• 제목/요약/키워드: Species-specific probe

검색결과 67건 처리시간 0.03초

Species classification of the toxic dinoflagellate Alexandrium tamarense and A. catenella based on their paralytic shellfish toxin profiles

  • Kim, Young-Soo;Kim, Chang-Hoon
    • 한국양식학회:학술대회논문집
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    • 한국양식학회 2003년도 추계학술발표대회 논문요약집
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    • pp.128-128
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    • 2003
  • The annually outbreak of paralytic shellfish poisoning (PSP) were caused by toxic dinolagellate A. tamarense and A. catenella in Korea. The purpose of this study were to investigate the distribution of PSP-causative organisms, A. tamarense and A. catenella and their species classification. Sediment (Saemangeum, the south open sea) and water samples (southeastern coast) were sampled to establish clonal isolates in 2003. After isolation and purification, strains were cultured under $17^{\circ}C$, f/2 media, 14:10=L:D cycle. PST analysis and species identification were performed by HPLC-FD method and specific DNA probe, respectively. Thirty-ons strains were isolated from the Saemangeum reclamation, southeastern coast including Jinhae Bay and south open sea. PSTs were detected in all cultured strains. In eight strains from south offshore, major toxin components are GTX5, C1/2 and minors are GTX3/4, dcGTX3, neoSTX. Sixteen strains from south coastal area have GTX1/4, neoSTX, C1/2 as major toxin components and GTX2/3 as minors. Seven strains from the Saemangeum reclamation have GTX5, C1/2 as major toxin components and GTX1/2/3/4 as minors. Thus, among eight south offshore isolates, four A. tamarense have more toxic (38.31~l19.16 fmol.$cell^{-1}$) than A. catenella (3.78~13.13 fmol.$cell^{-1}$). With the previous results of different toxin composition, toxin components and toxin contents, .it is toxin profile that could used to diagnosis of regional toxic population and geographical distribution of both A. tamarense and A. catenella and their toxigenic strains.

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살수여상에서의 질소, 인 제거 미생물 분포 및 질산화 활성 조사 (Analysis on the distribution of nitrogen and phosphorus removing microorganisms and nitrifying activity in a trickling filter)

  • 김동진;유익근;안대희
    • 한국환경과학회지
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    • 제18권6호
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    • pp.691-698
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    • 2009
  • Trickling filter has been extensively studied for the domestic wastewater treatment especially for the small scale plants in rural area. The performance of the trickling filter depends on the microbial community and their activity in the biofilms on the media. Nitrification. denitrification, and phosphorus removal of the trickling filter from the wastewater depend on the activity and the amount of the specific microorganisms responsible for the metabolism. For the estimation of the performance of a trickling filter, batch nitrification experiment and fluorescence in situ hybridization (FISH) were carried out to measure the microbial activity and its distribution on the media of the trickling filter. Batch nitrification activity measurement showed that the top part of the 1st stage trickling filter had the highest nitrification activity and the maximum activity was 0.002 g $NH_4$-N/g MLVSS${\cdot}$h. It is thought that higher substrate (ammonia) concentration yields more nitrifying bacteria in the biofilms. The dominant ammonia oxidizer and nitrite oxidizer in the biofilm were Nitrosomonas species and genus Nitrospira, respectively, by FISH analysis. Less denitrifiers were found than nitrifiers in the biofilm by the probe Rrp1088 which specifically binds to Rhodobacter, Rhodovulum, Roseobacter, and Paracoccus. Phosphorus accumulating bacteria were mostly found at the surface of the biofilm by probe Rc988 and PAO651 which specifically binds to Rhodocyclus group and their biomass was less than that of nitrifiers.

Convex Probe 소독 필요성 검증에 관한 연구 (A Study on the Necessity Verification of Convex Probe Disinfection)

  • 최관용;유세종;이준호;홍성용
    • 한국방사선학회논문지
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    • 제13권2호
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    • pp.193-200
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    • 2019
  • 본 연구는 대전, 충청지역 초음파실 종사자를 대상으로 병원감염관리에 관한 설문 조사를 실시하여 분석하였고, ATP를 이용하여 임상에서 사용되는 초음파 Probe의 오염도를 측정하였으며, 70% 알코올 이용하여 소독한 후 결과를 확인하였다. 기본적인 조사 대상자의 일반적인 특성 및 직종 별 대상자의 특성으로 나누어 학력, 직종, 초음파 전문자격증 보유 유무, 기관 내 감염 담당 부서 및 감염 교육의 여부를 분석하였다. 검사 후 젤 제거 여부 및 방법, Probe의 소독여부 및 변수 별 상관분석을 수행하여 초음파 Probe의 세균감염에 관한 인식 및 세척 및 소독에 대한 수행 정도를 분석하였다. 검사 후 Probe 세척에 관하여 수건을 가장 많이 사용하였으며, Gel 용기는 3개월 이상 교환하지 않는 것으로 나타났다. 70% 알코올 소독 후 ATP 오염도는 $1055.4{\pm}944.2$에서 $133.5{\pm}93.2$으로 감소하였고 통계적으로 유의한 것으로 분석되었다.(${\rho}<0.01$) 병원균종은 CNS, Gram positive bacillus, Micrococcus species 검출되었다. 이를 해결하기 위해 시중에서 손쉽게 구할 수 있는 70% 알코올을 이용하여 소독을 실시하였으며 소독 후 병원균종은 검출되지 않았다. 연구 결과 초음파실을 관리하는 의료인 또는 의료기사 등은 감염관리에 대한 주기적인 교육과 감염예방에 대한 노력이 필요하다고 볼 수 있으며, 70% 알코올은 병원균 사멸에 효과적인 것으로 나타났다. 따라서 의료기관은 적극적인 병원감염관리 교육을 실시하여 종사자들의 병원감염에 관한 인식을 개선하고, 환자 감염 예방에 기여해야 할 것이다. 또한 본 연구 결과를 적절히 활용한다면 초음파 Probe를 매개로 한 감염 예방에 도움이 될 것으로 사료된다.

Efficient Isolation of Intact RNA from the Soft Coral Scleronephthya gracillimum $(K\ddot{u}kenthal)$ for Gene Expression Analyses

  • Woo, Seo-Nock;Yum, Seung-Shic;Yoon, Moon-Geun;Kim, Sa-Heung;Lee, Jong-Rak;Kim, Jeong-Ha;Lee, Taek-Kyun
    • Animal cells and systems
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    • 제9권4호
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    • pp.205-209
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    • 2005
  • A rapid, simple and efficient method to extract RNA from the adult polyps of a soft coral, marine cnidarian, Scleronephthya gracillimum $(K\ddot{u}kenthal)$; was developed in this study. The highest yield and purity of RNA was obtained with the lysis solution containing 35 mM EDTA, 0.7 M LiCl, 7.0% SDS, and 200 mM Tris-Cl (pH 9.0). Approximately $40{\mu}g$ of total RNA was extracted from 200 mg of liquid nitrogen-pulverized polyp tissue. The ratio of absorbance at 260 nm and 280 nm ranged from 1.8 to 2.0. The results of the reverse transcription polymerase chain reaction (RTPCR) with ${\beta}-actin$ gene specific primers and Northern blot analysis using the same gene probe revealed that the RNA extracted by our method had high quality, and was sufficient for subsequent molecular biological analyses. This method was effective for RNA extraction from other soft coral species which belong to the genus Dendronephthya.

사염화탄소로 유도된 Cytochrome P-450 활성도의 전환으로 본 Hedera rhombea 잎의 메탄올 추출물의 간독성 감소작용 (Chemoprotective Effect of Methanol Extract of Hedera rhombea Loaves on the Reversal of Cytochrome P-450 Activities Induced by Carbon Tetrachloride)

  • 홍영숙;김형래;배영숙;박상신
    • Biomolecules & Therapeutics
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    • 제3권4호
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    • pp.245-250
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    • 1995
  • The carbon tetrachloride($CCl_4$) has been demonstrated to have a hepatotoxic effect in human or many other species. To investigate the enzyme induction of mixed function oxygenases in liver of male Sprague-Dawley rats a single 0.1, 0.5 mι/kg dose of carbon tetrachloride were given. At 24 hr after a single dose of 0.1 mι CC1$_4$/kg weight, methanol extract of Hedera rhombea leaves was administered with 100, 500 mg/kg weight. Assays of 7-ethoxyresorufin-Ο-deethylation(EROD),7-benzyloxyresorufin-Ο-deathylation(BROD),4-nitro-phenol-UDP-glucuronosyltransferase(UDPGT), Western blot and RNA slot blot were used as representatives of the activities of cytochrome P-450 enzymes. The change of the activity of CYP1A1 form measured by EROD assay and Western analysis using 1-7-1 monoclonal antibody was not observed. The activity CYP2B1 form by BROD assay and using 2-66-3 monoclonal antibody was remarkably increased. Elevated level of CYP2B1 mRNA was shown by slot hybridization with 2B1-specific probe. Administration of methanol extract of Hedera rhombea leaves reversed the enzyme activity and the level of mRNA, which suggest the chemoprotective effect of methanol extracts of Hedera rhombea leaves to carbon tetrachloride hepatotoxlcity.

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Application of Chemical Probes to Detect Superoxide Anion and Singlet Oxygen in Biological Systems during Gamma Irradiation

  • Lee, Min Hee;Cho, Eun Ju;Kim, Ji Hong;Kim, Ji Eun;Chung, Byung Yeoup;Cho, Jae-Young;Lee, Kang-Soo;Kim, Jin-Hong
    • 방사선산업학회지
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    • 제5권3호
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    • pp.221-225
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    • 2011
  • To detect superoxide anion ($O_2{\cdot}^-$) or singlet oxygen ($^1O_2$) in biological systems during gamma irradiation, specific chemical probes, 4,5-dihydroxy-1,3-benzene disulfonic acid (Tiron) or 2,2,6,6-tetramethyl-piperidine (TEMP), were evaluated. Tiron or TEMP spin adducts was structurally stable in aqueous solution during gamma irradiation up to 500 or 1,000 Gy, respectively. The signal of Tiron semiquinone radical, a spin adduct of Tiron upon reaction with $O_2{\cdot}^-$, was slightly increased by gamma irradiation. This trend was dose-dependently manifested in $O_2$-saturated aqueous solution using nitro blue tetrazolium (NBT), a common probe for both hydrated electron ($e{^-}_{aq}$) and $O_2{\cdot}^-$. In contrast, a spin adduct of TEMP, was never inducible by gamma irradiation, while its signal was substantially enhanced by photosensitization of riboflavin. These results suggest that Tiron and NBT or TEMP could be utilized to detect $O_2{\cdot}^-$ or $^1O_2$ in biological systems during gamma irradiation, although $O_2{\cdot}^-$ or $^1O_2$ are not the main reactive oxygen species produced by water radiolysis.

Preliminary Application of Molecular Monitoring of the Pacific Herring (Clupea pallasii) Based on Real-time PCR Assay Utilization on Environmental Water Samples

  • Kim, Keun-Yong;Heo, Jung Soo;Moon, Seong Yong;Kim, Keun-Sik;Choi, Jung-Hwa;Yoo, Joon-Taek
    • 생태와환경
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    • 제54권3호
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    • pp.209-220
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    • 2021
  • Pacific herring, Clupea pallasii, a keystone species with significant ecological and commercial importance, is declining globally throughout much of its range. While traditional fishing equipment methods remain limited, new sensitive and rapid detection methods should be developed to monitor fisheries resources. To monitor the presence and quantity of C. pallasii from environmental DNA (eDNA) extracted from seawater samples, a pair of primers and a TaqMan® probe specific to this fish based on mitochondrial cytochrome b (COB) sequences were designed for the real-time PCR (qPCR) assay. The combination of our molecular markers showed high specificity in the qPCR assay, which affirmed the success of presenting a positive signal only in the C. pallasii specimens. The markers also showed a high sensitivity for detecting C. pallasii genomic DNA in the range of 1 pg~100 ng rxn-1 and its DNA plasmid containing COB amplicon in the range of 1~100,000copies rxn-1, which produced linear standard calibration curves (r2=0.99). We performed a qPCR assay for environmental water samples obtained from 29 sampling stations in the southeastern coastal regions of South Korea using molecular markers. The assay successfully detected the C. pallasii eDNA from 14 stations (48.2%), with the highest mean concentration in Jinhae Bay with a value of 76.09±18.39 pg L-1 (246.20±58.58 copies L-1). Our preliminary application of molecular monitoring of C. pallasii will provide essential information for efficient ecological control and management of this valuable fisheries resource.

Design, Optimization and Verification of 16S rRNA Oligonucleotide Probes of Fluorescence in-situ Hybridization for Targeting Clostridium spp. and Clostridium kluyveri

  • Hu, Lintao;Huang, Jun;Li, Hui;Jin, Yao;Wu, Chongde;Zhou, Rongqing
    • Journal of Microbiology and Biotechnology
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    • 제28권11호
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    • pp.1823-1833
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    • 2018
  • Fluorescence in-situ hybridization (FISH) is a common and popular method used to investigate microbial communities in natural and engineered environments. In this study, two specific 16S rRNA-targeted oligonucleotide probes, CLZ and KCLZ, were designed and verified to quantify the genus Clostridium and the species Clostridium kluyveri. The optimal concentration of hybridization buffer solution for both probes was 30% (w/v). The specificity of the designed probes was high due to the use of pellets from pure reference strains. Feasibility was tested using samples of Chinese liquor from the famed Luzhou manufacturing cellar. The effectiveness of detecting target cells appears to vary widely in different environments. In pit mud, the detection effectiveness of the target cell by probes CLZ and KCLZ was 49.11% and 32.14%, respectively. Quantitative analysis by FISH technique of microbes in pit mud and fermented grains showed consistency with the results detected by qPCR and PCR-DGGE techniques, which showed that the probes CLZ and KCLZ were suitable to analyze the biomass of Clostridium spp. and C. kluyveri during liquor fermentation. Therefore, this study provides a method for quantitative analysis of Clostridium spp. and C. kluyveri and monitoring their community dynamics in microecosystems.

Spatial and seasonal distributions of the phototrophic dinoflagellate Biecheleriopsis adriatica (Suessiaceae) in Korea: quantification using qPCR

  • Kang, Hee Chang;Jeong, Hae Jin;Ok, Jin Hee;You, Ji Hyun;Jang, Se Hyeon;Lee, Sung Yeon;Lee, Kyung Ha;Park, Jae Yeon;Rho, Jung-Rae
    • ALGAE
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    • 제34권2호
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    • pp.111-126
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    • 2019
  • The phototrophic dinoflagellate Biecheleriopsis adriatica is a small suessioid species characterized by a fragile thin wall. Although the morphology of this dinoflagellate is well established, there is currently little information available on its distribution and the environmental factors that influence this distribution. Thus, to investigate the spatial and seasonal distributions of the vegetative cells of B. adriatica in Korean waters, surface water samples were collected on a seasonal basis from 28 stations in the East, West, and South Sea of Korea and Jeju Island from April 2015 to October 2018, and abundances of the vegetative cells of B. adriatica were quantified using quantitative real-time polymerase chain reactions, for which we developed the species-specific primer and probe set. Simultaneously, major environmental parameters, including temperature, salinity, nutrient concentrations, and dissolved oxygen concentrations were measured. The vegetative cells of B. adriatica were detected at 20 of the 28 sampling stations: 19 stations in summer and 6 in autumn, although from no stations in either spring or winter. The ranges of water temperature and salinity at sites where this species was detected were $17.7-26.4^{\circ}C$ and 9.9-34.3, respectively, whereas those of nitrate and phosphate concentrations were not detectable-96.2 and $0.18-2.66{\mu}M$, respectively. Thus, the sites at which this species is found are characterized by a narrow range of temperature, but wide ranges of salinity and concentrations of nitrate and phosphate. The highest abundance of the vegetative cells of B. adriatica was $41.7cells\;mL^{-1}$, which was recorded in Jinhae Bay in July 2018. In Jinhae Bay, the abundance of vegetative cells was significantly positively correlated with the concentration of nitrate, but was negatively correlated with salinity. On the basis of these findings, it appears that the abundance of B. adriatica vegetative cells shows strong seasonality, and in Jinhae Bay, could be affected by the concentrations of nitrate.

Detection of Campylobacter jejuni in food and poultry visors using immunomagnetic separation and microtitre hybridization

  • Simard, Ronald-E.
    • 한국어업기술학회:학술대회논문집
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    • 한국어업기술학회 2000년도 춘계수산관련학회 공동학술대회발표요지집
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    • pp.71-73
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    • 2000
  • Campylobacter jejuni is most frequently identified cause of cause of acute diarrhoeal infections in developeed countries, exceeding rates of illness caused by both salmonella and shigilla(Skirrow, 1990 ; Lior 1994). Previous studies on campylobacter jejuni contamination of commercial broiler carcasses in u.s.(Stern, 1992). Most cases of the disease result from indirect transmission of Campylobactor from animals via milk, water and meat. In addition to Campylobactor jejuni. the closely relates species Campylobactor coli and Campylobactor lari have also been implicated as agents of gastroenteritis in humans. Campylobactor coli represented only approximately 3% of the Campylobactor isolates from patients with Campylobactor enteritis(Griffiths and Park, 1990) whereas Campylobactor coli is mainly isolated from pork(Lmmerding et al., 1988). Campylobactor jejuni has also been isolated from cases of bacteremia, appendicitis and, recently, has been associated with Guillai-Barre syndrome(Allos and Blaser, 1994; von Wulffen et al., 1994; Phillips, 1995). Studies in volunteers indicated that the infectious dose for Campylobactor jejuni is low(about 500 organisms)(Robinson, 1981). The methods traditionally used to detect Campylobactor ssp. in food require at least two days of incubation in an enrichment broth followed by plating and two days of incubation on complex culture media containing many antibiotics(Goossens and Butzler, 1992). Finnaly, several biochemical tests must be done to confirm the indentification at the species level. Therfore, sensitive and specific methods for the detection of small numbers of Campylobactor cells in food are needed. Polymerase chain reaction(PCR) assays targeting specific DNA sequences have been developed for the detection of Campylobactor(Giesendorf and Quint, 1995; Hemandex et al., 1995; Winter and Slavidk, 1995). In most cases, a short enrichment step is needed to enhance the sensitivity of the assay prior to detection by PCR as the number of bacteria in the food products is low in comparison with those found in dinical samples, and because the complex composition of food matrices can hinder the PCR and lower its sensitivity. However, these PCR systems are technically demanding to carry out and cumbersome when processing a large number of samples simutaneously. In this paper, an immunomagnetic method to concentrate Campylobactor cells present in food or clinical samples after an enrichment step is described. To detect specifically the thermophilic Campylobactor. a monoclonal antibody was adsorbed on the surface of the magnetic beads which react against a major porin of 45kDa present on the surface of the cells(Huyer et al., 1986). After this partial purification and concentration step, detection of bound cells was achieved using a simple, inexpensive microtitre plate-based hybridization system. We examined two alternative detection systems, one specific for thermophilic Campylobactor based on the detection of 23S rRNA using an immobilized DNA probe. The second system is less specific but more sensitive because of the high copy number of the rRNA present in bacterial cell($10^3-10^4$). By using specific immunomagnetic beads against thermophilic Campylobactor, it was possible to concentrate these cells from a heterogeneous media and obtain highly specific hybridization reactions with good sensitivity. There are several advantages in using microtitre plates instead of filter membranes or other matrices for hybridization techniques. Microtitre plates are much easier to handle than filter membranes during the adsorption, washing, hybridization and detection steps, and their use faciilitates the simultanuous analysis of multiple sample. Here we report on the use of a very simple detection procedure based on a monoclonal anti-RNA-DNA hybrid antibody(Fliss et al., 1999) for detection of the RNA-DNA hybrids formed in the wells.

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