• Title/Summary/Keyword: Sequence-to-Sequence

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A comprehensive analysis of temporal characteristics in independent rainstorm events in Seoul: focusing on changes in unit time and secondary peak constant (서울특별시 내 독립 호우사상의 시간분포 특성 분석: 분 단위와 차첨두 상수의 조건 변화를 중심으로)

  • Cha, Hoyoung;Lee, Jinwook;Jun, Changhyun;Byun, Jongyun;Baik, Jongjin
    • Journal of Korea Water Resources Association
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    • v.56 no.11
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    • pp.785-799
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    • 2023
  • In this study, we proposed a new concept termed the Secondary Peak Constant (SPC) and discerned the temporal characteristics of independent rainstorm events based on unit time and SPC about 24 observation stations in Seoul. Utilizing rainfall observations from 2000 to 2022, independent rainstorm events discreted from rainfall data per unit time. The temporal characteristics of these events were derived according to unit time, and temporal characteristics of the peak rainfall were identified through the SPC. Finally, the temporal characteristics of independent rainstorm events were examined distinctively when analyzed by unit time and SPC. Independent rainstorm events with smaller unit time showed significantly larger total rainfall, rainfall duration, and rainfall intensity. The temporal characteristics of the largest peak rainfall (1st Peak) within independent rainstorm events followed a sequence of Q4>Q2>Q3>Q1. Additionally, the 2nd Peak rainfall predominantly occurred the location where the 1st Peak appeared. The proportion of independent rainstorm events with multiple peak rainfalls exceeded 50.0% when the SPC was 0.7 or lower. The average number of peak rainfalls within independent rainstorm events ranged from 1.5 to 3.4. This study identified the temporal characteristics of independent rainstorm events based on unit time. Then, the peak rainfall of temporal characteristics was quantified by SPC on this study. Hence, it is evident that the temporal characteristics of independent rainstorm events for specific area can be anlayzed and quantified based on unit time and SPC.

Biosorption and Desorption of Heavy Metals using Undaria sp. (미역 폐기물의 중금속 흡탈착 특성)

  • Cho, Ju-Sik;Park, Il-Nam;Heo, Jong-Soo;Lee, Young-Seak
    • Korean Journal of Environmental Agriculture
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    • v.23 no.2
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    • pp.92-98
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    • 2004
  • The adsorption and desorption of Pb, Cd, Co, Zn, Cr, Co, Ni, and Mo on the waste Undaria sp. were studied. Except for Pb. the mono adsorption rate for all heavy metals were lower than that of the heavy metals mixed. However, the adsorption capacity of the heavy metals by 1g of biosorption, in mixed heavy metals increased According to FT-IR analysis of the biosorbent after heavy metal biosorption, the replacement of the functional group by the heavy metals ions could be confirmed and the inverted peaks became larger after heavy metals adsorption. The adsorption equilibrium of heavy metals was reached in about 1 hour. The equilibrium parameters were determined based on Langmuir and Freundlich isotherms. The affinity of metals on the biosorbent decreased in the following order: Pb>Cu>Cr>Cd>Co. The desorption rate decreased in the following sequence: NTA>$H_2SO_4$>HCl>EDTA. The desorption rate of heavy metals by NTA increased with increase in the concentration from 0.1 to 0.3% but the desorption rate became constant beyond 0.3%. Therefore, it represented that desorption rate of heavy metals was suitable under optimized condition ($30^{\circ}C$, pH 2 and 0.3% NTA solution) and was fast with 80% or more the uptake occurring within 10 min of contact time.

Identification of Streptomyces scopuliridis KR-001 and Its Herbicidal Characteristics (Streptomyces scopuliridis KR-001의 분리 동정 및 잡초 방제효과)

  • Lee, Boyoung;Kim, Jae Deok;Kim, Young Sook;Ko, Young Kwan;Yon, Gyu Hwan;Kim, Chang-Jin;Koo, Suk Jin;Choi, Jung Sup
    • Weed & Turfgrass Science
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    • v.2 no.1
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    • pp.38-46
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    • 2013
  • With increasing environmental issues from synthetic chemical herbicides, microbe-originated herbicides could be a fascinating alternative in current agriculture. We isolated Streptomyces strains that produced herbicidal active metabolite(s) against a grass weed Digitaria sanguinalis. According to the result from 16S rDNA sequence comparison with the close strains, the best isolate (Code name MS-80673) was identified as Streptomyces scopuliridis KR-001. The closest type strain was Streptomyces scopuliridis RB72 which was previously reported as a bacteriocin producer. The optimal culture condition of S. scopuliridis KR-001 was $28^{\circ}C$, pH 7.0 and culture period 4 to7 days. Both of soil and foliar application of the crude culture broth concentrate was effective on several troublesome or noxious weed species such as a Sciyos angulatus in a greenhouse and field condition. Phytotoxic symptoms of the culture broth concentrate of S. scopuliridis KR-001 by foliar application were wilting and burndown of leaves, and stems followed by discoloration and finally plant death. In crops such as rice, wheat, barley, hot pepper and tomato, growth inhibition was observed. These results suggest that the new S. scopuliridis KR-001 strain producing herbicidal metabolites may be a new bio-herbicide candidate and/or may provide a new lead molecule for a more efficient herbicide.

Microbial profile of asymptomatic and symptomatic teeth with primary endodontic infections by pyrosequencing (원발성 치근단 치주염을 갖는 감염근관에서 증상유무에 따른 세균분포의 pyrosequencing 분석)

  • Lim, Sang-Min;Lee, Tae-Kwon;Kim, Eun-Jeong;Park, Jun-Hong;Lee, Yoon;Bae, Kwang-Shik;Kum, Kee-Yeon
    • Restorative Dentistry and Endodontics
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    • v.36 no.6
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    • pp.498-505
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    • 2011
  • Objectives: The purpose of this in vivo study was to investigate the microbial diversity in symptomatic and asymptomatic canals with primary endodontic infections by using GS FLX Titanium pyrosequencing. Materials and Methods: Sequencing was performed on 6 teeth (symptomatic, n = 3; asymptomatic, n = 3) with primary endodontic infections. Amplicons from hypervariable region of the small-subunit ribosomal RNA gene were generated by polymerized chain reaction (PCR), and sequenced by means of the GS FLX Titanium pyrosequencing. Results: On average, 10,639 and 45,455 16S rRNA sequences for asymptomatic and symptomatic teeth were obtained, respectively. Based on Ribosomal Database Project Classifier analysis, pyrosequencing identified the 141 bacterial genera in 13 phyla. The vast majority of sequences belonged to one of the seven phyla: Actinobacteria, Bacteroidetes, Firmicutes, Fusobacteria, Proteobacteria, Spirochetes, and Synergistetes. In genus level, Pyramidobacter, Streptococcus, and Leptotrichia constituted about 50% of microbial profile in asymptomatic teeth, whereas Neisseria, Propionibacterium, and Tessaracoccus were frequently found in symptomatic teeth (69%). Grouping the sequences in operational taxonomic units (3%) yielded 450 and 1,997 species level phylotypes in asymptomatic and symptomatic teeth, respectively. The total bacteria counts were significantly higher in symptomatic teeth than that of asymptomatic teeth (p < 0.05). Conclusions: GS FLX Titanium pyrosequencing could reveal a previously unidentified high bacterial diversity in primary endodontic infections.

Isolation of Agarivorans sp. KC-1 and Characterization of Its Thermotolerant β-Agarase (한천분해세균 Agarivorans sp. KC-1의 분리 및 내열성 β-아가라제의 특성 규명)

  • Min, Kyung-Cheol;Lee, Chang-Eun;Lee, Dong-Geun;Lee, Sang-Hyeon
    • Journal of Life Science
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    • v.28 no.9
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    • pp.1056-1061
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    • 2018
  • This article reports an agar-degrading marine bacterium and characterizes its agarase. The agar-degrading marine bacterium, KC-1, was isolated from seawater on the shores of Sacheon, in Gyeongnam province, Korea, using Marine Broth 2216 agar medium. To identify the agar-degrading bacterium as Agarivorans sp. KC-1, phylogenetic analysis based on the 16S rRNA gene sequence was used. An extracellular agarase was prepared from a culture medium of Agarivorans sp. KC-1, and used for the characterization of enzyme. The relative activities at 20, 30, 40, 50, 60, and $70^{\circ}C$ were 65, 91, 96, 100, 77, and 35%, respectively. The relative activities at pH 5, 6, 7, and 8 were 93, 100, 87, and 82%, respectively. The extracellular agarase showed maximum activity (254 units/l) at pH 6.0 and $50^{\circ}C$ in 20 mM of Tris-HCl buffer. The agarase activity was maintained at 90% or more until 2 hr exposure at $20^{\circ}C$, $30^{\circ}C$ and $40^{\circ}C$, but it was found that the activity decreased sharply from $60^{\circ}C$. A zymogram analysis showed that Agarivorans sp. KC-1 produced 3 agar-degrading enzymes that had molecular weights of 130, 80, and 69 kDa. A thin layer chromatography analysis suggested that Agarivorans sp. KC-1 produced extracellular ${\beta}$-agarases as it hydrolyzed agarose to produce neoagarooligosaccharides, including neoagarohexaose (21.6%), neoagarotetraose (32.2%), and neoagarobiose (46.2%). These results suggest that Agarivorans sp. KC-1 and its thermotolerant ${\beta}$-agarase would be useful for the production of neoagarooligosaccharides that inhibit bacterial growth and delay starch degradation.

Comparison of PCR-RFLP and Real-Time PCR for Allelotyping of Single Nucleotide Polymorphisms of RRM1, a Lung Cancer Suppressor Gene (폐암 억제유전자 RRM1의 단일염기다형성 검사를 위한 PCR-RFLP법과 Real-Time PCR법의 유용성 비교)

  • Jeong, Ju-Yeon;Kim, Mi-Ran;Son, Jun-Gwang;Jung, Jong-Pil;Oh, In-Jae;Kim, Kyu-Sik;Kim, Young-Chul
    • Tuberculosis and Respiratory Diseases
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    • v.62 no.5
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    • pp.406-416
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    • 2007
  • Background: Single nucleotide polymorphisms (SNPs), which consist of a substitution of a single nucleotide pair, are the most abundant form of genetic variations occurring with a frequency of approximately 1 per 1000 base pairs. SNPs by themselves do not cause disease but can predispose humans to disease, modify the extent or severity of the disease or influence the drug response and treatment efficacy. Single nucleotide polymorphisms (SNPs), particularly those within the regulatory regions of the genes often influence the expression levels and can modify the disease. Studies examining the associations between SNP and the disease outcome have provided valuable insight into the disease etiology and potential therapeutic intervention. Traditionally, the genotyping of SNPs has been carried out using polymerase chain reaction-restriction fragment length polymorphism(PCR-RFLP), which is a low throughput technique not amenable for use in large-scale SNP studies. Recently, TaqMan real-time PCR chemistry was adapted for use in allelic discrimination assays. This study validated the accuracy and utility of real-time PCR technology for SNPs genotyping Methods: The SNPs in promoter sequence (-37 and -524) of lung cancer suppressor gene, RRM1 (ribonucleotide reductase M1 subunit) with the genomic DNA samples of 89 subjects were genotyped using both real-time PCR and PCR-RFLP. Results: The discordance rates were 2.2% (2 mismatches) in -37 and 16.3% (15 mismatches) in -524. Auto-direct sequencing of all the mismatched samples(17 cases) were in accord with the genotypes read by real-time PCR. In addition, 138 genomic DNAs were genotyped using real-time PCR in a duplicate manner (two separated assays). Ninety-eight percent of the samples showed concordance between the two assays. Conclusion: Real-time PCR allelic discrimination assays are amenable to high-throughput genotyping and overcome many of the problematic features associated with PCR-RFLP.

Selection of (Ac/Ds) insertion mutant lines by abiotic stress and analysis of gene expression pattern of rice (Oryza sativar L.) (비생물학적 스트레스 관련 벼 Ac/Ds 삽입 변이체의 선발 및 유전자 발현 분석)

  • Jung, Yu-Jin;Park, Seul-Ah;Ahn, Byung-Ohg;Yun, Doh-Won;Ji, Hyeon-So;Lee, Gang-Sup;Park, Young-Whan;Suh, Seok-Cheol;Baek, Hyung-Jin;Lee, Myung-Chul
    • Journal of Plant Biotechnology
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    • v.35 no.4
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    • pp.307-316
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    • 2008
  • Transposon-mediated insertional mutagenesis is one of powerful strategy for assessing functions of genes in higher plants. In this report, we have selected highly susceptible and tolerance plant by screening about high salt (3% NaCl) and cold stresses ($4^{\circ}C$) from F2 seeds of 30,000 Ac/Ds insertional mutagenesis lines in rice (Oryza sativa L. cv. Dongjin). In order to identify the gene tagging, insertion of Ds element was analyzed by Southern blot and these results revealed that 19 lines were matched genotype of selected lines with phenotype from the first selected 212 lines, and 13 lines have one copy of Ds elements. The Franking Sequence Tags (FSTs) of selected mutant lines showed high similarities with the following known function genes: signal transduction and regulation of gene expression (transpoter, protease family protein and apical meristem family protein), osmotic stress response (heat shock protein, O-methyltransferase, glyceraldehyde-3-phosphate dehydrogenase and drought stress induce protein), vesicle trafficking (SYP 5 family protein) and senescence associated protein. The expression pattern of 19 genes were analyzed using RT-PCR under the abiotic stresses of 9 class; 250mM NaCl, osmotic, drought, 3% $H_2O_2$, $100{\mu}M$ ABA, $100{\mu}M$ IAA, 0.1 ppm 2,4-D, $4^{\circ}C$ cold and $38^{\circ}C$ high temperature. Isolated knock-out genes showed the positive response about 250 mM NaCl, drought, $H_2O_2$, PEG, IAA, 2,4-D, ABA treatment and low ($4^{\circ}C$) and high temperature ($38^{\circ}C$). The results from this study indicate that function of selected knock-out genes could be useful in improving of tolerance to abiotic stresses as an important transcriptional activators in rice.

Sex Determination of Porcine IVF Embryos by Polymerase Chain Reaction (PCR) (중합효소연쇄반응을 이용한 돼지 체외수정란의 성감별)

  • 강미선;김용준;이해이;유일정
    • Journal of Embryo Transfer
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    • v.16 no.3
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    • pp.203-211
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    • 2001
  • This study was carried out to determine sex of porcine embryos produced by in vitro fertilization. Porcine oocyte-cumulus complexes were cultured in BSA-free North Carolina State University (NCSU) 23 medium containing porcine follicular fluid (10%), cystein (0.1 mg/ml) and hormonal supplement (10 IU eCG and 10 IU hCG per ml) for 20~22 hrs. They were then cultured in the same medium but without hormonal supplement for additional 20~22 hrs. After culture, cumulus cells were removed and oocytes were co-incubated for 6 hrs with four different concentrations (5$\times$10$^4$, 2.5$\times$ 10$^{5}$ , 5.0$\times$10$^{5}$ and l0$\times$10$^{5}$ ) of porcine sperm. After fertilization, oocytes were transferred into NCSU 23 with 0.4% BSA medium. The cleavage and blastocyst formation rates were evaluated at 48 and 144 hrs, respectively. In this study, the polymerase chain reaction (PCR) was used to determine the sex of porcine embryos in the stage of blastocyst. The PCR was performed using a set of oligonucleotide primers (5‘-TCATGGACCAGGTAGGGAAT-3', 5’-GAAAGACACGTCCTTGGA GA-3') for 491 bp fragment of porcine male-specific DNA sequence. In the flour different sperm concentration (5$\times$10$^4$, 2.5$\times$10$^{5}$ , 5.0$\times$10$^{5}$ and l0$\times$10$^{5}$ ) for fertilization condition, the cleavage rate was 55.95, 67.88, 60.18 and 47.60%, respectivety, and the development rate of blastocysts was 16.03, 20.40, 21.41 and 12.37%, respectively. At 5.0$\times$10$^4$and 2.5$\times$10$^{5}$ of sperm concentrations per ml cleavage rate and development rate of blastocyst were higher than those of 5.0$\times$10$^4$and l0$\times$10$^{5}$ of sperm concentration (P<0.01). The male of porcine embryos was detected at 491 bp by PCR, and 18 of the 31 porcine blastocysts were the male (58.1%) and the rest 13 were the female(41.9%).

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Neurochemical Profile Quantification of Regional Adult Mice Brain Using: ex vivo $^1H$ High-Resolution Magic Angle Spinning NMR Spectroscopy (생체 외 조직 고 분해능 Magic Angle Spinning을 이용한 정상 Adult Mice에서의 뇌 부위별 뇌 신경화학 대사물질 정량분석)

  • Lee, Do-Wan;Woo, Dong-Cheol;Lee, Sung-Ho;Kim, Sang-Young;Kim, Goo-Young;Rhim, Hyang-Shuk;Choi, Chi-Bong;Kim, Hwi-Yool;Lee, Chang-Wook;Choe, Bo-Young
    • Progress in Medical Physics
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    • v.21 no.1
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    • pp.35-41
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    • 2010
  • The purpose of this study is to quantitate regional neurochemical profile of regional normal adult mice brain and assess regional metabolic differences by using ex vivo $^1H$ high-resolution magic angle spinning nuclear magnetic resonance spectroscopy ($^1H$ HR-MAS NMRS). The animals were matched in sex and age. The collected brain tissue included frontal cortex, temporal cortex, thalamus, and hippocampus. Quantitative 1D spectra were acquired on 40 samples with the CPMG pulse sequence (8 kHz spectral window, TR/TE = 5500/2.2 ms, NEX = 128, scan time: 17 min 20 sec). The mass of brain tissue and $D_2O$+TSP solvent were 8~14 mg and 7~13 mg. A total of 16 metabolites were quantified as follow: Acet, NAA, NAAG, tCr, Cr, tCho, Cho, GPC + PC, mIns, Lac, GABA, Glu, Gln, Tau and Ala. As a results, Acet, Cho, NAA, NAAG and mIns were showed significantly different aspects on frontal cortex, hippocampus, temporal cortex and thalamus respectively. The present study demonstrated that absolute metabolite concentrations were significantly different among four brain regions of adult mice. Our finding might be helpful to investigate brain metabolism of neuro-disease in animal model.

Female External Genitalia and Urethra on MR Imaging: Optimal Pulse Sequence and Comparison of Anatomy in Premenopausal and Postmenopausal Women (여성 외부 생식기와 요도의 자기공명영상 소견: 적합한 영상기법과 폐경 전후의 해부학적 변화 비교)

  • Whang, Shin-Young;Ahn, Kyung-Sik;Sung, Deuk-Jae;Park, Beom-Jin;Kim, Min-Ju;Cho, Sung-Bum;Lee, Nam-Joon
    • Investigative Magnetic Resonance Imaging
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    • v.15 no.2
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    • pp.146-153
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    • 2011
  • Purpose : To describe normal anatomy and compare the differences of external genital organs and urethra on MR imaging in pre- and postmenopausal women. Materials and Methods : A total of 19 pre- and 18 postmenopausal healthy women underwent pelvis MR imaging at 1.5 T. Two radiologists retrospectively scored and compared the image quality of female external genitalia and urethra on axial T2-weighted images (T2WI) and axial fat-suppressed contrast-enhanced T1-weighted images (FSCE-T1WI) by using Wilcoxon signed ranks test. The radiologists compared the wall thickness or size of external genital organs and urethra on FSCE-T1WI between two groups by using Student t test. Results : Image quality was better with FSCE-T1WI than with T2WI in all subjects (p < 0.05). The vestibular bulb, clitoris and labium minor were more clearly visualized on FSCE-T1WI in premenopausal subjects rather than in postmenopausal subjects (p < 0.05). The urethra had a target-like appearance with three layers in premenopausal and postmenopausal subjects. Postmenopausal subjects were observed to have significantly smaller vaginal wall thickness, urethral wall thickness and vestibular bulb width than premenopausal subjects (p < 0.05). Conclusion : The anatomy and morphologic changes of female external genital organs and urethra were well discernible on FSCE-T1WI.