• Title/Summary/Keyword: BLAST Analysis

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Proposal of Vertical Direction Deck Delay Time for Efficient Formation of Free Surface of Bottom Deck (효율적 하부데크의 자유면 형성을 위한 수직방향 데크 단차 제안)

  • Seung-Won Jung;Seung-Joong Lee;Jin-Hyuk Song;Young-Ho Kim;Young-Suk Song;Nam-Sun Hwang
    • Explosives and Blasting
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    • v.41 no.4
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    • pp.41-50
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    • 2023
  • This study, a vertical double-deck method using an electronic detonator was applied to increase excavation volume and reduce blast pollution. In the double deck method, there is a possibility that blasting efficiency may be reduced if bottom deck blasting is carried out without the free surface being completely formed after upper deck blasting. And for this reason, the blasting efficiency of the double deck method varies depending on the deck delay time. Therefore, in this study, we proposed four deck delay times applying 1 to 5 times the hole delay time. And blasting efficiency was evaluated according to fragmentation analysis. As a result of the fragmentation evaluation, the fragmentation of pattern 4 (deck delay time = hole delay time×5) was the best, but it was confirmed that fragmentation efficiency increased significantly from pattern 3 (deck delay time = hole delay time×3). Accordingly, it is analyzed that when blasting a vertical double deck, the deck delay time must be at least three times the hole delay time to obtain an efficient blasting effect.

Estimating the tensile strength of geopolymer concrete using various machine learning algorithms

  • Danial Fakhri;Hamid Reza Nejati;Arsalan Mahmoodzadeh;Hamid Soltanian;Ehsan Taheri
    • Computers and Concrete
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    • v.33 no.2
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    • pp.175-193
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    • 2024
  • Researchers have embarked on an active investigation into the feasibility of adopting alternative materials as a solution to the mounting environmental and economic challenges associated with traditional concrete-based construction materials, such as reinforced concrete. The examination of concrete's mechanical properties using laboratory methods is a complex, time-consuming, and costly endeavor. Consequently, the need for models that can overcome these drawbacks is urgent. Fortunately, the ever-increasing availability of data has paved the way for the utilization of machine learning methods, which can provide powerful, efficient, and cost-effective models. This study aims to explore the potential of twelve machine learning algorithms in predicting the tensile strength of geopolymer concrete (GPC) under various curing conditions. To fulfill this objective, 221 datasets, comprising tensile strength test results of GPC with diverse mix ratios and curing conditions, were employed. Additionally, a number of unseen datasets were used to assess the overall performance of the machine learning models. Through a comprehensive analysis of statistical indices and a comparison of the models' behavior with laboratory tests, it was determined that nearly all the models exhibited satisfactory potential in estimating the tensile strength of GPC. Nevertheless, the artificial neural networks and support vector regression models demonstrated the highest robustness. Both the laboratory tests and machine learning outcomes revealed that GPC composed of 30% fly ash and 70% ground granulated blast slag, mixed with 14 mol of NaOH, and cured in an oven at 300°F for 28 days exhibited superior tensile strength.

Development of a sequence-characterized amplified region (SCAR) marker for female off-season flowering detection in date palm (Phoenix dactylifera L.)

  • Lalita Kethirun;Puangpaka Umpunjun;Ngarmnij Chuenboonngarm;Unchera Viboonjun
    • Journal of Plant Biotechnology
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    • v.50
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    • pp.190-199
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    • 2023
  • Date palm (Phoenix dactylifera L.: Arecaceae) is a dioecious species where only female trees bear fruits. In their natural state, date palms produce dates once a year. However, in Thailand, some trees were observed to produce dates during the off-season, despite no variations in morphology. The availability of such off-season fruits can significantly increase their market value. Interestingly, most female off-season date palms investigated in this study were obtained through micropropagation. Hence, there is an urgent need for genetic markers to distinguish female offseason flowering plantlets within tissue culture systems. In this study, we aimed to develop random amplification of polymorphic DNA-sequence characterized amplified region (RAPD-SCAR) markers for the identification of female off-season flowering date palms cultivated in Thailand. A total of 160 random decamer primers were employed to screen for specific RAPD markers in off-season flowering male and female populations. Out of these, only one primer, OPN-02, generated distinct genomic DNA patterns in female off-season flowering (FOFdp) individuals compared to female seasonal flowering genotypes. Based on the RAPD-specific sequence, specific SCAR primers denoted as FOFdpF and FOFdpR were developed. These SCAR primers amplified a single 517-bp DNA fragment, predominantly found in off-season flowering populations, with an accuracy rate of 60%. These findings underscore the potential of SCAR marker technology for tracking offseason flowering in date palms. Notably, a BLAST analysis revealed a substantial similarity between the SCAR marker sequence and the transcript variant mRNA from Phoenix dactylifera encoding the SET DOMAIN GROUP 40 protein. In Arabidopsis, this protein is involved in the epigenetic regulation of flowering time. The genetic potential of the off-season flowering traits warrants further elucidation.

Application of Molecular Biological Technique for Development of Stability Indicator in Uncontrolled Landfill (불량매립지 안정화 지표 개발을 위한 분자생물학적 기술의 적용)

  • Park, Hyun-A;Han, Ji-Sun;Kim, Chang-Gyun;Lee, Jin-Young
    • Journal of Korean Society of Environmental Engineers
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    • v.28 no.2
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    • pp.128-136
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    • 2006
  • This study was conducted for developing the stability parameter in uncontrolled landfill by using a biomolecular investigation on the microbial community growing through leachate plume. Landfill J(which is in Cheonan) and landfill T(which is in Wonju) were chosen for this study among a total of 244 closed uncontrolled landfills. It addressed the genetic diversity of the microbial community in the leachate by 165 rDNA gene cloning using PCR and compared quantitative analysis of denitrifiers and methanotrophs with the conventional water quality parameters. From the BLAST search, genes of 47.6% in landfill J, and 32.5% in landfill T, respectively, showed more than 97% of the similarity where Proteobacteria phylum was most significantly observed. It showed that the numbers of denitrification genes, i.e. nirS gene and cnorB gene in the J site are 7 and 4 times higher than those in T site, which is well reflecting from a difference of site closure showing 7 and 13 years after being closed, respectively. In addition, the quantitative analysis on methane formation gene showed that J1 spot immediately bordering with the sources has the greatest number of methane formation bacteria, and it was decreased rapidly according to distribute toward the outer boundary of landfill. The comparative investigation between the number of genes, i.e. nirS gene, cnorB gene and MCR gene, md the conventional monitoring parameters, i.e. TOC, $NH_3-N,\;NO_3-N,\;NO_2-N,\;Cl^-$, alkalinity, addressed that more than 99% of the correlation was observed except for the $NO_3-N$. It was concluded that biomolecular investigation was well consistent with the conventional monitoring parameters to interpret their influences and stability made by leachate plume formed in downgradient around the uncontrolled sites.

Genetic and Physiological Discrepancies from Isolates of Sclerotinia homoeocarpa causing Zoysiagrass Dollar Spot Disease (한국잔디에 발생하는 동전마름병 원인균의 유전 및 생리적 특성차이)

  • Park, Dae-Sup;Kim, Kyung-Duck;Kihl, Joon-Yeong;Pyee, Jae-Ho
    • Asian Journal of Turfgrass Science
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    • v.20 no.1
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    • pp.65-76
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    • 2006
  • Scz1, an isolate of Sclerotinia homoeocarpa, was recently reported as a novel pathogen responsible for dollar spot disease in Zoysiagrass, a warm season turfgrass. Scz1 possessed different characteristics on mycelial pigment, mycelial affinity and host pathogenecity compared to those of Scb1, a typical isolate, obtained from creeping bentgrass, a cool season turfgrass. In this study, only three isolates, Scz1, Scz2(another analogous isolate of Sclerotinia homoeocarpa from zoysiagrass), and Scb1, were examined at the molecular level using the internal transcribed spacer(ITS) and random amplified polymorphic DNA(RAPD) assays to verify their identification and genetic variation. As a result of ITS assay, partial ITS sequences of three isolates showed 94-97% similarity with a standardized ITS sequence of S. homoeocarpa registered on BLAST. In the analysis of RAPD, range value through similarity matrix was 0.167 between Scz1 and Scb1, 0.139 between Scz2 and Scb1, and 0.713 between Scz1 and Scz2, respectively. Furthermore, tendegram analysis indicated that Scz1 and Scz2, unlike Scb1, were clustered together as accompanying a high genetic similarity. In in vitro fungicide bioassay, $EC_{50}$ value representing the sensitivity degree to propiconazole, a well-known fungicide for dollar spot disease, was 0.012 ${\mu}g/ml$ for Sczl, 0.003 ${\mu}g/ml$ for Scz2, and 0.030 ${\mu}g/ml$ for Scb1. From all data taken, we concluded that both Scz1 and Scz2 belonged to one group of S. homoeocarpa, since they exhibit the same host range and high level of genetic similarity, whereas their chemical competences to a fungicide were different. This study would provide further approach for assessing genetic diversity of S. homoeocarpa isolates as well as characterizing individual isolate against chemical exposure.

Screening and Identification of a Cesium-tolerant Strain of Bacteria for Cesium Biosorption (환경유래의 세슘 저항성 균주 선별 및 세슘 흡착제거 연구)

  • Kim, Gi Yong;Jang, Sung-Chan;Song, Young Ho;Lee, Chang-Soo;Huh, Yun Suk;Roh, Changhyun
    • Korean Journal of Environmental Biology
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    • v.34 no.4
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    • pp.304-313
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    • 2016
  • One of the issues currently facing nuclear power plants is how to store spent nuclear waste materials which are contaminated with radionuclides such as $^{134}Cs$, $^{135}Cs$, and $^{137}Cs$. Bioremediation processes may offer a potent method of cleaning up radioactive cesium. However, there have only been limited reports on $Cs^+$ tolerant bacteria. In this study, we report the isolation and identification of $Cs^+$ tolerant bacteria in environmental soil and sediment. The resistant $Cs^+$ isolates were screened from enrichment cultures in R2A medium supplemented with 100 mM CsCl for 72 h, followed by microbial community analysis based on sequencing analysis from 16S rRNA gene clone libraries(NCBI's BlastN). The dominant Bacillus anthracis Roh-1 and B. cereus Roh-2 were successfully isolated from the cesium enrichment culture. Importantly, B. cereus Roh-2 is resistant to 30% more $Cs^+$ than is B. anthracis Roh-1 when treated with 50 mM CsCl. Growth experiments clearly demonstrated that the isolate had a higher tolerance to $Cs^+$. In addition, we investigated the adsorption of $0.2mg\;L^{-1}$ $Cs^+$ using B. anthracis Roh-1. The maximum $Cs^+$ biosorption capacity of B. anthracis Roh-1 was $2.01mg\;g^{-1}$ at pH 10. Thus, we show that $Cs^+$ tolerant bacterial isolates could be used for bioremediation of contaminated environments.

Current Status and Future Prospect of Plant Disease Forecasting System in Korea (우리 나라 식물병 발생예찰의 현황과 전망)

  • Kim, Choong-Hoe
    • Research in Plant Disease
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    • v.8 no.2
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    • pp.84-91
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    • 2002
  • Disease forecasting in Korea was first studied in the Department of Fundamental Research, in the Central Agricultural Technology Institute in Suwon in 1947, where the dispersal of air-borne conidia of blast and brown spot pathogens in rice was examined. Disease forecasting system in Korea is operated based on information obtained from 200 main forecasting plots scattered around country (rice 150, economic crops 50) and 1,403 supplementary observational plots (rice 1,050, others 353) maintained by Korean government. Total number of target crops and diseases in both forecasting plots amount to 30 crops and 104 diseases. Disease development in the forecasting plots is examined by two extension agents specialized in disease forecasting, working in the national Agricul-tural Technology Service Center(ATSC) founded in each city and prefecture. The data obtained by the extension agents are transferred to a central organization, Rural Development Administration (RDA) through an internet-web system for analysis in a nation-wide forecasting program, and forwarded far the Central Forecasting Council consisted of 12 members from administration, university, research institution, meteorology station, and mass media to discuss present situation of disease development and subsequent progress. The council issues a forecasting information message, as a result of analysis, that is announced in public via mass media to 245 agencies including ATSC, who informs to local administration, the related agencies and farmers for implementation of disease control activity. However, in future successful performance of plant disease forecasting system is thought to be securing of excellent extension agents specialized in disease forecasting, elevation of their forecasting ability through continuous trainings, and furnishing of prominent forecasting equipments. Researches in plant disease forecasting in Korea have been concentrated on rice blast, where much information is available, but are substan-tially limited in other diseases. Most of the forecasting researches failed to achieve the continuity of researches on specialized topic, ignoring steady improvement towards practical use. Since disease forecasting loses its value without practicality, more efforts are needed to improve the practicality of the forecasting method in both spatial and temporal aspects. Since significance of disease forecasting is directly related to economic profit, further fore-casting researches should be planned and propelled in relation to fungicide spray scheduling or decision-making of control activities.

Construction of cDNA Library and EST Analysis Related to Seed-hair Characteristics in Carrot (당근 종모 형질 관련 cDNA Library 작성 및 EST 분석)

  • Oh, Gyu-Dong;Shim, Eun-Jo;Jun, Sang-Jin;Park, Young-Doo
    • Horticultural Science & Technology
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    • v.31 no.6
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    • pp.782-789
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    • 2013
  • Carrot (Daucus carota L. var. sativa) is one of the most widely used crops in the world and is nutritionally important crop. However, seed-hair which is generated in epidermal cell of seeds causes the difficulty of the seedling process, because of the seed germination and absorption inhibitions. For these reasons, carrot seeds are commercialized after mechanical hair removal process. However, in this process, various damage and seed loss occur and breeding of hairless-seed carrot cultivar is needed to overcome these various weaknesses and additional seed production costs. In this study, cDNA libraries using 2 combinations, which were composed of short-hair seed CT-ATR 615 OP 666-13 & long-hair seed CT-ATR 615 OP 671-9, and short-hair seed CT-SMR 616 OP 659-1 & long-hair seed CT-SMR 616 OP 677-14, were constructed and EST sequences of each individuals were analyzed to reveal carrot seed-hair characteristics. Firstly, analyzed EST sequences were classified into FunCat functional categories. As a result, significant differences have been identified in metabolism category, protein folding and stabilization, protein binding, C-compound binding category from both of two combinations. Secondly, several candidate EST sequences related to seed trichome differentiation and cellulose biosynthetic process were selected based on GO data of EST sequences. These differences based on FunCat categories and candidate EST obtained by GO data analysis are thought to be involved in the formation of carrot seed hair. Finally, 741 SSR sites and 33 SNP sites were identified from analyzed EST sequences of two combinations. Then we designed SNP and SSR primer sets to develop molecular markers. These molecular markers will be used for classification of carrot cultivars and study seed-hair characteristic.

Molecular Phylogenetic Study of the Endangered Land Snail Satsuma myomphala Based on Metallothionein Gene. (Metallothionein 유전자를 기초로 한 멸종위기 육상 달팽이 Satsuma myomphala (거제외줄달팽이) 의 분자계통학적 연구)

  • Sang, Min Kyu;Kang, Se Won;Hwang, Hee-Ju;Chung, Jong Min;Song, Dae Kwon;Min, Hye Rin;Park, Jie Eun;Ha, Hee Cheol;Lee, Hyun Jun;Hong, Chan Eui;Ahn, Young Mo;Park, So Young;Park, Young-Su;Park, Hong Seog;Han, Yeon Soo;Lee, Jun Sang;Lee, Yong Seok
    • The Korean Journal of Malacology
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    • v.32 no.4
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    • pp.263-268
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    • 2016
  • Metallothionein (MT) family of metal-binding proteins are involved in maintaining homeostasis and heavy metal poisoning. Recently, MT has been considered as a biomarker that can identify a particular species, very similar to the use of cytochrome oxidase I (COI) gene. Satsuma myomphala species of land snails have been reported from North-East Asia, including South Korea and Japan. In particular, the land snail species have been known from only a limited area of Geoje Island, Gyeongsangnam-do province of South Korea. Genetic studies of S. myomphala has been limited with only 6 nucleotide, 2 protein registered on the NCBI server. For elucidating the genetic information of S. myomphala, we conducted RNA sequencing analysis using Illumina HiSeq 2500 next-generation platform. We screened the MT gene from the RNA-Seq database to confirm the molecular phylogenetic relationship. After sequencing, the de novo analysis and clustering generated 103,774 unigenes. After annotation against PANM database using BLAST program, we obtained MT sequence of 74 amino acid residues containing the coding region of 222 bp. Based on this sequence, we found about 53 sequences using the BLAST program in NCBI nr database. Using ClustalX alignment, Maximum-Likehood Tree of MEGA program, we confirmed the molecular phylogenetic relationships that showed similarity with mollusks such as Helix pomatia and H. aspersa, Megathura crenulata.

Effects of acid-treatment conditions on the surface properties of the RBM treated titanium implants (산-처리 조건이 RBM처리한 티타늄 임플란트의 표면 특성에 주는 영향)

  • Lee, Han-Ah;Seok, Soohwang;Lee, Sang-Hyeok;Lim, Bum-Soon
    • Korean Journal of Dental Materials
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    • v.45 no.4
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    • pp.257-274
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    • 2018
  • The purpose of this study was to evaluate the effect of acid-treatment conditions on the surface properties of the RBM (Resorbable Blast Media) treated titanium. Disk typed cp-titanium specimens were prepared and RBM treatments was performed with calcium phosphate ceramic powder. Acid solution was mixed using HCl, $H_2SO_4$ and deionized water with 4 different volume fraction. The RBM treated titanium was acid treated with different acid solutions at 3 different temperatures and for 3 different periods. After acid-treatments, samples were cleaned with 1 % Solujet solution for 30 min and deionized water for 30 min using ultrasonic cleanser, then dried in the electrical oven ($37^{\circ}C$). Weight of samples before and after acid-treatment were measured using electric balance. Surface roughness was estimated using a confocal laser scanning microscopy, crystal phase in the surface of sample was analyzed using X-ray diffractometer. Surface morphology and components were evaluated using Scanning Electron Microscope (SEM) with Energy Dispersive X-ray spectroscopy (EDX) and X-ray Photoemission Spectroscopy (XPS). Values of the weight changes and surface roughness were statistically analyzed using Tukey-multiple comparison test (p=0.05). Weight change after acid treatments were significantly increased with increasing the concentration of $H_2SO_4$ and temperature of acid-solution. Acid-treatment conditions (concentration of $H_2SO_4$, temperature and time) did not produce consistent effects on the surface roughness, it showed the scattered results. From XRD analysis, formation of titanium hydrides in the titanium surface were observed in all specimens treated with acid-solutions. From XPS analysis, thin titanium oxide layer in the acid-treated specimens could be evaluated. Acid solution with $90^{\circ}C$ showed the strong effect on the titanium surface, it should be treated with caution to avoid the over-etching process.