• Journal of Microbiology and Biotechnology
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• v.20 no.1
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• pp.21-29
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• 2010

The phenolic compounds are a major contaminant class often found in industrial wastewaters and the biological treatment is an alternative tool commonly employed for their removal. In this sense, monitoring microbial community dynamics is crucial for a successful wastewater treatment. This work aimed to monitor the structure and activity of the bacterial community during the operation of a laboratory-scale continuous submerged membrane bioreactor (SMBR), using PCR and RT-PCR followed by denaturing gradient gel electrophoresis (DGGE) and 16S rRNA libraries. Multivariate analyses carried out using DGGE profiles showed significant changes in the total and metabolically active dominant community members during the 4-week treatment period, explained mainly by phenol and ammonium input. Gene libraries were assembled using 16S rDNA and 16S rRNA PCR products from the fourth week of treatment. Sequencing and phylogenetic analyses of clones from the 16S rDNA library revealed a high diversity of taxa for the total bacterial community, with predominance of Thauera genus (ca. 50%). On the other hand, a lower diversity was found for metabolically active bacteria, which were mostly represented by members of Betaproteobacteria (Thauera and Comamonas), suggesting that these groups have a relevant role in the phenol degradation during the final phase of the SMBR operation.

• Reproductive and Developmental Biology
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• v.39 no.4
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• pp.105-115
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• 2015

Toll-like receptor 7 (TLR7) is critical for the triggering of innate immune response by recognizing the conserved molecular patterns of single-stranded RNA (ssRNA) viruses and mediated antigenic adaptive immunity. To understand how TLR7 distinguish pathogen-derived molecular patterns from the host self, it is essential to be able to identify TLR7 receptor interaction interfaces, such as active sites or R848-agonist binding sites. The functional interfaces of TLR7 can serve as targets for structure-based drug design in studying the TLR7 receptor's structure-function relationship. In contrast to mammalian TLR7, chicken TLR7 (chTLR7) is unknown for its important biological function. Therefore, it has been targeted to mediate contrasting evolutionary patterns of positive selection into non-synonymous SNPs across eleven species using TLR7 conservation patterns (evolutionary conserved and class-specific trace residues), where protein sequence differences to the TLR7 receptors of interest record mutation that have passed positive section across the species. In this study, we characterized the Lys609 residue on chTLR7-ECD homodimer interfaces to reflect the current tendency of evolving positive selection to be transfer into a stabilization direction of the R848-agonist/chTLR7-ECDs complex under the phylogenetically variable position across species and we suggest a potential indicator for contrasting evolutionary patterns of both the species TLR-ECDs.

• Asian Pacific Journal of Cancer Prevention
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• v.17 no.11
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• pp.4985-4989
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• 2016

Long non-coding RNAs (lncRNAs) are a novel class of non-protein coding RNAs that are involved in a wide variety of biological processes. There are limited data regarding the impact of lnc-LAMC2-1:1 rs2147578 as well as CASC8 rs10505477 T>C polymorphisms on cancer development. Here we examined for the first time whether rs2147578 and rs10505477 polymorphisms are associated with childhood acute lymphoblastic leukemia (ALL) in a total of 110 cases and 120 healthy controls. Genotyping was achieved by the polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) method. The rs2147578 variant increased the risk of ALL in codominant (OR=4.33, 95%CI=2.00-9.37, p<0.0001, CG vs CC, and OR=5.81, 95%CI=2.30-14.69, p=0.0002, GG vs CC), dominant (OR=4.63, 95%CI=2.18-9.86, p<0.0001, CG+GG vs CC), overdominant (OR=1.74, 95%CI=1.02-2.97, p=0.0444, CG vs CC+GG) and allele (OR=1.91, 95%CI=1.32-2.77, p=0.0008, G vs C) inheritance models tested. No significant association was found between the CASC8 rs10505477 T>C variant and risk of childhood ALL. In conclusion, the present study revealed that the lnc-LAMC2-1:1 rs2147578 polymorphism may be a risk factor for developing childhood ALL. Further studies with larger sample sizes with different ethnicities are now required to confirm our findings.

• Journal of Microbiology and Biotechnology
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• v.20 no.7
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• pp.1053-1060
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• 2010

Cordyceps militaris, an entomopathogenic fungus belonging to the class Ascomycetes, has been reported to have beneficial biological activities such as hypoglycemic, anti-inflammatory, antitumor, antimetastatic, hypolipidemic, immunomodulatory, and antioxidant effects. In this study, the crude water-soluble polysaccharide CMP, which was obtained from the fruiting body of C. militaris by hot water extraction and ethanol precipitation, was fractionated by DEAE-cellulose and Sepharose CL-6B column chromatographies. This process resulted in three polysaccharide fractions, termed CMP Fr I, CMP Fr II, and CMP Fr III. Of these fractions, CMP Fr II, with an average molecular mass of 127 kDa, was able to upregulate effectively the phenotypic functions of macrophages such as NO production and cytokine expression. The chemical property of the stimulatory polysaccharide, CMP Fr II, was determined based on its monosaccharide composition, which consisted of glucose (56.4%), galactose (26.4%), and mannose (17.2%). Its structural characteristics were investigated by a combination of chemical and instrumental analyses, including methylation, reductive cleavage, acetylation, Fourier transform infrared spectroscopy (FTIR), and gas chromatography-mass spectrometry (GCMS). Results indicated that CMP Fr II consisted of the (1${\rightarrow}$4) or (1${\rightarrow}$2) linked glucopyranosyl or galactopyranosyl residue with a (1${\rightarrow}$2) or (1${\rightarrow}$6) linked mannopyranosyl, glucopyranosyl, or galactopyranosyl residue as a side chain. The configuration of the ${\beta}$-linkage and random coil conformation of CMP Fr II were confirmed using a Fungi-Fluor kit and Congo red reagent, respectively.

• Journal of the Institute of Electronics and Information Engineers
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• v.51 no.5
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• pp.51-57
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• 2014

In this paper, we introduce the adaptive threshold detection scheme based on an evolutionary arithmetic algorithm for the M-ary holographic data storage(HDS) system. The genetic algorithm is a particular class of evolutionary arithmetic based on the process of biological evolution, which is a very promising technique for optimization problem and estimation applications. In this study, to improve the detection performance that is degraded by the HDS channel environment and the pixel misalignment, the threshold value was assumed to be a population set of the evolutionary algorithm. The proposed method can find an appropriate population set of bit threshold, which minimizes bit error rate(BER) as increased generation. For performance evaluation, we consider severe misalignment effect in the 4-ary holographic data storage system. Furthermore, we measure the BER performance and compare the proposed methods with the conventional threshold detection scheme, which verifies the superiority of the proposed scheme.

• Korean Journal of Agricultural Science
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• v.37 no.3
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• pp.435-449
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• 2010

Soils in the sloping uplands in Korea are subject to intensive land use with high input of agrochemicals and are vulnerable to soil erosion. Development of the environmentally sound land management strategy is essential for a sustainable production system in the sloping upland. This report addresses the status of upland agriculture and the best management practices for the uplands toward the sustainable agriculture. More than 60% of Korean lands are forest and only 21% are cultivating paddy and upland. Uplands are about 7% of the total lands and about 62% of the uplands are in the slopes higher than 7%. Due to the site-specificity of the upland, many managerial and environmental problems are occurring, such as severe erosion, shallow surface soils with rocky fragments, and loadings of non-point source (NPS) contaminants into the watershed. Based on the field trials, most of the sloping uplands were classified as Suitability Class III-V and the major limiting factor was slope and rock fragments. Due to this, soils were over-applied with N fertilizer, even though N rate was the recommendation. This resulted in decreases in yield, degradation of soil quality and increases in N loading to the leachate. Various case studies drew management practices toward sustainable production systems. The suggested BMP on the managerial, vegetative, and structural options were to practice buffer strips along the edges of fields and streams, winter cover crop, contour and mulching farming, detention weir, diversion drains, grassed waterway, and slope arrangement. With these options, conservation effects such as reductions in raindrop impact, flow velocity, runoff and sediment loss, and rill and gully erosion were observed. The proper management practice is a key element of the conservation of the soil and water in the sloping upland.

• Molecules and Cells
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• v.38 no.3
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• pp.243-250
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• 2015

Patterning of the polar axis during the early leaf developmental stage is established by cell-to-cell communication between the shoot apical meristem (SAM) and the leaf primordia. In a previous study, we showed that the DRL1 gene, which encodes a homolog of the Elongator-associated protein KTI12 of yeast, acts as a positive regulator of adaxial leaf patterning and shoot meristem activity. To determine the evolutionally conserved functions of DRL1, we performed a comparison of the deduced amino acid sequence of DRL1 and its yeast homolog, KTI12, and found that while overall homology was low, well-conserved domains were presented. DRL1 contained two conserved plant-specific domains. Expression of the DRL1 gene in a yeast KTI12-deficient yeast mutant suppressed the growth retardation phenotype, but did not rescue the caffeine sensitivity, indicating that the role of Arabidopsis Elongator-associated protein is partially conserved with yeast KTI12, but may have changed between yeast and plants in response to caffeine during the course of evolution. In addition, elevated expression of DRL1 gene triggered zymocin sensitivity, while overexpression of KTI12 maintained zymocin resistance, indicating that the function of Arabidopsis DRL1 may not overlap with yeast KTI12 with regards to toxin sensitivity. In this study, expression analysis showed that class-I KNOX genes were downregulated in the shoot apex, and that YAB and KAN were upregulated in leaves of the Arabidopsis drl1- 101 mutant. Our results provide insight into the communication network between the SAM and leaf primordia required for the establishment of leaf polarity by mediating histone acetylation or through other mechanisms.

• BMB Reports
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• v.35 no.3
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• pp.348-351
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• 2002

AquI DNA methyltransferase, M.AquI, catalyses the transfer of a methyl group from S-adenosyl-L-methionine to the C5 position of the outermost deoxycytidine base in the DNA sequence 5'CYCGRG3'. M.AquI is encoded by two overlapping ORFs (termed $\alpha$ and $\beta$) instead of the single ORF that is customary for Class II methyltransferase genes. The structural organization of the M.AquI protein sequence is quite similar to that of other bacterial C5-DNA methyltransferases. Ten conserved motifs are also present in the correct order, but only on two polypeptides. We separately subcloned the genes that encode the $\alpha$ and $\beta$ subunits of M.AquI into expression vectors. The overexpressed His-fusion $\alpha$ and $\beta$ subunits of the enzyme were purified to homogeneity in a single step by Nickel-chelate affinity chromatography. The purified recombinant proteins were assayed for biological activity by an in vitro DNA tritium transfer assay. The $\alpha$ and $\beta$ subunits of M.AquI alone have no DNA methyltransferase activity, but when both subunits are included in the assay, an active enzyme that catalyses the transfer of the methyl group from S-adenosyl-L-methionine to DNA is reconstituted. We also showed that the $\beta$ subunit alone contains all of the information that is required to generate recognition of specific DNA duplexes in the absence of the $\alpha$ subunit.

• Korean Journal of Fisheries and Aquatic Sciences
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• v.40 no.6
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• pp.367-373
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• 2007

We assessed the stock of the southern bluefin tuna (SBT, Thunnus maccoyii) by applying the MULTIFAN-CL model. The model is spatially disaggregated, with the population and fisheries stratified into a number of regions within the overall stock range. Catch, effort, length-frequency, and tagging data from 1965 to 2003 were stratified by three regions and four quarters (Jan-Mar, Apr-Jun, Jul-Sept and Oct-Dec). These data were used to estimate the instantaneous fishing mortality (F), biomass, spawning biomass, recruitment, and so on. The Commission for the Conservation of Southern Bluefin Tuna (CCSBT) used only Japanese data and did not consider migration for the SBT stock assessment. By contrast, we used Japanese, Australian, New Zealand, Taiwanese, and Korean data, and considered migration. As a result, the estimated annual average F of all age classes was 0.073/yr and the F of age class 6-10 was the highest. The results also showed that the biomass and recruitment of SBT had declined significantly after 1965. Compared with the CCSBT results, the estimated spawning biomass in this study was lower and more uncertain. However, we will conduct a sensitivity analysis to get more accurate biological parameters and results. In addition, we need to use the bootstrap resampling method to quantify the uncertainty.

• Asian Pacific Journal of Cancer Prevention
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• v.14 no.2
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• pp.765-768
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• 2013

Background and Aims: Prostate cancer is the most commonly diagnosed cancer in males in many populations. Metformin is the most widely used anti-diabetic drug in the world, and there is increasing evidence of a potential efficacy of this agent as an anti-cancer drug. Metformin inhibits the proliferation of a range of cancer cells including prostate, colon, breast, ovarian, and glioma lines. MicroRNAs (miRNAs) are a class of small, non-coding, single-stranded RNAs that downregulate gene expression. We aimed to evaluate the effects of metformin treatment on changes in miRNA expression in PC-3 cells, and possible associations with biological behaviour. Materials and Methods: Average cell viability and cytotoxic effects of metformin were investigated at 24 hour intervals for three days using the xCELLigence system. The $IC_{50}$ dose of metformin in the PC-3 cells was found to be 5 mM. RNA samples were used for analysis using custom multi-species microarrays containing 1209 probes covering 1221 human mature microRNAs present in miRBase 16.0 database. Results: Among the human miRNAs investigated by the arrays, 10 miRNAs were up-regulated and 12 miRNAs were down-regulated in the metformin-treated group as compared to the control group. In conclusion, expression changes in miRNAs of miR-146a, miR-100, miR-425, miR-193a-3p and, miR-106b in metformin-treated cells may be important. This study may emphasize a new role of metformin on the regulation of miRNAs in prostate cancer.