• Journal of Nutrition and Health
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• v.33 no.3
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• pp.271-278
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• 2000

Fecal microflora of 12 breast-fed(BF) and 15 formula-fed(FF) infants were investigated at 1 year after birth and the results were compared to those that had previously been obtained from the same subjects at 1 week after birth, and before and after weaning. At 1 year the two lactation groups showed no significant differences both in frequencies and numbers of each major bacterical species, except eubacteria, which showed higher frequency in FF infants. Bifidobacteria appeared as dominant species in 50% BF infants, heres bacteroides in 73.3% FF infants. Fecal pH was lower, though insignificant, in BF infants(6.5$\pm$0.4) than in FF infants(6.8$\pm$0.5). In BF infants, the number of bifidobacteria, clostridia, and E. coli deceased from birth up to 1 year, whereas the number of bacteroides similar trends to BF infants except that the number of bifidobacteria increased, but insignificantly. This research showed that the floral differences resulted not from the age, but from the types of feeding and that breast feeding and that breast feeding could be better than formula feeding in the BF infants had more stable floral composition and bowels with lower pH, which can play a protection role against pathogen infection.

• ALGAE
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• v.18 no.3
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• pp.183-190
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• 2003

Except for a group I intron in trnL-uaa occuring in eubacteria and plastids, group I introns are rarely documented in plastid genomes. Here, we report that a green alga, Caulerpa sertularioides, contains three group IA3 introns in the 16S gene (cpSSU), CS-cpSSU.i1, CS-cpSSU.i2 and CS-cpSSU.i3. Each intron has an open reading frame with LAGLIDADG motifs. CS-cpSSU.i1orf and CS-cpSSU.i3orf occur at Loop 6 in the intron secondary structure and CScpSSU. i2orf at Loop 8. CS-cpSSU.i1orf and CS-cpSSU.i2orf contain both LAGLI-DADG motifs but CS-cpSSU.i3orf has only one. CS-cpSSU.i1 and CS-cpSSU.i2 share the insetion sites and the ORFs at Loop 6 and 8 with CpSSU·1 and CpSSU·2 introns of Chlamydomonas pallidostigmatica (Chlorophyceae). In contrast, CS-cpSSU.i3, containing 28 copies of GAAATAT at Loop 6, is a novel intron found only in Caulerpa sertularioides. Possible scenarios of the evolution of the three introns and their possible use in systematic research are discussed.

• BMB Reports
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• v.33 no.1
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• pp.54-58
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• 2000

Recent research results regarding the very long chain transmembrane ${\alpha},{\omega}-dicarboxylic$ components in the membrane of extremophilic eubacteria, such as Sarcina ventriculi, Thennotoga maritima, and Thermoanaerobacter ethanolicus have raised interesting questions concerning the physical and biochemical function on these components in the membrane. In order to understand the dynamic characteristics of these acids which reside in the bilayer membrane, 580 ps molecular dynamic simulations at 300 K were performed for two model systems. These systems were the bilayer with regular chain (C16:0 or C18:1) fatty acid methyl esters and the fatty acid bilayer containing very long chain transmembrane dicarboxylic acid methyl esters (${\alpha},{\omega}-15,16-dimethyltriacotane-dioate$ dimethyl ester; C32:0). Our analyses indicate that very long chain transmembrane dicarboxylic acids have a noticeable influence on the bilayer dynamics at a sub-nanosecond time scale. The center-ofmass mean-squared-displacement (MSD) of regular chain fatty acids adjacent to the very long chain transmembrane dicarboxylic acids decreased, the long-axis order parameter increased, and the reorientational motions of methylene groups were slowed along the hydrocarbon chains. These results indicate that the very long chain transmembrane dicarboxylic acids reduce the molecular order of the whole bilayer membrane.

• Journal of Microbiology and Biotechnology
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• v.8 no.3
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• pp.280-283
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• 1998

We have cloned the RNA polymerase sigma-like factors from a wide range of actinomycetes by using specific primers with the polymerase chain reaction (PCR). The specific oligonucleotide primers were designed on the basis of amino acid sequences of conserved regions from HrdA, B, D of Streptomyces griseus as well as from the rpoD box of many eubacteria. The consensus sequences were from the rpoD box and helix-turn-helix motif involved in -35 recognition. The designed primers were successfully applied to amplify the DNA fragments of the hrd homolog genes from 8 different strains of actinomycetes which produce a wide variety of important antibiotics. The 480 bp of the DNA fragment was amplified from all 8 strains, and it was identified as a part of hrdA and hrdB as we designed. The deduced amino acid sequence of PCR-amplified DNA fragments were highly homologous to those of other known RNA polymerase sigma factors of S. griseus and Streptomyces aureofaciens. Therefore, this study with specifically designed primers will support rapid cloning of the RNA polymerase sigma factors which recognize different classes of promoters from actinomycetes, and it will also be helpful in understanding the relationship of promoters and sigma factors leading to heterogeneity of RNA polymerases in actinomycetes.

• Journal of Dairy Science and Biotechnology
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• v.21 no.2
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• pp.125-137
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• 2003

Bifidobacteria are normal inhabitants of the human gastrointestinal tract throughout lift, starting just days after birth, and are one of several predominant species of the colonic microflora, along with Peptostreptococcus, Eubacteria, Clostridia, and Bacteroides. Bifidobacteria differ from lactic acid bacteria in that they produce not only lactic acid but also acetic acid as major fermentation products. The classification of bifidobacteria has changed numerous times since they were discovered in 1899 in the feces of breast-fed infants. Since 1994, three additional species have been included in the list (B. lactis, B. inopinatum, and B. denticolens), with a current total of 32 species. A variety of probiotic effects of bifidobacteria are currently being investigated. Research reports suggests several potential probiotic advantages, in particular antimicrobial effects, immune-modulation reduction of the cancer risk, and modulation of gastrointestinal flora. As technological challenges related to viability and enumeration are being overcome, milks fermented with these anaerobic microorganisms(alone or in combination with lactic acid bacteria) are more able to provide consistently satisfying with large numbers of viable microorganisms. Over 70 products containing bifidobacteria are currently offered around the world, including fermented milks, cheese, buttermilk frozen desserts, candy, and pharmaceutical preparations.

• Molecules and Cells
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• v.20 no.1
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• pp.1-16
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• 2005

The peptidyl transferase center (PTC) is located in a protein free environment, thus confirming that the ribosome is a ribozyme. This arched void has dimensions suitable for accommodating the 3'ends of the A-and the P-site tRNAs, and is situated within a universal sizable symmetry-related region that connects all ribosomal functional centers involved in amino-acid polymerization. The linkage between the elaborate PTC architecture and the A-site tRNA position revealed that the A-to P-site passage of the tRNA 3'end is performed by a rotatory motion, which leads to stereochemistry suitable for peptide bond formation and for substrate mediated catalysis, thus suggesting that the PTC evolved by genefusion. Adjacent to the PTC is the entrance of the protein exit tunnel, shown to play active roles in sequence-specific gating of nascent chains and in responding to cellular signals. This tunnel also provides a site that may be exploited for local co-translational folding and seems to assist in nascent chain trafficking into the hydrophobic space formed by the first bacterial chaperone, the trigger factor. Many antibiotics target ribosomes. Although the ribosome is highly conserved, subtle sequence and/or conformational variations enable drug selectivity, thus facilitating clinical usage. Comparisons of high-resolution structures of complexes of antibiotics bound to ribosomes from eubacteria resembling pathogens, to an archaeon that shares properties with eukaryotes and to its mutant that allows antibiotics binding, demonstrated the unambiguous difference between mere binding and therapeutical effectiveness. The observed variability in antibiotics inhibitory modes, accompanied by the elucidation of the structural basis to antibiotics mechanism justifies expectations for structural based improved properties of existing compounds as well as for the development of novel drugs.

• Journal of Microbiology and Biotechnology
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• v.27 no.1
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• pp.130-140
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• 2017

It is vital to understand the changing characteristics of interphase microbial communities and interspecies synergism during the fermentation of Chinese liquors. In this study, microbial communities in the three indispensable phases (pit mud, zaopei, and huangshui) of Luzhou-flavored liquor manufacturing pits and their shifts during cellars use were first investigated by polyphasic culture-independent approaches. The archaeal and eubacterial communities in the three phases were quantitatively assessed by combined phospholipid ether lipids/phospholipid fatty acid analysis and fluorescence in situ hybridization. In addition, qualitative information regarding the microbial community was analyzed by PCR-denaturing gradient gel electrophoresis. Results suggested that the interphase microbial community profiles were quite different, and the proportions of specific microbial groups evolved gradually. Anaerobic bacteria and gram-positive bacteria were dominant and their numbers were higher in pit mud ($10^9$ cells/g) than in huangshui ($10^7$ cells/ml) and zaopei ($10^7$ cells/g). Hydrogenotrophic methanogenic archaea were the dominant archaea, and their proportions were virtually unchanged in pit mud (around 65%), whereas they first increased and then decreased in zaopei (59%-82%-47%) and increased with pit age in huangshui (82%-92%). Interactions between microbial communities, especially between eubacteria and methanogens, played a key role in the formation of favorable niches for liquor fermentation. Furthermore, daqu (an essential saccharifying and fermentative agent) and metabolic regulation parameters greatly affected the microbial community.

• Journal of Life Science
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• v.13 no.6
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• pp.856-864
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• 2003

The 16S rRNA gene is the most common gene in the phylogenetic analysis of procaryotes. However very high conservative of 16S rRNA has limitation in the discrimination of highly related organisms, hence other molecule was applied in this study and the result was compared with that of 16S rRNA. Three COGs (Clusters of Orthologous of protein) were only detected in 42 procaryotes ; transcription elongation facto. (COG0195), bacterial DNA primase (COG0358) and uridylate kinase (COG0528). Uridylate kinase gene was selected because of the similarity and one single copy number in each genome. Bacteria, belong to same genus, and Archaebacteria were same position with high bootstrap value in phylogenetic tree like the tree of 16S rRNA. However, alpha and epsilon Proteobcteria showed different position and Spirochaetales of Eubarteria was grouped together with Archaebacteria unlike the result of 16S rRNA. Uridylate kinase may compensate the problem of very high conservative of 16S rRNA gene and it would help to access more accurate discrimination and phylogenetic analysis of bacteria.

• Journal of Korean Society of Environmental Engineers
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• v.27 no.12
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• pp.1311-1320
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• 2005

The purpose of this research is to survey characteristics of microbial community and the removal efficiency of organic materials for biological activated carbon in water treatment plant. Coal based activated carbon retained more attached bacterial biomass on the surface of the activated carbon than the other activated carbon with operating time and materials. The heterotrophic plate count(HPC), eubacteria(EUB) and 4,6-diamidino-2-phenylindole(DAPI) counts were ranged from $0.95{\times}10^7$ to $52.4{\times}10^7$ CFU/g, from $3.8{\times}10^8$ to $134.2{\times}10^8$ cells/g and from $7.0{\times}10^8$ to $250.2{\times}10^8$ cells/g, respectively. The biomass of EUB and DAPI appeared to be much more $10^2$ than HPC, which were increasing in bed volume of 20,000 at the stage of steady-state. The change of microbial community by analyzing fluorescent in situ hybridization(FISH) method with rRNA-targeted oligonucleotide probes, the dominant group was $\alpha$-proteobacteria($\alpha$ group) and high G+C content bacteria(HGC) the lowest distributing rate before reaching the bed volume of 20,000. After reaching the bed volume of 20,000, $\alpha$ group and other groups of bacteria became decreased, on the other hand, the proportion of both $\beta$-proteobacteria($\beta$ group) and $\gamma$-proteobacteri($\gamma$ group) were increasing. Coconut and wood based activated carbons had similar trend with coal based activated carbon, but the rate of $\alpha$ group on coal based activated carbon had gradually increased. Bacterial production with the operating period appeared highest in coal based activated carbon at the range of $1.2{\sim}3.4\;mg-C/m^3{\cdot}h$ while the coconut and wood based activated carbon were ranged from 1.1 to 2.6 $mg-C/m^3{\cdot}h$ and from 0.7 to 3.5 $mg-C/m^3{\cdot}h$ respectively. The removal efficiency of assimilable organic carbon(AOC) showed to be highly correlated with bacterial production. The correlation coefficient between removal efficiency of AOC and bacterial production were 0.679 at wood based activated carbon, 0.291 at coconut based activated carbon and 0.762 at coal based activated carbon, respectively.

• Journal of Life Science
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• v.25 no.9
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• pp.1007-1013
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• 2015

A COG (Cluster of Orthologous Groups of proteins) algorithm was applied to detect conserved genes in 711 prokaryotes. Only COG0080 (ribosomal protein L11) was common among all the 711 prokaryotes analyzed and 58 COGs were common in more than 700 prokaryotes. Nine COGs among 58, including COG0197 (endonuclease III) and COG0088 (ribosomal protein L4), were conserved in a form of one gene per one organism. COG0008 represented 1356 genes in 709 of the prokaryotes and this was the highest number of genes among 58 COGs. Twenty-two COGs were conserved in more than 708 prokaryotes. Of these, two were transcription related, four were tRNA synthetases, eight were large ribosomal subunits, seven were small ribosomal subunits, and one was translation elongation factor. Among 58 conserved COGs in more than 700 prokaryotes, 50 (86.2%) were translation related, and four (6.9%) were transcription related, pointing to the importance of protein-synthesis in prokaryotes. Among these 58 COGs, the most conserved COG was COG0060 (isoleucyl tRNA synthetase), and the least conserved was COG0143 (methionyl tRNA synthetase). Archaea and eubacteria were discriminated in the genomic analysis by the average distance and variation in distance of common COGs. The identification of these conserved genes could be useful in basic and applied research, such as antibiotic development and cancer therapeutics.