• Genomics & Informatics
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• v.16 no.2
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• pp.22-29
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• 2018

Incorporation of unique barcodes into fission yeast gene deletion collections has enabled the identification of gene functions by growth fitness analysis. For fine tuning, it is important to examine barcode sequences, because mutations arise during strain construction. Out of 8,708 barcodes (4,354 strains) covering 88.5% of all 4,919 open reading frames, 7,734 barcodes (88.8%) were validated as high-fidelity to be inserted at the correct positions by Sanger sequencing. Sequence examination of the 7,734 high-fidelity barcodes revealed that 1,039 barcodes (13.4%) deviated from the original design. In total, 1,284 mutations (mutation rate of 16.6%) exist within the 1,039 mutated barcodes, which is comparable to budding yeast (18%). When the type of mutation was considered, substitutions accounted for 845 mutations (10.9%), deletions accounted for 319 mutations (4.1%), and insertions accounted for 121 mutations (1.6%). Peculiarly, the frequency of substitutions (67.6%) was unexpectedly higher than in budding yeast (~28%) and well above the predicted error of Sanger sequencing (~2%), which might have arisen during the solid-phase oligonucleotide synthesis and PCR amplification of the barcodes during strain construction. When the mutation rate was analyzed by position within 20-mer barcodes using the 1,284 mutations from the 7,734 sequenced barcodes, there was no significant difference between up-tags and down-tags at a given position. The mutation frequency at a given position was similar at most positions, ranging from 0.4% (32/7,734) to 1.1% (82/7,734), except at position 1, which was highest (3.1%), as in budding yeast. Together, well-defined barcode sequences, combined with the next-generation sequencing platform, promise to make the fission yeast gene deletion library a powerful tool for understanding gene function.

• Molecules and Cells
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• v.37 no.7
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• pp.547-553
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• 2014

Glioblastoma multiforme (GBM) is one of the most common brain malignancies and has a very poor prognosis. Recent evidence suggests that the presence of cancer stem cells (CSC) in GBM and the rare CSC subpopulation that is resistant to chemotherapy may be responsible for the treatment failure and unfavorable prognosis of GBM. A garlic-derived compound, Z-ajoene, has shown a range of biological activities, including anti-proliferative effects on several cancers. Here, we demonstrated for the first time that Z-ajoene specifically inhibits the growth of the GBM CSC population. CSC sphere-forming inhibition was achieved at a concentration that did not exhibit a cytotoxic effect in regular cell culture conditions. The specificity of this inhibitory effect on the CSC population was confirmed by detecting CSC cell surface marker CD133 expression and biochemical marker ALDH activity. In addition, stem cell-related mRNA profiling and real-time PCR revealed the differential expression of CSC-specific genes, including Notch, Wnt, and Hedgehog, upon treatment with Z-ajoene. A proteomic approach, i.e., reverse-phase protein array (RPPA) and Western blot analysis, showed decreased SMAD4, p-AKT, 14.3.3 and FOXO3A expression. The protein interaction map (http://string-db.org/) of the identified molecules suggested that the AKT, ERK/p38 and $TGF{\beta}$ signaling pathways are key mediators of Z-ajoene's action, which affects the transcriptional network that includes FOXO3A. These biological and bioinformatic analyses collectively demonstrate that Z-ajoene is a potential candidate for the treatment of GBM by specifically targeting GBM CSCs. We also show how this systemic approach strengthens the identification of new therapeutic agents that target CSCs.

• Journal of Korean Society of Occupational and Environmental Hygiene
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• v.19 no.3
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• pp.213-232
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• 2009

This document was prepared to review and summarize the analytical methods for airborne and bulk asbestos. Basic principles, shortcomings and advantages for asbestos analytical instruments using phase contrast microscopy(PCM), polarized light microscopy(PLM), X-ray diffractometer (XRD), transmission electron microscopy(TEM), scanning electron microscopy(SEM) were reviewed. Both PCM and PLM are principal instrument for airborne and bulk asbestos analysis, respectively. If needed, analytical electron microscopy is employed to confirm asbestos identification. PCM is used originally for workplace airborne asbestos fiber and its application has been expanded to measure airborne fiber. Shortcoming of PCM is that it cannot differentiate true asbestos from non asbestos fiber form and its low resolution limit ($0.2{\sim}0.25{\mu}m$). The measurement of airborne asbestos fiber can be performed by EPA's Asbestos Hazard Emergency Response Act (AHERA) method, World Health Organization (WHO) method, International Standard Organization (ISO) 10312 method, Japan's Environmental Asbestos Monitoring method, and Standard method of Indoor Air Quality of Korea. The measurement of airborne asbestos fiber in workplace can be performed by National Institute for Occupational Safety and Health (NIOSH) 7400 method, NIOSH 7402 method, Occupational Safety and Health Administration (OSHA) ID-160 method, UK's Health and Safety Executive(HSE) Methods for the determination of hazardous substances (MDHS) 39/4 method and Korea Occupational Safety and Health Agency (KOSHA) CODE-A-1-2004 method of Korea. To analyze the bulk asbestos, stereo microscope (SM) and PLM is required by EPA -600/R-93/116 method. Most bulk asbestos can be identified by SM and PLM but one limitation of PLM is that it can not see very thin fiber (i.e., < $0.25{\mu}m$). Bulk asbestos analytical methods, including EPA-600/M4-82-020, EPA-600/R-93/116, OSHA ID-191, Laboratory approval program of New York were reviewed. Also, analytical methods for asbestos in soil, dust, water were briefly discussed. Analytical electron microscope, a transmission electron microscope equipped with selected area electron diffraction (SAED) and energy dispersive X-ray analyser(EDXA), has been known to be better to identify asbestiform than scanning electron microscope(SEM). Though there is no standard SEM procedures, SEM is known to be more suitable to analyze long, thin fiber and more cost-effective. Field emission scanning electron microscope (FE-SEM) imaging protocol was developed to identify asbestos fiber. Although many asbestos analytical methods are available, there is no method that can be applied to all type of samples. In order to detect asbestos with confidence, all advantages and disadvantages of each instrument and method for given sample should be considered.

• Korean Journal of Soil Science and Fertilizer
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• v.41 no.4
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• pp.267-272
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• 2008

Mid-infrared (MIR) spectroscopy, particularly Fourier transform infrared spectroscopy (FTIR), has emerged as an important analytical tool in quantification as well as identification of multi-atomic inorganic ions such as nitrate. In the present study, the possibility of quantifying soil nitrate via diffuse reflectance infrared Fourier transform spectroscopy (DRIFTS) without change of a sample phase or with least treated samples was examined. Four types of soils were spectrally characterized in terms of unique bands of soil contents and interferences with nitrate bands in the range of $2000-1000cm^{-1}$. In order to reduce the effects of soil composition on calibration model for nitrate, spectra transformed to the 1st order derivatives were used in the partial least squared regression (PLSR) model and the classification procedure associated with input soil types was involved in calibration system. PLSR calibration models for each soil type provided better performance results ($R^2$>0.95, RPD>6.0) than the model considering just one type of soil as a standard.

• Analytical Science and Technology
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• v.13 no.2
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• pp.136-150
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• 2000

For the identification of unknown drugs in biological samples, we attempted rapid high performance thin layer chromatographic method which is sensitive and selective chromatographic analysis of high performance thin layer chromatography (HPTLC) with automated TLC sampler and ultra-violet (UV) scanner. We constructed HPTLC database (DB) on two hundred five drugs by using the data of Rf values and UV spectra (scan 200-360 nm) as well as gas chromatography/mass spectrometry (GC/MS) DB on ninety six drugs by using the data of relative retention time (RRT) on lidocain and mass spectra. After extracting drugs in biological sample by solid phase extraction (Clean Screen ZSDAU020), we applied them to HPTLC and GC/MS DB. Drugs, especially extracted from biological samples, showed good matching ratio to HPTLC DB and these drugs were confirmed by GC/MS. In conclusion, this DB system is thought to be very useful method for the screening of unknown drugs in biological samples.

• Korean Journal of Microbiology
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• v.35 no.2
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• pp.158-163
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• 1999

A ploygalacturonase-produchg yeast was isolated from Cheju soil by selective eivichment media. One strain which has the highesl activity of polygalacturonase was selected. The characle~ishcs of the strain CS-2 were as follows: CS-2 utilized xylose. sucrose, maltose, u.ehalose, cellobiose. melibiose, lactose, raffinose, inosiiol, dulicilol, and dextrose, but did not utilized galactose, nitrate. nit~te, and lysine. Growth of CS-2 was inhibited by cyclohexamide, 1% acetic acid, and high concenaation (over 50%) of glucose. It grew at $30^{\circ}C$ but did 'IIOL $35^{\circ}C$. The cell size ofthe strain CS-2 was 2.9 p ~ n in length and 1.3 $\mu$ in diameter. Vegetable reproductmn was multiple budding and ascospre was present I to 4. Pseudomycelia or true myceliua formation were not observed In any of the cullureq. These results suggest that strain CS-2 is most likely a strain related Cryptococcus spp. (Cryptococcu spp. CS-2). When polygalacturonase or ihe yeast was induced by addition of polygalactoronic acid, polygalacturonase activity was detected in culture supernatent. There was a peak of specific activity a1 he mid-stationary phase(3 days culture) of growth. Polygalacturonase specific activity of Crylmcoccus sp. CS-2 was 2.96 unitsling. The molecular weighl ol'polygalacturonase was showed to be 46 KDa by both SDS-PAGE and activity stailling.

• Economic and Environmental Geology
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• v.40 no.5
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• pp.563-574
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• 2007

Laser induced breakdown spectroscopy (LIBS) is a recently developed analytical technique that is based upon the measurement of emission lines generated by atomic species close to the surface of the sample, thus allowing their chemical detection, identification and quantification. With powerful advantages of LIBS compared to the conventional analytical methodology, this technique can be applied in the detection of heavy metals in the field. LIBS allows the rapid analysis by avoiding laborious chemical steps. LES have already been applied for the determination of element concentration in a wide range of materials in the solid, liquid and gaseous phase with simplicity of the instrument and diversity of the analytical application. These feasibility of rapid multi elemental analysis are appealing proprieties for the in-situ analytical technique in geochemical investigation, exploration and environmental analysis. There remain still some limitations to be solved for LIBS to be applied in soil environment as an in-situ analytical technology. We would like to provide the basic principle related to the plasma formation and laser-induced breakdown of sample materials. In addition, the matrix effect, laser properties and the various factors affecting on the analytical signal of LIBS was dealt with to enhance understanding of LIBS through literature review. Ultimately, it was investigated the feasibility of LIBS application in soil environment monitoring by considering the basic idea to enhance the data quality of LIBS including the calibration method for the various effects on the analytical signal of LIBS.

• Analytical Science and Technology
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• v.27 no.5
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• pp.243-247
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• 2014

Formaldehyde is defined as carcinogen causing leukaemia, lymphoma or nasopharyngeal carcinoma at high level of exposure. Furniture-manufacturing workers can be exposed to formaldehyde, which implies serious impact on health of the workers. The authors carried out ambient monitoring of formaldehyde in the field, and identified the source of formaldehyde generated during the working process by testing the condition in the laboratory settings. After sampling formaldehyde in the air with 2,4-DNPH (2,4-dinitrophenylhydrazine) coated silica gel, we extracted formaldehyde derivative with acetonitrile and analyzed the extract using HPLC with UV detector at 360 nm. Formaldehyde was separated by ACQUITY UPLC BEH $C_{18}$ column at a flow rate of 0.5 mL/min using 45% acetonitrile as mobile phase. The workers were exposed to higher level of formaldehyde than normal air. Formaldehyde up to 0.31 ppm was detected in the process of veneer attachment, which exceeded 0.3 ppm, the ceiling value of ACGIH standard. The laboratory test of measuring formaldehyde generated from the glue and veneer used in the attachment process resulted in more formaldehyde generation as the temperature increased, and more from the veneer. Heating the veneer to $100-150^{\circ}C$ following the real condition of the manufacturing site generated 1.14-2.70 ppm of formaldehyde from the sample, which was 2-5 times higher level than Korean limit of exposure (0.5 ppm). As the workers handling and processing the veneer which was produced by wet process had high possibility to be exposed to formaldehyde, urgent improvement and management of working environment of furniture manufacturer is demanded.

• Journal of Food Hygiene and Safety
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• v.6 no.3
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• pp.147-155
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• 1991

Enterotoxigenic E. coli is one of the major causative agents of the infantile diarrhea and traveler's diarrhea. The heat-stable enterotoxin(ST) is thought to be a virulence factor in the pathogenesis of the diarrhea and to be a maker for identification of the enterotoxingeic E. coli from non pathogenic E. coli. The isolate of enterotoxigenlc E. coli was isolated from swine during 1989 year(from 5 to 10 month) in the Kyong-gi and Chung-Cheong provinces, and three strains(KM-4, KM-7 and KM-12) was selected from 189 isolates of ST producing E. coli. The detection of a ST produced of the isolated E. coli was performed by the infant mouse assay(IMA). This study was designed to know optimal conditions for the production of the ST and the molecular properties of plasmids of the enterotoxigenic E. coli. Amount of ST produced were the most at initial pH 8.5~9.0 of succinate salts medium culture. The cultural time of the same medium was accumulated the highest level of ST was at the 14 to 16 hours, and then stationary phase was at the 20 hours. From this experiment the KM-7 strain was selected among ST producing strains by IMA. Partial plasmid-curing experiment was done to select plasmid encoding for ST among other plasmids and then comparing the plasmid pattern of ST producing strain(KM-7) with those of other ST non-producing strains, it is found that ST gene exists on the about 80 Kbp plasmid. Each fragment of this plasmid digested with EcoRl was ligated to vector pBR 322 and transformed into E. coli K-12. A clone producing ST(eKT 53) was selected by IMA. The EcoRl digestion pattern of the isolated plasmid(pKD 37) from the ST producing clone it is indicated that the size of the inserted fragment in eKT 53 strain is 16 Kbp. The cultured supernatant of eKT 53 strain was positive result of ST production in IMA.

• Korean Journal of Food Science and Technology
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• v.7 no.1
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• pp.15-21
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• 1975

Soong-Neung is a Korean traditional beverage served after meals and is made from cooked and roasted rice produced on the bottom of the container during the rice cooking process. The volatiles from the extract of cooked and roasted rice were separated into pyrazine and carbonyl fractions and qualitatively investigated. The pyrazine fraction was characterized by gas chromatography and combined gas chromatography-mass spectrometry and five pyrazines were positively identified. Pyrazine compounds identified are 2-methylpyrazine, 2,3-dimethylpyrazine, 2,5-dimethylpyrazine, 2-ethyl-5-methylpyrazine and 2-ethyl-3-methylpyrazine. Carbonyls were converted to their 2,4-dinitrophenylhydrazones and identified by gas chromatography, combined gas chromatography-mass spectrometry and thin layer chromatography. Acetaldehyde, propionaldehyde, iso-butyraldehyde and iso-valeraldehyde were positively identified in the carbonyl compounds. The aroma of the fractions indentified as 2,3-dimethylpyrazine and 2,5-dimethylpyrazine had a nut-like or roasted cereal-like flavor, which is one of the characteristic flavors of Soong-Neung.