• Environmental Mutagens and Carcinogens
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• v.18 no.2
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• pp.83-88
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• 1998

To detect the mutation in a given sequence, there are variety of methods developed by use of the gel electrophoresis. One of the methods, TGGE (Temperature Gradient Gel Electrophoresis), is a popular technique because it can detect mutations in DNA fragment with ease and at low cost. This study used 200 bp BamHI-digested DNA fragment containing the human $\varepsilon$-globin promoter which was mutated[$\varepsilon$ F1*(-141), GATA- I*(-163), and GATA-1* & $\varepsilon$F1]. This BamHI-digested DNA fragment was directly used to detect the mutated DNA fragment on 50% denaturant gel with temperature gradient of 45$^{\circ}C$ through $53^{\circ}C$. In agreement with the theoretical result of MELTSCAN program (Brossette and Wallet, 1994) the mobilities of mutated DNA fragments were shown to be nearly distinguished on the temperature gradient gel. In contrast to the above result the heteroduplex analysis under the temperature gradient condition was shown to detect the mutated DNA fragments through the heteroduplex formation between strands of mutated DNA and wild-type DNA.

• Journal of Life Science
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• v.12 no.2
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• pp.208-212
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• 2002

Human $\varepsilon$-globin DNA fragment was used to determine the thermal stabilities of base pairs at d(CXG) and d(GXC) by Temperature Gradient Gel Electrophoresis(TGGE). The base pair stability depends on the hydrogen bonding interaction and base stacking interaction of neighbor base sequence. The orders of base pair stabilities were T.AG.A = A.G>C.T>T.C>C.A>A.C for d(GXC).d(GYC).

• Journal of Life Science
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• v.14 no.2
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• pp.309-314
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• 2004

Cyclic AMP receptor protein (CRP) is involved in the transcriptional regulation of more than 100 genes in E. coli. CRP dimer is converted into active form via the sequential conformation change of cAMP binding pocket, hinge region and HTH DNA binding motif by binding of cAMP. The temperature gradient gel electrophoresis (TGGE) was applied to CRP protein to know whether it was an efficient technique to study the conformational transitions and the thermal stability. TGGE showed the unfolding process of wild-type and S83G CRP proteins with the temperature gradient set from 29 to 71$^{\circ}C$ on nondenaturing polyacrylamide gel. Melting temperature (Tm) was 57$\pm$1 and 55$\pm$1$^{\circ}C$ for wild-type and S83G CRP, respectively in acidic buffer[89.8 mM Glycine and 24 mM Boric acid (pH 5.8)].

• Journal of Microbiology and Biotechnology
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• v.20 no.9
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• pp.1322-1330
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• 2010

Three types of nuruk were made from rice, wheat, and a rice-glasswort (6:4) mixture. Nuruk, makgeolli, and vinegar were manufactured with rice nuruk (RN), wheat nuruk (WN), and rice-glasswort nuruk (RGN). The variable region of 18S or 16S rDNA amplified with genomic DNA extracted directly from nuruk-, makgeolli-, and vinegar-making cultures was analyzed via temperature gradient gel electrophoresis (TGGE). The sequence of the 18S rDNA variable region extracted from the TGGE gel for nuruk was 99% homologous with Aspergillus sp. and that for the makgeolli-making culture was 99% homologous with Saccharomyces sp. and Saccharomycodes sp. The sequence of the 16S rDNA variable region extracted from TGGE gel for the vinegar-making culture was 98% homologous, primarily with the Acetobacter sp. The eukaryotic and prokaryotic diversities in the nuruk-, makgeolli-, and vinegar-making cultures was not significantly altered by the addition of glasswort. Prokaryotic diversity was higher than eukaryotic diversity in the nuruk, but eukaryotic diversity was higher than prokaryotic diversity in the makgeolli-making culture, on the basis of the TGGE patterns. No 18S rDNA was amplified from the DNA extracted from the vinegar-making culture. The diversity of the microbial community in the process from nuruk to vinegar was slightly affected by the type of raw material utilized for nuruk-making. The saccharifying activity and ethanol productivity of nuruk, polyphenol content in makgeolli, and acetic acid and polyphenol content in the vinegar were increased as a result of the addition of glasswort. In conclusion, the glasswort may be not simply an activator for the growth of microorganisms during the fermentation of nuruk, makgeolli, or vinegar, but also a nutritional supplement that improves the quality of vinegar.

• Journal of Microbiology and Biotechnology
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• v.19 no.12
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• pp.1665-1671
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• 2009

Anaerobic digestion sludge was cultivated in an electrochemical bioreactor (ECB) to enrich the hydrogenotrophic methanogens. A modified graphite felt cathode with neutral red (NR-cathode) was charged with electrochemical reducing power generated from a solar cell. The methane and carbon dioxide collected in a Teflon bag from the ECB were more than 80 ml/l of reactant/day and less than 20 ml/l of reactant/day, respectively, whereas the methane and carbon dioxide collected from a conventional bioreactor (CB) was around 40 ml/l of reactant/day, respectively. Moreover, the maximal volume ratios of methane to carbon dioxide (M/C ratio) collected in the Teflon bag from the ECB and CB were 7 and 1, respectively. The most predominant methanogens isolated from the CB on the $20^{th}$, $80^{th}$, and $150^{th}$ days of incubation were hydrogenotrophs. The methanogenic diversity analyzed by temperature gradient gel electrophoresis (TGGE) of the 16S rDNA variable region was higher in the ECB than in the CB. The DNA extracted from the TGGE bands was more than 95% homologous with hydrogenotrophic methanogens in the ECB, but was an aceticlastic methanogen in the CB. In conclusion, the ECB was demonstrated as a useful system for enriching hydrogenotrophic methanogens and increasing the M/C ratio of the gas product.

• Korean Journal of Soil Science and Fertilizer
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• v.49 no.2
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• pp.144-156
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• 2016

Soil is a dynamic biological system, in which it is difficult to determine the composition of microbial communities. Knowledge of microbial diversity and function in soils are limited because of the taxonomic and methodological limitations associated with studying the organisms. In this review, approaches to measure microbial diversity in soil were discussed. Research on soil microbes can be categorized as structural diversity, functional diversity and genetic diversity studies, and these include cultivation based and cultivation independent methods. Cultivation independent technique to evaluate soil structural diversity include different techniques such as Phospholipid Fatty Acids (PLFA) and Fatty Acid Methyl Ester (FAME) analysis. Carbon source utilization pattern of soil microorganisms by Community Level Physiological Profiling (CLPP), catabolic responses by Substrate Induced Respiration technique (SIR) and soil microbial enzyme activities are discussed. Genetic diversity of soil microorganisms using molecular techniques such as 16S rDNA analysis Denaturing Gradient Gel Electrophoresis (DGGE) / Temperature Gradient Gel Electrophoresis (TGGE), Terminal Restriction Fragment Length Polymorphism (T-RFLP), Single Strand Conformation Polymorphism (SSCP), Restriction Fragment Length Polymorphism (RFLP) / Amplified Ribosomal DNA Restriction Analysis (ARDRA) and Ribosomal Intergenic Spacer Analysis (RISA) are also discussed. The chapter ends with a final conclusion on the advantages and disadvantages of different techniques and advances in molecular techniques to study the soil microbial diversity.

• Journal of Microbiology and Biotechnology
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• v.21 no.6
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• pp.590-598
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• 2011

Bacterial assimilation of $CO_2$ into stable biomolecules using electrochemical reducing power may be an effective method to reduce atmospheric $CO_2$ without fossil fuel combustion. For the enrichment of the $CO_2$-fixing bacteria using electrochemical reducing power as an energy source, a cylinder-type electrochemical bioreactor with a built-in anode compartment was developed. A graphite felt cathode modified with neutral red (NR-graphite cathode) was used as a solid electron mediator to induce bacterial cells to fix $CO_2$ using electrochemical reducing power. Bacterial $CO_2$ consumption was calculated based on the variation in the ratio of $CO_2$ to $N_2$ in the gas reservoir. $CO_2$ consumed by the bacteria grown in the electrochemical bioreactor (2,000 ml) reached a maximum of approximately 1,500 ml per week. Time-coursed variations in the bacterial community grown with the electrochemical reducing power and $CO_2$ in the mineral-based medium were analyzed via temperature gradient gel electrophoresis (TGGE) of the 16S rDNA variable region. Some of the bacterial community constituents noted at the initial time disappeared completely, but some of them observed as DNA signs at the initial time were clearly enriched in the electrochemical bioreactor during 24 weeks of incubation. Finally, Alcaligenes sp. and Achromobacter sp., which are capable of autotrophically fixing $CO_2$, were enriched to major constituents of the bacterial community in the electrochemical bioreactor.