• Title/Summary/Keyword: Multi-species

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Probe-based qPCR Assay for Rapid Detection of Predominant Candida glabrata Sequence Type in Korea

  • Bae, Jinyoung;Lee, Kyung Eun;Jin, Hyunwoo
    • Biomedical Science Letters
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    • v.25 no.4
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    • pp.407-416
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    • 2019
  • Recent years have seen an increase in the incidence of candidiasis caused by non-albicans Candida (NAC) species. In fact, C. glabrata is now second only to C. albicans as the most common cause of invasive candidiasis. Therefore, the rapid genotyping specifically for C. glabrata is required for early diagnosis and treatment of candidiasis. A number of genotyping assays have been developed to differentiate C. glabrata sequence types (STs), but they have several limitations. In the previous study, multi-locus sequence typing (MLST) has performed with a total of 101 C. glabrata clinical isolates to analyze the prevalent C. glabrata STs in Korea. A total of 11 different C. glabrata STs were identified and, among them, ST-138 was the most commonly classified. Thus, a novel probe-based quantitative PCR (qPCR) assay was developed and evaluated for rapid and accurate identification of the predominant C. glabrata ST-138 in Korea. Two primer pairs and hybridization probe sets were designed for the amplification of internal transcribed spacer 1 (ITS1) region and TRP1 gene. Analytical sensitivity of the probe-based qPCR assay was 100 ng to 10 pg and 100 ng to 100 pg (per 1 μL), which target ITS1 region and TRP1 gene, respectively. This assay did not react with any other Candida species and bacteria except C. glabrata. Of the 101 clinical isolates, 99 cases (98%) were concordant with MLST results. This novel probe-based qPCR assay proved to be rapid, sensitive, highly specific, reproducible, and cost-effective than other genotyping assay for C. glabrata ST-138 identification.

Podophyllotoxin Induces ROS-Mediated Apoptosis and Cell Cycle Arrest in Human Colorectal Cancer Cells via p38 MAPK Signaling

  • Lee, Seung-On;Joo, Sang Hoon;Kwak, Ah-Won;Lee, Mee-Hyun;Seo, Ji-Hye;Cho, Seung-Sik;Yoon, Goo;Chae, Jung-Il;Shim, Jung-Hyun
    • Biomolecules & Therapeutics
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    • v.29 no.6
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    • pp.658-666
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    • 2021
  • Podophyllotoxin (PT), a lignan compound from the roots and rhizomes of Podophyllum peltatum, has diverse pharmacological activities including anticancer effect in several types of cancer. The molecular mechanism of the anticancer effects of PT on colorectal cancer cells has not been reported yet. In this study, we sought to evaluate the anticancer effect of PT on human colorectal cancer HCT116 cells and identify the detailed molecular mechanism. PT inhibited the growth of cells and colony formation in a concentration-dependent manner and induced apoptosis as determined by the annexin V/7-aminoactinomycin D double staining assay. PT-induced apoptosis was accompanied by cell cycle arrest in the G2/M phase and an increase in the generation of reactive oxygen species (ROS). The effects of PT on the induction of ROS and apoptosis were prevented by pretreatment with N-acetyl-L-cysteine (NAC), indicating that an increase in ROS generation mediates the apoptosis of HCT116 cells induced by PT. Furthermore, Western blot analysis showed that PT upregulated the level of phospho (p)-p38 mitogen-activated protein kinase (MAPK). The treatment of SB203580, a p38 inhibitor, strongly prevented the apoptosis induced by PT, suggesting that PT-induced apoptosis involved the p38 MAPK signaling pathway. In addition, PT induced the loss of mitochondrial membrane potential and multi-caspase activation. The results suggested that PT induced cell cycle arrest in the G2/M phase and apoptosis through the p38 MAPK signaling pathway by upregulating ROS in HCT116 cells.

Picropodophyllotoxin Induces G1 Cell Cycle Arrest and Apoptosis in Human Colorectal Cancer Cells via ROS Generation and Activation of p38 MAPK Signaling Pathway

  • Lee, Seung-On;Kwak, Ah-Won;Lee, Mee-Hyun;Seo, Ji-Hye;Cho, Seung-Sik;Yoon, Goo;Chae, Jung-Il;Joo, Sang Hoon;Shim, Jung-Hyun
    • Journal of Microbiology and Biotechnology
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    • v.31 no.12
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    • pp.1615-1623
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    • 2021
  • Picropodophyllotoxin (PPT), an epimer of podophyllotoxin, is derived from the roots of Podophyllum hexandrum and exerts various biological effects, including anti-proliferation activity. However, the effect of PPT on colorectal cancer cells and the associated cellular mechanisms have not been studied. In the present study, we explored the anticancer activity of PPT and its underlying mechanisms in HCT116 cells. The 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide (MTT) assay was used to monitor cell viability. Flow cytometry was used to evaluate cell cycle distribution, the induction of apoptosis, the level of reactive oxygen species (ROS), assess the mitochondrial membrane potential (Δψm), and multi-caspase activity. Western blot assays were performed to detect the expression of cell cycle regulatory proteins, apoptosis-related proteins, and p38 MAPK (mitogen-activated protein kinase). We found that PPT induced apoptosis, cell cycle arrest at the G1 phase, and ROS in the HCT116 cell line. In addition, PPT enhanced the phosphorylation of p38 MAPK, which regulates apoptosis and PPT-induced apoptosis. The phosphorylation of p38 MAPK was inhibited by an antioxidant agent (N-acetyl-L-cysteine, NAC) and a p38 inhibitor (SB203580). PPT induced depolarization of the mitochondrial inner membrane and caspase-dependent apoptosis, which was attenuated by exposure to Z-VAD-FMK. Overall, these data indicate that PPT induced G1 arrest and apoptosis via ROS generation and activation of the p38 MAPK signaling pathway.

Designing a novel mRNA vaccine against Vibrio harveyi infection in fish: an immunoinformatics approach

  • Islam, Sk Injamamul;Mou, Moslema Jahan;Sanjida, Saloa;Tariq, Muhammad;Nasir, Saad;Mahfuj, Sarower
    • Genomics & Informatics
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    • v.20 no.1
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    • pp.11.1-11.20
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    • 2022
  • Vibrio harveyi belongs to the Vibrio genus that causes vibriosis in marine and aquatic fish species through double-stranded DNA virus replication. In humans, around 12 Vibrio species can cause gastroenteritis (gastrointestinal illness). A large amount of virus particles can be found in the cytoplasm of infected cells, which may cause death. Despite these devastating complications, there is still no cure or vaccine for the virus. As a result, we used an immunoinformatics approach to develop a multi-epitope vaccine against most pathogenic hemolysin gene of V. harveyi. The immunodominant T- and B-cell epitopes were identified using the hemolysin protein. We developed a vaccine employing three possible epitopes: cytotoxic T-lymphocytes, helper T-lymphocytes, and linear B-lymphocyte epitopes, after thorough testing. The vaccine was developed to be antigenic, immunogenic, and non-allergenic, as well as having a better solubility. Molecular dynamics simulation revealed significant structural stiffness and binding stability. In addition, the immunological simulation generated by computer revealed that the vaccination might elicit immune reactions in the actual life after injection. Finally, using Escherichia coli K12 as a model, codon optimization yielded ideal GC content and a higher codon adaptation index value, which was then included in the cloning vector pET2+ (a). Altogether, our experiment implies that the proposed peptide vaccine might be a good option for vibriosis prophylaxis.

Mapping of the Righteous Tree Selection for a Given Site Using Digital Terrain Analysis on a Central Temperate Forest (수치지형해석(數値地形解析)에 의한 온대중부림(溫帶中部林)의 적지적수도(適地適樹圖) 작성(作成))

  • Kang, Young-Ho;Jeong, Jin-Hyun;Kim, Young-Kul;Park, Jae-Wook
    • Journal of Korean Society of Forest Science
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    • v.86 no.2
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    • pp.241-250
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    • 1997
  • The study was conducted to make a map for selecting righteous tree species for each site by digital terrain analysis. We set an algorithmic value for each tree species' characteristics with distribution pattern analysis, and the soil types were digitized from data indicated on soil map. Mean altitude, slope, aspect and micro-topography were estimated from the digital map for each block which had been calculated by regression equations with altitude. The results obtained from the study could be summarized as follows 1. We could develope a method to select righteous tree species for a given site with concern of soil, forest condition and topographic factors on Muju-Gun in Chonbuk province(2,500ha) by the terrain analysis and multi-variate digital map with a personal computer. 2. The brown forest soils were major soil types for the study area, and 29 tree species were occurred with Pinus densiflora as a dominant species. The differences in site condition and soil properties resulted in site quality differences for each tree species. 3. We tried to figure out the accuracy of a basic program(DTM.BAS) enterprised for this study with comparing the mean altitude and aspect calculated from the topographic terrain analysis map and those from surveyed data. The differences between the values were less than 5% which could be accepted as a statistically allowable value for altitude, as well as the values for aspect showed no differences between both the mean altitude and aspect. The result may indicate that the program can be used further in efficiency. 4. From the righteous-site selection map, the 2nd group(R, $B_1$) took the largest area with 46% followed by non-forest area (L) with 23%, the 5th group with 7% and the 4th group with 5%, respectively. The other groups occupied less than 6%. 5. We suggested four types of management tools by silvicultural tree species with considering soil type and topographic conditions.

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Target candidate fish species selection method based on ecological survey for hazardous chemical substance analysis (유해화학물질 분석을 위한 생태조사 기반의 타깃 후보어종 선정법)

  • Ji Yoon Kim;Sang-Hyeon Jin;Min Jae Cho;Hyeji Choi;Kwang-Guk An
    • Korean Journal of Environmental Biology
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    • v.41 no.2
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    • pp.109-125
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    • 2023
  • This study was conducted to select target fish species as baseline research for accumulation analysis of major hazardous chemicals entering the aquatic ecosystem in Korea and to analyze the impact on fish community. The test bed was selected from a sewage treatment plant, which could directly confirm the impact of the inflow of harmful chemicals, and the Geum River estuary where harmful chemicals introduced into the water system were concentrated. A multivariable metric model was developed to select target candidate fish species for hazardous chemical analysis. Details consisted of seven metrics: (1) commercially useful metric, (2) top-carnivorous species metric, (3) pollution fish indicator metric, (4) tolerance fish metric, (5) common abundant metric, (6) sampling availability (collectability) metric, and (7) widely distributed fish metric. Based on seven metric models for candidate fish species, eight species were selected as target candidates. The co-occurring dominant fish with target candidates was tolerant (50%), indicating that the highest abundance of tolerant species could be used as a water pollution indicator. A multi-metric fish-based model analysis for aquatic ecosystem health evaluation showed that the ecosystem health was diagnosed as "bad conditions". Physicochemical water quality variables also influenced fish feeding and tolerance guild in the testbed. Eight water quality parameters appeared high at the T1 site, indicating a large impact of discharging water from the sewage treatment plant. T2 site showed massive algal bloom, with chlorophyll concentration about 15 times higher compared to the reference site.

Characterization of $\beta$-Ketoadipate Pathway from Multi-Drug Resistance Bacterium, Acinetobacter baumannii DU202 by Proteomic Approach

  • Park, Soon-Ho;Kim, Jae-Woo;Yun, Sung-Ho;Leem, Sun-Hee;Kahng, Hyung-Yeel;Kim, Seung-Il
    • Journal of Microbiology
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    • v.44 no.6
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    • pp.632-640
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    • 2006
  • In this study, the biodegradative activities of monocyclic aromatic compounds were determined from the multi-drug resistant (MDR) Acinetobacter baumannii, which were studied in the form of clinical isolates from a hospital in Korea. These bacteria were capable of biodegrading monocyclic aromatic compounds, such as benzoate and p-hydroxybenzoate. In order to determine which pathways are available for biodegradation in these stains, we conducted proteome analyses of benzoate, and p-hydroxybenzoate-cultured A. baumannii DU202, using 2-DE/MS analysis. As genome DB of A. baumannii was not yet available, MS/MS analysis or de novo sequencing methods were employed in the identification of induced proteins. Benzoate branch enzymes [catechol 1,2-dioxygenase (CatA) and benzoate dioxygenase $\alpha$ subunit (BenA)] of the $\beta$-ketoadipate pathway were identified under benzoate culture condition and p-hydroxybenzoate branch enzymes [protocatechuate 3,4-dioxygenas $\alpha$ subunit (PcaG) and 3-carboxy-cis,cis-muconate cycloisomerase (PcaR)] of the $\beta$-ketoadipate pathway were identified under p-hydroxybenzoate culture condition, respectively, thereby suggesting that strain DU202 utilized the $\beta$-ketoadipate pathway for the biodegradation of monocyclic aromatic compounds. The sequence analysis of two purified dioxygenases (CatA and PcaGH) indicated that CatA is closely associated with the CatA of Acinetobacter radiresistance, but PcaGH is only moderately associated with the PcaGH of Acinetobacter sp. ADPI. Interestingly, the fused form of PcaD and PcaC, carboxymuconolactone decarboxylase (PcaCD), was detected on benzoate-cultured A. baumannii DU202. These results indicate that A. baumannii DU202 exploits a different $\beta$-ketoadipate pathway from other Acinetobacter species.

Numerical Study for the Influence of Environment Temperature on Offshore Arctic Pipeline and Impingement Erosion Analysis by using Thermal Flow Simulation (극지 해양 파이프라인 내부 유체의 온도별 영향 및 내부 충돌침식 분석)

  • Jo, Chul Hee;Lee, Jun-Ho;Jang, Choon-Man;Heang, Su-Jin
    • Journal of Advanced Marine Engineering and Technology
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    • v.39 no.3
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    • pp.201-205
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    • 2015
  • This paper describes thermal flow characteristic in various pipelines: straight pipeline and curved pipeline. In the Arctic and ocean area, pipelines are exposed to a extremely low temperature ($0{\sim}-40^{\circ}C$). In this situation, three-dimensional flow analysis should be analyzed to investigate thermal effects such as pressure drop, temperature change, velocity deficit and distribution change of liquid droplet of internal fluid. Also, due to freezing of water droplet, impingement erosion is expected in the curved pipeline. The stability of the pipelines can be influenced by impingement erosion. In this paper, multi-phase and multi-species analysis was introduced to analyze the flow characteristics and impingement erosion of Arctic and ocean pipelines.

Emission Characteristics of Elemental Constituents in Fine Particulate Matter Using a Semi-continuous Measurement System (준 실시간 측정시스템을 이용한 미세입자 원소성분 배출특성 조사)

  • Park, Seung-Shik;Ondov, John M.
    • Journal of Korean Society for Atmospheric Environment
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    • v.26 no.2
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    • pp.190-201
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    • 2010
  • Fine particulate matter < $1.8{\mu}m$ was collected as a slurry using the Semicontinuous Elements in Aerosol Sampler with time resolution of 30-min between May 23 and 27, 2002 at the Sydney Supersite, Florida, USA. Concentrations of 11 elements, i.e., Al, As, Cd, Cr, Cu, Fe, Mn, Ni, Pb, Se, and Zn, in the collected slurry samples were determined off-line by simultaneous multi-element graphite furnace atomic absorption spectrometry. Temporal profiles of $SO_2$ and elemental concentrations combined with meteorological parameters such as wind direction and wind speed indicate that some transient events in their concentrations are highly correlated with the periods when the plume from an animal feed supplement processing facility influenced the Sydney sampling site. The peaking concentrations of the elemental species during the transient events varied clearly as the plume intensity varied, but the relative concentrations for As, Cr, Pb, and Zn with respect to Cd showed almost consistent values. During the transient events, metal concentrations increased by factors of >10~100 due to the influence of consistent plumes from an individual stationary source. Also the multi-variate air dispersion receptor model, which was previously developed by Park et al. (2005), was applied to ambient $SO_2$ and 8 elements (Al, As, Cd, Cr, Cu, Fe, Pb, and Zn) measurements between 20:00 May 23 and 09:30 May 24 when winds blew from between 70 and $85^{\circ}$, in which animal feed processing plant is situated, to determine emission and ambient source contributions rates of $SO_2$ and elements from one animal feed processing plant. Agreement between observed and predicted $SO_2$ concentrations was excellent (R of 0.99; and their ratio, $1.09{\pm}0.35$) when one emission source was used in the model. Average ratios of observed and predicted concentrations for As, Cd, Cr, Pb, and Zn varied from $0.83{\pm}0.26$ for Pb to $1.12{\pm}0.53$ for Cd.

Multi-type and shape data meta management and dynamic user configurable interface method (다종다형 자료 메타 관리 및 사용자 동적 구성 가능한 검색 인터페이스 제공 방안)

  • Choi, Myungjin;Kim, Taeyoung;Lee, Minseob;Yang, Yunjung;Yoon, Kyoungwon;Kim, Moongi
    • Journal of Satellite, Information and Communications
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    • v.12 no.1
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    • pp.81-87
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    • 2017
  • In this paper, we present the system that user can search and manage data using united interface and user can define search field dynamically. The feature of this system is that it is possible to manage multiple polymorphic meta information first. Second, there is a database integration bus that can support easy integration between the various systems. Third, it is possible to set the search item for each user which can customize polymorphism data for each user. The system studied in this paper is expected to be capable of managing big data, which is currently well received in the field of ICT. In addition, it will be possible to effectively manage multi-species polymorphic data in various fields in the future and to easily integrate between systems having various environments.