was conducted to develop economic injury level (EIL) of onion thrips, Thrips tabaci, on welsh onion (Allium fistulosum L. var) in the early transplanting stage. The changes of welsh onion biomass, yield loss, and T. tabaci density were investigated according to the inoculation periods of T. tabaci. In the early transplanting stage of welsh onion, the yield loss (%) increased with increasing inoculation periods: 17.0, 53.3, 38.4, and 80.8% yield loss in 5, 10, 15, and 20 d inoculation periods, respectively. The relationship between Cumulative Insect Days (CID) of T. tabaci and yield loss (%) of welsh onion was well described by a nonlinear logistic equation. Using the estimated equation, EIL of T. tabaci on welsh onion was estimated to 30 CID per plant based on the yield loss 12% (an empirical gain threshold 5% + marketable rate 93% of welsh onion). ET was calculated to 24 CID, which corresponds to 80% of EIL. Until a more defined EIL-model is developed, the present results should be useful for T. tabaci management in early growth stage of welsh onion. The effect of T. tabaci attack on the yield of welsh onion in late growing season (120 days after transplanting) was also examined. The yield of welsh onion increased at a low population density of T. tabaci and decreased at higher densities, showing a typical over-compensatory response.

THE VLBI MONITORING PROJECT FOR 6.7 GHz METHANOL MASERS USING THE JVN/EAVN

  • SUGIYAMA, KOICHIRO;FUJISAWA, KENTA;HACHISUKA, KAZUYA;YONEKURA, YOSHINORI;MOTOGI, KAZUHITO;SAWADA-SATOH, SATOKO;MATSUMOTO, NAOKO;SAITO, YU;HIRANO, DAIKI;HAYASHI, KYONOSUKE;SHEN, ZHIQIANG;HONMA, MAREKI;HIROTA, TOMOYA;MURATA, YASUHIRO;DOI, AKIHIRO;NIINUMA, KOTARO;DODSON, RICHARD;RIOJA, MARIA;ELLINGSEN, SIMON;CHEN, XI;KIM, KEE-TAE;OGAWA, HIDEO
    • Publications of The Korean Astronomical Society
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    • v.30 no.2
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    • pp.645-647
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    • 2015
  • We have initiated a Very Long Baseline Interferometer (VLBI) monitoring project of 36 methanol maser sources at 6.7 GHz using the Japanese VLBI Network (JVN) and East-Asian VLBI Network (EAVN), starting in August 2010. The purpose of this project is to systematically reveal 3-dimensional (3-D) kine-matics of rotating disks around forming high-mass protostars. As an initial result, we present proper mo- tion detections for two methanol maser sources showing an elliptical spatial morphology, G 002.53+00.19 and G 006.79-00.25, which could be the best candidates associated with the disk. The detected proper motions indicate a simple rotation in G 002.53+00.19 and rotation with expansion in G 006.79-00.25, respectively, on the basis of disk model fits with rotating and expanding components. The expanding motions might be caused by the magnetic-centrifugal wind on the disk.

Chromosome Analysis in Clinical Samples by Chromosome Diagnostic System Using Fluorescence in Situ Hybridization (국산 Fluorescence in Situ Hybridization 시스템을 이용한 다양한 검체에서의 염색체 분석)

  • Moon, Shin-Yong;Pang, Myung-Geol;Oh, Sun-Kyung;Ryu, Buom-Yong;Hwang, Do-Yeong;Jung, Byeong-Jun;Choe, Jin;Sohn, Cherl;Chang, Jun-Keun;Kim, Jong-Won;Kim, Seok-Hyun;Choi, Young-Min
    • Clinical and Experimental Reproductive Medicine
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    • v.24 no.3
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    • pp.335-340
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    • 1997
  • Fluorescence in situ hybridization (FISH) techniques allow the enumeration of chromosome abnormalities and from a great potential for many clinical applications. In order to produce quantitative and reproducible results, expensive tools such as a cooled CCD camera and a computer software are required. We have developed a Chromosome Image Processing System (Chips) using FISH that allows the detection and mapping of the genetic aberrations. The aim of our study, therefore, is to evaluate the capabilities of our original system using a black-and-white video camera. As a model system, three repetitive DNA probes (D18Z1, DXZ1, and DYZ3) were hybridized to variety different clinical samples such as human metaphase spreads and interphase nuclei obtained from uncultured peripheral blood lymphocytes, uncultured amniocytes, and germ cells. The visualization of the FISH signals was performed using our system for image acquisition and pseudocoloring. FISH images were obtained by combining images from each of probes and DAPI counterstain captured separately. Using our original system, the aberrations of single or multiple chromosomes in a single hybridization experiment using chromosomes and interphase nuclei from a variety of cell types, including lymphocytes, amniocytes, sperm, and biopsied blastomeres, were enabled to evaluate. There were no differences in the image quality in accordance with FISH method, fluorochrome types, or different clinical samples. Always bright signals were detected using our system. Our system also yielded constant results. Our Chips would permit a level of performance of FISH analysis on metaphase chromosomes and interphase nuclei with unparalleled capabilities. Thus, it would be useful for clinical purposes.

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The Present Status and Future Prospect on Education of Fisheries High School in Japan -I. Distribution of Schools and Arrangement of Curriculum (일본(日本) 수산계(水產系) 고등학교교육(高等學校敎育)의 현황(現況)과 전망(展望) -I. 학교(學校)의 분포(分布)와 교육과정(敎育課程)의 편제(編制))

  • Lee, Byoung-Gee
    • Journal of Fisheries and Marine Sciences Education
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    • v.4 no.1
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    • pp.75-87
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    • 1992
  • Cultivation of competent manpower is recognized as one of the important factors in the development of fisheries as well as of other industries. For reference to the development of education of fisheries high schools in the Republic of Korea, the author carried out a study on the education in Japan. The reason is why the education on fisheries had been initiated in Japan and her educational system has played the role of a model for neighboring countries. Even though the education on fisheries tends to shrink a little in recent years by diffusing the unwilling tendency to engage in 3D (dirty, difficult and dangerous) jobs, there are fifty-one high schools educating fisheries in Japan. Thirty-eight of them are specialized fisheries high schools and the others are comprehensive high schools to put common course and fisheries course together. In the first step of study, the goal of education on fisheries, organization of department and arrangement of curriculum are analysed. 1. In the newly arranged curriculum which will come into effect from 1994, the goal of education on fisheries is set up as "By educating fundamental knowledge and technology on the production and circulation in the field of fisheries, have students understand the significance and role of fisheries, and so cultivate ability and active attitude to the development of fisheries". The goal means that the circulation of fishery products are regarded as important as the production itself, and active attitude to the development of fisheries is also stressed, different from the present goal. 2. Standard departments directed by the Government are set up as five-Departments of Marine Fishing, of Fisheries Engineering, of Information Communication, of Fish Culture, of Sea Foods. But they are actually organized and named by the founders of schools-local government. Then there are many unique-named departments and the management of schools are somewhat flexible according to the situation of local district. 3. Special subjects are revised to twenty-four in the new curriculum from twenty-two in the present curriculum. Among them the contents are widely revised in the subjects such as Introduction to Fisheries, Fisheries Engineering, Communication Engineering, Communication Technology, Fish Culture. On the other hand, five subjects such as Information Treatment on Fisheries, Information Technology on Fisheries, Subjective Study, Fisheries Economics, Circulation of Sea Foods are newly set up to meet the changing phase of the time.

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Comparative Analysis of Construction Productivity for Modernized Korean Housing (Hanok) (보급형 신한옥 개발을 위한 건설 생산성 분석)

  • Kim, Min;Kim, Yesol;Lee, YunSub;Jung, Youngsoo
    • Korean Journal of Construction Engineering and Management
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    • v.14 no.3
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    • pp.107-114
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    • 2013
  • The interest in traditional Korean housing has greatly increasing in Korean housing market. However, it is difficult to wildly disseminate for a high construction cost reason. In order to effectively facilitate the Hanok construction, Korean government has initiated a project that develops a new style Korean housing, which meets the requirements of low cost and modernized life style. Cost of building is mainly affected by materials and construction methods. Hanok has some special commodities those significantly impact the cost. In order to effectively cut down the costs, well-organized planning for costs is very important. Also, improving the productivity by utilizing new materials and methods can result in cost down. In this context, this paper compared and analyzed two different types of Korean housing; one is a modernized Korean house which used new materials and methods, the other is a traditional Korean house which was build up by purely traditional methods. Productivity has also been compared and analyzed for 5 major commodities between two types of models. Based on these comparative data, effect of cost down by new model has been analyzed. As a result it is confirmed that by using the new materials and methods could highly effect to increasing productivity and cost down. Especially, the cost of Roofing have been more influenced by using new material while the Wood and Finishes have been influenced by new construction method. Construction cost of Foundation (Earthwork, Concrete, Masonry) and Openings were influenced both factors, changing of materials and methods.

GPS-based monitoring and modeling of the ionosphere and its applications for high accuracy correction in China

  • Yunbin, Yuan;Jikun, Ou;Xingliang, Huo;Debao, Wen;Genyou, Liu;Yanji, Chai;Renggui, Yang;Xiaowen, Luo
    • Proceedings of the Korean Institute of Navigation and Port Research Conference
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    • v.2
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    • pp.203-208
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    • 2006
  • The main research conducted previously on GPS ionosphere in China is first introduced. Besides, the current investigations include as follows: (1) GPS-based spatial environmental, especially the ionosphere, monitoring, modeling and analysis, including ground/space-based GPS ionosphere electron density (IED) through occultation/tomography technologies with GPS data from global/regional network, development of a GNSS-based platform for imaging ionosphere and atmosphere (GPFIIA), and preliminary test results through performing the first 3D imaging for the IED over China, (2) The atmospheric and ionospheric modeling for GPS-based surveying, navigation and orbit determination, involving high precisely ionospheric TEC modeling for phase-based long/median range network RTK system for achieving CM-level real time positioning, next generation GNSS broadcast ionospheric time-delay algorithm required for higher correction accuracy, and orbit determination for Low-Earth-orbiter satellites using single frequency GPS receivers, and (3) Research products in applications for national significant projects: GPS-based ionospheric effects modeling for precise positioning and orbit determination applied to China's manned space-engineering, including spatial robot navigation and control and international space station intersection and docking required for related national significant projects.

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The Response Prediction of Flexible Pavements Considering Nonlinear Pavement Foundation Behavior (비선형 포장 하부 거동을 고려한 연성 포장의 해석)

  • Kim, Min-Kwan
    • International Journal of Highway Engineering
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    • v.11 no.1
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    • pp.165-175
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    • 2009
  • With the current move towards adopting mechanistic-empirical concepts in the design of pavement structures, state-of-the-art mechanistic analysis methodologies are needed to determine accurate pavement responses, such as stress, strain, and deformation. Previous laboratory studies of pavement foundation geomaterials, i.e., unbound granular materials used in base/subbase layers and fine-grained soils of a prepared subgrade, have shown that the resilient responses followed by nonlinear, stress-dependent behavior under repeated wheel loading. This nonlinear behavior is commonly characterized by stress-dependent resilient modulus material models that need to be incorporated into finite element (FE) based mechanistic pavement analysis methods to predict more realistically predict pavement responses for a mechanistic pavement analysis. Developed user material subroutine using aforementioned resilient model with nonlinear solution technique and convergence scheme with proven performance were successfully employed in general-purpose FE program, ABAQUS. This numerical analysis was investigated in predicted critical responses and domain selection with specific mesh generation was implemented to evaluate better prediction of pavement responses. Results obtained from both axisymmetric and three-dimensional (3D) nonlinear FE analyses were compared and remarkable findings were described for nonlinear FE analysis. The UMAT subroutine performance was also validated with the instrumented full scale pavement test section study results from the Federal Aviation Administration's National Airport Pavement Test Facility (FAA's NAPTF).

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Development of Valuation Framework for Estimating the Market Value of Media Contents (미디어 콘텐츠의 시장가치 산정을 위한 가치평가 프레임워크 개발)

  • Sung, Tae-Eung;Park, Hyun-Woo
    • Journal of Service Research and Studies
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    • v.6 no.3
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    • pp.29-40
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    • 2016
  • Since the late 20th century, there has been much effort to improve the market value of media contents which are commercialized in a digital format, by fusing digital data of video, audio, numerals, characters with IT technology together. Then by what criteria and methodologies could the market value for the drama "Sons of the Sun" or the animated film 'Frozen', often referred to in the meida, be estimated? In the circumstances there has been little or no research on the valuation framework of media contents and the status of their valuation system development to date, we propose a practical valuation models for various purposes such as contents trading, review of investment adequacy, etc., by formalizing and presenting a contents valuation framework for the four types of media of movies, online games, and broadcasting commercials, and animations. Therefore, we develope computational methods of cash flows which includes production cost by media content types, provide reference databases associated with key variables of valuation (economic life cycle, discount rates, contents contribution and royalty rates), and finally propose the valuation framework of media contents based on both income approach and relief-from-royalty method which has been applied to valuation of intangible assets so far.

Analysis of a Gas Mask Using CFD Simulation (CFD모사기법을 이용한 가스 여과기 성능 해석)

  • Jeon, Rakyoung;Kwon, Kihyun;Yoon, Soonmin;Park, Myungkyu;Lee, Changha;Oh, Min
    • Korean Chemical Engineering Research
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    • v.57 no.4
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    • pp.475-483
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    • 2019
  • Special chemical warfare agents are lethal gases that attack the human respiratory system. One of such gases are blood agents that react with the irons present in the electron transfer system of the human body. This reaction stops internal respiration and eventually causes death. The molecular sizes of these agents are smaller than the pores of an activated carbon, making chemical adsorption the only alternative method for removing them. In this study, we carried out a Computational Fluid Dynamics simulation by passing a blood agent: cyanogen chloride gas through an SG-1 gas mask canister developed by SG Safety Corporation. The adsorption bed consisted of a Silver-Zinc-Molybdenum-Triethylenediamine activated carbon impregnated with copper, silver, zinc and molybdenum ions. The kinetic analysis of the chemical adsorption was performed in accordance with the test procedure for the gas mask canister and was validated by the kinetic data obtained from experimental results. We predicted the dynamic behaviors of the main variables such as the pressure drop inside the canister and the amount of gas adsorbed by chemisorption. By using a granular packed bed instead of the Ergun equation that is used to model porous materials in Computational Fluid Dynamics, applicable results of the activated carbon were obtained. Dynamic simulations and flow analyses of the chemical adsorption with varying gas flow rates were also executed.