• Title/Summary/Keyword: Clone Detection

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Paralytic Shellfish Toxin Profiles of the Dinoflagellate Alexandrium Species Isolated from Benthic Cysts in Jinhae Bay, Korea (진해만산 와편모조류 Alexandrium속 휴면포자 발아체의 마비성패독 조성)

  • KIM Chang-Hoon
    • Korean Journal of Fisheries and Aquatic Sciences
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    • v.28 no.3
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    • pp.364-372
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    • 1995
  • On the outbreak of paralytic shellfish poisoning in April 1993 in most of shellfish harvesting areas in Jinhae Bay, Korea, to clarify the toxin production of causative organism Alexandrium species, 19 axenic clonal isolates established from the benthic resting cysts in three different stations of those culture grounds were subjected to PSP toxin analysis by HPLC. Individual toxin content per cell was highly variable among the strains isolated from a sampling area and originated from an individual cyst. Average toxin contents in those areas revealed higher values of 54-70 fmol/cell. Toxin profiles included C1/C2(epiGTX8/GTX8), GTX1/GTX4 and neoSTX as the major components, and GTX2/GTX3, GTX5, C4, dcSTX and STX as the minor or sporadic ones. neoSTX on the dominant toxins showed not only most diverse compositional changes comprising $5-54 mol\%$ ranges but also no detection on the half of the strains examined, which were implicated in arising of heterogeneity with a genetic trait within a geographical region. When average toxin composition was compared, carbamate toxins comprised large proportions of $57\%,\;54\%\;and\;67\%$ as total toxin in St. 1, St. 2 and St. 4, respectively. These results suggested that an extensive paralytic shellfish toxification in Jinhae Bay could be largely due to the production of highly potent carbamate toxins in the causative dinoflagellate Alexandrium species.

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Current status of Ac/Ds mediated gene tagging systems for study of rice functional genomics in Korea (Ac/Ds 삽입 변이체를 이용한 벼 유전자 기능 연구)

  • Lee, Gang-Seob;Park, Sung-Han;Yun, Do-Won;Ahn, Byoung-Ohg;Kim, Chang-Kug;Han, Chang-Deok;Yi, Gi-Hwan;Park, Dong-Soo;Eun, Moo-Young;Yoon, Ung-Han
    • Journal of Plant Biotechnology
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    • v.37 no.2
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    • pp.125-132
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    • 2010
  • Rice is the staple food of more than 50% of the worlds population. Cultivated rice has the AA genome (diploid, 2n=24) and small genome size of only 430 megabase (haploid genome). As the sequencing of rice genome was completed by the International Rice Genome Sequencing Project (IRGSP), many researchers in the world have been working to explore the gene function on rice genome. Insertional mutagenesis has been a powerful strategy for assessing gene function. In maize, well characterized transposable elements have traditionally been used to clone genes for which only phenotypic information is available. In rice endogenous mobile elements such as MITE and Tos (Hirochika. 1997) have been used to generate gene-tagged populations. To date T-DNA and maize transposable element systems has been utilized as main insertional mutagens in rice. A main drawback of a T-DNA scheme is that Agrobacteria-mediated transformation in rice requires extensive facilities, time, and labor. In contrast, the Ac/Ds system offers the advantage of generating new mutants by secondary transposition from a single tagged gene. Revertants can be utilized to correlate phenotype with genotype. To enhance the efficiency of gene detection, advanced gene-tagging systems (i.e. activation, gene or enhancer trap) have been employed for functional genomic studies in rice. Internationally, there have been many projects to develop large scales of insertionally mutagenized populations and databases of insertion sites has been established. Ultimate goals of these projects are to supply genetic materials and informations essential for functional analysis of rice genes and for breeding using agronomically important genes. In this report, we summarize the current status of Ac/Ds-mediated gene tagging systems that has been launched by collaborative works from 2001 in Korea.

Diversity of Acid-Tolerant Epiphytic Bacterial Communities on Plant Leaves in the Industrial Area and the Natural Forest Area Based on 16S rDNA (16S rDNA 염기서열에 의한 청정지역 및 공단지역 내 식물잎권의 내산성세균 군집의 다양성)

  • 정필문;신광수;임종순;이인수;박성주
    • Korean Journal of Microbiology
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    • v.37 no.4
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    • pp.265-272
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    • 2001
  • The diversity of acid-tolerant epiphytic bacterial communities on deciduous oak tree (Quercus dentate Thunb.) leaves was examined both in the natural forest area with a clean air and in the industrial estate to assess effects of acidic depositions to the phyllosphere using 16S rDNA sequence data. A total of 444 acid-tolerant epiphytic bacterial clones were obtained, resulting in 17 phylotypes by performing a analysis of restriction fragment length polymorphism (RFLP) for PCR-amplified 16S rDNA products. A very low diversity of dominating acid tolerant bacterial communities in both areas was found, just 2 subphyla groups, $\gamma$-Proteobacteria and low-G+C gram-positive bacteria. As tree leaves grow older, diversities of acid-tolerant bacteria on them significantly increased. The community structure of acid-tolerant epiphytic bacteria consisted of Pseudomonas and Enterobacteriaceae groups in the $\gamma$-Proteobacteria subphylum, and Streptococcaceae and Staphylococcus groups in the low-G+C gram-positive bacteria subphylum. The direct influence of acidic depositions on bacterial phylogenetic composition could not be detected especially when higher taxonomic levels such as subphylum, but at narrower or finer levels it could be observed by a detection of Xanthomonadales group belonged to the $\gamma$-Proteobacteria only in the industrial area and of Acetobacteraceae group belonged to the $\alpha$-Proteobacteria. There remains that these specific acid-tolerant epiphytic bacterial groups could be used as indicators for assessing effects of acidic depositions on the phyllosphere.

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Rapid Diagnosis of Iridovirus Infection by Polymerase Chain Reaction (Polymerase Chain Reaction(PCR)을 이용한 Iridovirus의 검색)

  • Cha, Seung-Ju;Do, Jeong-Wan;Kim, Hyun-Ju;Cho, Wha-Ja;Mun, Chang-Hoon;Park, Jeong-Min;Park, Myoung-Ae;Kim, Su-Mi;Sohn, Sang-Gyu;Bang, Jong-Deuk;Park, Jeong-Woo
    • Journal of fish pathology
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    • v.11 no.1
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    • pp.61-67
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    • 1998
  • For rapid detection of iridovirus infection, a PCR-based diagnostic method was developed. The genomic DNA from mortality-associated iridovirus was cloned into pUC19 vector. The nucleotide sequences of these clones were compared with sequences of other genes from EMBL/GenBank databank. Based on the nucleotide sequences, PCR primers were prepared and used for PCR. The DNA amplification did not occur from the normal fish cells. In contrast, DNA was amplified from the iridovirus-infected fish cells and purified iridovirus. These results suggest that mortality-associated iridovirus can be detected from virus-infected cells within short time and this PCR-based diagnostic system provides a simple and accurate method for detecting the presence of iridovirus infection.

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Immunocytochemistry, In situ hybridization and electron microscopy for early diagnosis of Aujeszky's in living pigs (오제스키병의 생체 조기진단을 위한 면역세포화학, In situ hybridization 및 전자현미경적 연구)

  • Moon, Oun-kyong;Kim, Soon-bok;Sur, Jung-hyang;Song, Geun-suk;Nho, Whan-gook
    • Korean Journal of Veterinary Research
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    • v.36 no.4
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    • pp.845-858
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    • 1996
  • The purpose of this study was to establish early diagnostic methods for the detection of Aujeszky's disease viral antigens and nucleic acid in nasal cells, and buffy coats from experimentally infected living pigs by a combination of immunocytochemistry, in situ hybridization with digoxigenin(DIG)-labled probe and electron microscopy. Forty days old piglets were inoculated intranasally with $10^{7.0}TCID_{50}$ of Aujeszky's disease virus (ADV, NYJ-1-87 strain). The viral antigens and nucleic acid of ADV were detected in nasal cells, and buffy coat for 20 days after inoculation by immunocytochemistry, in situ hybridization with DIG-labeled probe and electron microscopical method. The results were compared with conventional methods such as a porcine Aujeszky's disease serodiagnostic(PAD) kit, neutralization test(NT) and virus isolation. 1. The viral antigens, nucleic acids and capsids of ADV were detected in nasal cells, buffy coats from 3 days to 20 days after inoculation by immunocytochemistry, in situ hybridization with DIG-labeled probe and electron microscopy, respectively. 2. When viral antigens were detected by the immunocytochemical technique, a diffuse brown deposit was observed in the nucleus and cytoplasm of nasal cells, buffy coats and PK-15 cells under a microscope. 3. DIG-labeled DNA probe was prepared by amplification of conserved sequence of recombinant ADV-gp50 clone with polymerase chain reacction. When ADV-DNA was detected by ISH with DIG-labeled probe, purplish blue pigmentation were observed in the nuclei and cytoplasms of ADV-infected cells under a microscope. Positive signals were observed in nasal cells and in the buffy coat and PK-15 cells at the first day after inoculation. 4. Where ADV-capsids were detected by transmission electron microscopical method, aggregation of capsids was observed in the nuclei and cytoplasms of nasal cells, buffy coats and PK-15 cells. The results suggested that these methods were considered as the highly sensitive and reliable tools for rapid and confirmative diagnosis of Aujeszky's disease in living pigs.

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Ttrosine Hydroxylase in Japanese Medaka (Oryzias latipes): cDNA Cloning and Molecular Monitoring of TH Gene Expression As a Biomarker (송사리 Tyrosine Hydroxylase: cDNA 클로닝 및 생물지표로서의 TH 유전자 발현의 분자생물학적 추적)

  • Shin, Sung-Woo;Kim, Jung-Sang;Chon, Tae-Soo;Lee, Sung-Kyu;Koh, Sung-Cheol
    • Environmental Analysis Health and Toxicology
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    • v.15 no.4
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    • pp.131-137
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    • 2000
  • The release of hazardous waste materials into the environment poses serious risks in humans and ecosystems. The risk assessment of environmental pollutants including hazardous chemicals requires a comprehensive measurement of hazard and exposure of the chemicals that can be achieved by toxicity evaluation using a biological system such as biomarkers. In this report we have tried to develop a biomarker used to elucidate a molecular basis of, and to monitor abnormal behaviors caused by diazinon in Japanese medaka (Oryzias latipes) as a model organism. First, an attempt was made to clone tyrosine hydroxylase gene from Japanese medaka that would be a candidate for a biomarker for neuronal modulations and behaviors. For monitoring experiments at behavioral and molecular biological levels, the fish were treated under different sublethal conditions of diazinon and their behavioral responses were observed . In this study we have successfully cloned a partial TH gene from the medaka fish through PCR screening of an ovary cDNA library. DNA sequencing analysis revealed that the amplified fragment was 327 bp encoding 109 amino acids. Comparing the DNA sequence of medaka TH with other species, TH gene revealed the DNA sequence was completely identical to that of rat TH. In the RT-PCR, 330 Up of mRNA was consistently amplified in all the treated samples including control There were no significant differences in the TH expression level regardless of treating concentrations (1∼5,000 ppb) and time (0∼48 hr) The reason appeared to be that RT-PCR was not performed using through a quantitative analysis normalized against an actin gene expression. Organ or tissue - specific detection of TH activity and mRNA as biomarkers will be a useful monitoring tool for neurobehavioral changes in fish influenced by toxic chemicals. Furthermore, quantitative analysis of locomotive patterns and its correlation with the neurochemical and molecular data would be highly useful in measuring toxicity and hazard ofvarious environmental pollutants.

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Field Studios of In-situ Aerobic Cometabolism of Chlorinated Aliphatic Hydrocarbons

  • Semprini, Lewts
    • Proceedings of the Korean Society of Soil and Groundwater Environment Conference
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    • 2004.04a
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    • pp.3-4
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    • 2004
  • Results will be presented from two field studies that evaluated the in-situ treatment of chlorinated aliphatic hydrocarbons (CAHs) using aerobic cometabolism. In the first study, a cometabolic air sparging (CAS) demonstration was conducted at McClellan Air Force Base (AFB), California, to treat chlorinated aliphatic hydrocarbons (CAHs) in groundwater using propane as the cometabolic substrate. A propane-biostimulated zone was sparged with a propane/air mixture and a control zone was sparged with air alone. Propane-utilizers were effectively stimulated in the saturated zone with repeated intermediate sparging of propane and air. Propane delivery, however, was not uniform, with propane mainly observed in down-gradient observation wells. Trichloroethene (TCE), cis-1, 2-dichloroethene (c-DCE), and dissolved oxygen (DO) concentration levels decreased in proportion with propane usage, with c-DCE decreasing more rapidly than TCE. The more rapid removal of c-DCE indicated biotransformation and not just physical removal by stripping. Propane utilization rates and rates of CAH removal slowed after three to four months of repeated propane additions, which coincided with tile depletion of nitrogen (as nitrate). Ammonia was then added to the propane/air mixture as a nitrogen source. After a six-month period between propane additions, rapid propane-utilization was observed. Nitrate was present due to groundwater flow into the treatment zone and/or by the oxidation of tile previously injected ammonia. In the propane-stimulated zone, c-DCE concentrations decreased below tile detection limit (1 $\mu$g/L), and TCE concentrations ranged from less than 5 $\mu$g/L to 30 $\mu$g/L, representing removals of 90 to 97%. In the air sparged control zone, TCE was removed at only two monitoring locations nearest the sparge-well, to concentrations of 15 $\mu$g/L and 60 $\mu$g/L. The responses indicate that stripping as well as biological treatment were responsible for the removal of contaminants in the biostimulated zone, with biostimulation enhancing removals to lower contaminant levels. As part of that study bacterial population shifts that occurred in the groundwater during CAS and air sparging control were evaluated by length heterogeneity polymerase chain reaction (LH-PCR) fragment analysis. The results showed that an organism(5) that had a fragment size of 385 base pairs (385 bp) was positively correlated with propane removal rates. The 385 bp fragment consisted of up to 83% of the total fragments in the analysis when propane removal rates peaked. A 16S rRNA clone library made from the bacteria sampled in propane sparged groundwater included clones of a TM7 division bacterium that had a 385bp LH-PCR fragment; no other bacterial species with this fragment size were detected. Both propane removal rates and the 385bp LH-PCR fragment decreased as nitrate levels in the groundwater decreased. In the second study the potential for bioaugmentation of a butane culture was evaluated in a series of field tests conducted at the Moffett Field Air Station in California. A butane-utilizing mixed culture that was effective in transforming 1, 1-dichloroethene (1, 1-DCE), 1, 1, 1-trichloroethane (1, 1, 1-TCA), and 1, 1-dichloroethane (1, 1-DCA) was added to the saturated zone at the test site. This mixture of contaminants was evaluated since they are often present as together as the result of 1, 1, 1-TCA contamination and the abiotic and biotic transformation of 1, 1, 1-TCA to 1, 1-DCE and 1, 1-DCA. Model simulations were performed prior to the initiation of the field study. The simulations were performed with a transport code that included processes for in-situ cometabolism, including microbial growth and decay, substrate and oxygen utilization, and the cometabolism of dual contaminants (1, 1-DCE and 1, 1, 1-TCA). Based on the results of detailed kinetic studies with the culture, cometabolic transformation kinetics were incorporated that butane mixed-inhibition on 1, 1-DCE and 1, 1, 1-TCA transformation, and competitive inhibition of 1, 1-DCE and 1, 1, 1-TCA on butane utilization. A transformation capacity term was also included in the model formation that results in cell loss due to contaminant transformation. Parameters for the model simulations were determined independently in kinetic studies with the butane-utilizing culture and through batch microcosm tests with groundwater and aquifer solids from the field test zone with the butane-utilizing culture added. In microcosm tests, the model simulated well the repetitive utilization of butane and cometabolism of 1.1, 1-TCA and 1, 1-DCE, as well as the transformation of 1, 1-DCE as it was repeatedly transformed at increased aqueous concentrations. Model simulations were then performed under the transport conditions of the field test to explore the effects of the bioaugmentation dose and the response of the system to tile biostimulation with alternating pulses of dissolved butane and oxygen in the presence of 1, 1-DCE (50 $\mu$g/L) and 1, 1, 1-TCA (250 $\mu$g/L). A uniform aquifer bioaugmentation dose of 0.5 mg/L of cells resulted in complete utilization of the butane 2-meters downgradient of the injection well within 200-hrs of bioaugmentation and butane addition. 1, 1-DCE was much more rapidly transformed than 1, 1, 1-TCA, and efficient 1, 1, 1-TCA removal occurred only after 1, 1-DCE and butane were decreased in concentration. The simulations demonstrated the strong inhibition of both 1, 1-DCE and butane on 1, 1, 1-TCA transformation, and the more rapid 1, 1-DCE transformation kinetics. Results of tile field demonstration indicated that bioaugmentation was successfully implemented; however it was difficult to maintain effective treatment for long periods of time (50 days or more). The demonstration showed that the bioaugmented experimental leg effectively transformed 1, 1-DCE and 1, 1-DCA, and was somewhat effective in transforming 1, 1, 1-TCA. The indigenous experimental leg treated in the same way as the bioaugmented leg was much less effective in treating the contaminant mixture. The best operating performance was achieved in the bioaugmented leg with about over 90%, 80%, 60 % removal for 1, 1-DCE, 1, 1-DCA, and 1, 1, 1-TCA, respectively. Molecular methods were used to track and enumerate the bioaugmented culture in the test zone. Real Time PCR analysis was used to on enumerate the bioaugmented culture. The results show higher numbers of the bioaugmented microorganisms were present in the treatment zone groundwater when the contaminants were being effective transformed. A decrease in these numbers was associated with a reduction in treatment performance. The results of the field tests indicated that although bioaugmentation can be successfully implemented, competition for the growth substrate (butane) by the indigenous microorganisms likely lead to the decrease in long-term performance.

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Comparison of the Uptakes of Tc-99m MIBI and Tc-99m Tetrofosmin in A549, an MRP-expressing Cancer Cell, In Vitro and In Vivo (MRP발현 인체 비소세포 폐암 A549에서 Tc-99m MIBI와 Tc-99m Tetrofosmin섭취의 비교)

  • Yoo, Jeong-Ah;Jeong, Shin-Young;Seo, Myung-Rang;Bae, Jin-Ho;Ahn, Byeong-Cheol;Lee, Kyu-Bo;Choi, Sang-Woon;Lee, Byung-Ho;Lee, Jae-Tae
    • The Korean Journal of Nuclear Medicine
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    • v.37 no.6
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    • pp.382-392
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    • 2003
  • Purpose: Uptakes of Tc-99m MIBI (MIBI) and Tc-99m tetrofosmin (tetrofosmin) in human non-small cell lung cancer A549, multidrug-resistance associated protein (MRP) expressing cell, were investigated in vitro and in vivo. Materials and Methods: Western blot analysis and immunohistochemistry were used for detection of MRP in A549 cells with anti-MRPr1 antibody. Cellular uptakes of two tracers were evaluated at $100{\mu}M$ of verapamil (Vrp), $50{\mu}M$ of cyclosporin A (CsA) and $25{\mu}M$ of butoxysulfoximide (BSO) after incubation with MIBI and tetrofosmin for 30 and 50 min at $37^{\circ}C$, using single cell suspensions at $1{\times}10^6cells/ml$. Radioactivities in supernatants and pellets were measured with gamma well counter. A549 cells were inoculated in each flanks of 24 nude mice. Group 1 (Gr1) and Gr3 mice were treated with only MIBI or tetrofosmin, and Gr2 and Gr4 mice were treated with 70mg/kg of CsA i.p. for 1 hour before injection of 370KBq of MIBI or tetrofosmin. Mice were sacrificed at 10, 60 and 240 min. Radioactivities of organs and tumors were expressed as percentage injected dose per gram of tissue (%ID/gm). Results: Western blot analysis of the A549 cells detected expression of MRPr1 (190 kDa) and immunohistochemical staining of tumor tissue for MRPr1 revealed brownish staining in cell membrane but not P-gp. Upon incubating A549 cells for 60 min with MIBI and tetrofosmin, cellular uptake of MIBI was higher than that of tetrofosmin. Coincubation with modulators resulted in an increase in cellular uptakes of MIBI and tetrofosmin. Percentage increase of MIBI was higher than that of tetrofosmin with Vrp by 623% and 427%, CsA by 753% and 629% and BSO by 219% and 140%, respectively. There was no significant difference in tumoral uptakes of MIBI and tetrofosmin between Gr1 and Gr3. Percentage increases in MIBI (114% at 10 min, 257% at 60 min, 396% at 240 min) and tetrofosmin uptake (110% at 10 min, 205% at 60 min, 410% at 240 min) were progressively higher by the time up to 240 min with CsA. Conclusion: These results indicate that MIBI and tetrofosmin are suitable tracers for imaging MRP-mediated drug resistance in A549 tumors. MIBI may be a better tracer than tetrofosmin for evaluating MRP reversal effect of modulators.