• The Plant Pathology Journal
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• v.22 no.2
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• pp.139-146
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• 2006

The 3' region of Potato virus X (PVX) has the 74 nt 3'-nontranslated region (NTR) that is conserved among all potexviruses and contains several cis-acting elements for minus-strand and plus-strand RNA accumulation. Three stem-loop structures (SL1-SL3), especially formation of SL3 and U-rich sequence of SL2, and near upstream elements in the 3' NTR were previously demonstrated as important cis-acting elements. To Investigate the binding of these cis-acting elements within 3' end with host protein, we used the electrophoretic mobility shift assays (EMSA) and UV-cross linking analysis. The EMSA with cellular extracts from tobacco and RNA transcripts corresponding to the 150 nt of the 3' end of PVX RNA showed that the 3' end of PVX formed complexes with cellular proteins. The specificity of protein binding was confirmed through competition assay by using with 50-fold excess of specific and non-specific probes. We also conducted EMSA with RNAs containing various mutants on those cis-acting elements (${\Delta}10$10, SL3B, SL2A and ${\Delta}21$; J Mol Biol 326, 701-720) required for efficient PVX RNA accumulation. These analyses supported that these cis-acting elements are required for interaction with host protein(s). UV-cross linking analysis revealed that at least three major host proteins of about 28, 32, and 42 kDa in mass bound to these cis-elements. These results indicate that cis-acting elements from 3' end which are important for minus and plus-strand RNA accumulation are also required for host protein binding.

• Mass Spectrometry Letters
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• v.4 no.2
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• pp.30-33
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• 2013

Chalcones are naturally occurring, biologically active molecules generating interest from a wide range of research applications including synthetic methodology development, biological activity investigation and studying fragmentation patterns. In this article, a series of chalcones has been synthesized and their fragmentation behavior was studied using modern ambient ionization technique Direct Analysis in Real Time (DART). DART ion source connected with an ion trap mass spectrometer was used for the fragmentation of various substituted chalcones. The chalcones were introduced to the DART source using a glass capillary without sample preparation step. All the chalcones showed prominent molecular ion peaks $[M]^{{\cdot}+}$ corresponding to the structures. Multistage mass spectral data $MS^n$ ($MS^2$ and $MS^3$) were collected for all the chalcones studied. The chalcones with substitutions at 3, 4 or 5 positions gave product ion peaks with the loss of a phenyl radical ($Ph^{\cdot}$) by radical initiated ${\alpha}$-cleavage, while substitution at 2 position of chalcone in the A-ring gave a product ion peak with the loss of substituted styryl radical (PhCH = $CH^{\cdot}$). In case of the chalcones with the substituent at 4 positions in A and B rings gave both types of fragmentation patterns. In conclusion, chalcones can be easily characterized using modern DART interface in very short time and efficiently without any cumbersome sample pretreatment.

• Asian-Australasian Journal of Animal Sciences
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• v.23 no.10
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• pp.1386-1398
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• 2010

Soybean contains a high concentration of carbohydrates that consist mainly of non-starch polysaccharides (NSP) and oligosaccharides. The NSP can be divided into insoluble NSP (mainly cellulose) and soluble NSP (composed mainly of pectic polymers, which are partially soluble in water). Monogastric animals do not have the enzymes to hydrolyze these carbohydrates, and thus their digestion occurs by means of bacterial fermentation. The fermentation of soybean carbohydrates produces short chain fatty acids that can be used as an energy source by animals. The utilization efficiency of the carbohydrates is related to the chemical structure, the level of inclusion in the diet, species and age of the animal. In poultry, soluble NSP can increase digesta viscosity, reduce the digestibility of nutrients and depress growth performance. In growing pigs, these effects, in particular the effect on gut viscosity, are often not so obvious. However, in weaning piglets, it is reported that soy oligosaccharides and soluble NSP can cause detrimental effects on intestinal health. In monogastrics, consideration must be given to the anti-nutritive effect of the NSP on nutrient digestion and absorption on one hand, as well as the potential benefits or detriments of intestinal fermentation products to the host. This mirrors the needs for i) increasing efficiency of utilization of fibrous materials in monogastrics, and ii) the maintenance and improvement of animal health in antibiotic-free production systems, on the other hand. For example, ethanol/water extraction removes the low molecular weight carbohydrate fractions, such as the oligosaccharides and part of the soluble pectins, leaving behind the insoluble fraction of the NSP, which is devoid of anti-nutritive activities. The resultant product is a high quality soy protein concentrate. This paper presents the composition and chemical structures of carbohydrates present in soybeans and discusses their nutritive and anti-nutritive effects on digestion and absorption of nutrients in pigs and poultry.

• Journal of the Korean Applied Science and Technology
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• v.29 no.1
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• pp.95-101
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• 2012

To manufacture of a completely biodegradable and compostable biomass -based blend polymer film, two types of cellulose acetates(DS=2.4 and DS=2.7) were blended with 5 - 50 wt% of low average molecular weight polylactide(PLA) by mixing each polymer solution having same viscosity in 10 wt% methanol/dichloromethane. Their surface morphology, thermal and mechanical properties were studied. The chemical structures of blend films were confirmed by the fourier transform IR spectroscopy with attenuated total reflection(FT-IR ATR) spectrophotometer. Scanning electron microscope(SEM) photos of blend films of both CAs with less than 5 % of PLA showed homogeneous morphology. On the contrary, the other blends with higher than 20 wt% of PLA content showed a large phase separation with spherical domains. The thermal property of blend films was also analyzed with thermogravimetric analysis(TGA) and differential scanning calorimeter(DSC). The tensile strength of CA/PLA blend films was increased up to $820kg_f/cm^2$ for TAC/PLA and $600kg_f/cm^2$ for DAC/PLA.

• Asian-Australasian Journal of Animal Sciences
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• v.29 no.12
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• pp.1696-1701
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• 2016

Japanese quail is still used as a model for poultry research because of their usefulness as laying, meat, and laboratory animals. Microsatellite markers are the most widely used molecular markers, due to their relative ease of scoring and high levels of polymorphism. The objective of the research was to determine genetic diversity and population genetic structures of selected Japanese quail lines (high body weight 1 [HBW1], HBW2, low body weight [LBW], and layer [L]) throughout 15th generations and an unselected control (C). A total of 69 individuals from five quail lines were genotyped by fifteen microsatellite markers. When analyzed profiles of the markers the observed ($H_o$) and expected ($H_e$) heterozygosity ranged from 0.04 (GUJ0027) to 0.64 (GUJ0087) and 0.21 (GUJ0027) to 0.84 (GUJ0037), respectively. Also, $H_o$ and $H_e$ were separated from 0.30 (L and LBW) to 0.33 (C and HBW2) and from 0.52 (HBW2) to 0.58 (L and LBW), respectively. The mean polymorphic information content (PIC) ranged from 0.46 (HBW2) to 0.52 (L). Approximately half of the markers were informative ($PIC{\geq}0.50$). Genetic distances were calculated from 0.09 (HBW1 and HBW2) to 0.33 (C and L). Phylogenetic dendrogram showed that the quail lines were clearly defined by the microsatellite markers used here. Bayesian model-based clustering supported the results from the phylogenetic tree. These results reflect that the set of studied markers can be used effectively to capture the magnitude of genetic variability in selected Japanese quail lines. Also, to identify markers and alleles which are specific to the divergence lines, further generations of selection are required.

• BMB Reports
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• v.37 no.6
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• pp.657-662
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• 2004

Oligoribonucleotides containing 8-oxo-7,8-dihydroguanosine (8-oxoG) and 8-oxo-7,8-dihydro-2'-O-methylguanosine (8-oxoG-Me) were synthesized. The base pairing properties of 8-oxoG and 8-oxoG-Me in oligoribonucleotide in cDNA synthesis by reverse transcriptases were studied. dCMP was preferentially incorporated into the site opposite 8-oxoG or 8-oxoG-Me than into other dNMPs. TMP and dCMP were inserted preferentially into sites opposite 8-oxoG or 8-oxoG by reverse transcriptases. HIV-RT did not incorporate TMP, but RAV2-RT incorporated 50% more TMP than dCMP into the site opposite 8-oxoG. In the site opposite 8-oxoG-Me TMP was substantially incorporated by HIV-RT or RAV2-RT. Thermodynamic analysis of the DNA. RNA heteroduplex containing 8-oxoG revealed that 8-oxoG and 8-oxoG-Me formed base pairs with cytidine and thymidine with similar stability. The thermodynamic parameter (${\Delta}G^{\circ}$) demonstrated that the formation of duplexes between 8-oxoG or 8-oxoG-Me and cytidine or thymidine is more thermodynamically favorable than with adenosine and guanosine. However, differences in the melting temperature and ${\Delta}G^{\circ}$'s of 8-oxoG/dC and 8-oxoG/T were much smaller than between G/dC and G/T. CD spectra showed that DNA . RNA containing 8-oxoG or 8-oxoG-Me duplexes showed similarities between the A-type RNA and B-type DNA conformations.

• KSBB Journal
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• v.24 no.5
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• pp.458-462
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• 2009

Silk fibroin is a structural protein from Bombyx mori and can be sulfated to provide biofunctional polypeptides showing antiviral and anticoagulating activities. However, the sulfated fibroins have not been characterized enough to present their compositions and structures. In this report, sulfation reaction was investigated by varying the reaction temperature and sulfuric acid concentration and analysis of the resulting peptides were carried out. The degree of sulfation was proportion to sulfuric acid concentration but the maximum product yield was obtained at $60^{\circ}C$ and 5% of sulfuric acid concentration. FT-IR spectrum, UV absorption and NMR spectrum support that o-sulfate ester was formed at the hydroxyl group of serine and tyrosine residues. Size exclusion chromatography identified that sulfated fibroin was composed of a highly hydrolyzed polypeptide mixtures and peptides of relatively higher molecular weight.

• Journal of Microbiology and Biotechnology
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• v.23 no.6
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• pp.739-749
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• 2013

The seasonal and spatial diversity of picocyanobacteria (Pcy) in lakes of the Great Mazurian Lakes (GLM) system was examined by DGGE analysis of molecular markers derived from the 16S-23S internal transcribed spacer (ITS) of the ribosomal operon and the phycocyanin operon (cpcBA-IGS). The study of nine lakes, ranging from mesotrophy to hypereutrophy, demonstrated seasonal variance of Pcy. The richness and Shannon diversity index calculated on the basis of both markers were higher in spring and lower in early and late summer. No statistically significant relationships were found between the markers and trophic status of the studied lakes or Pcy abundance. There were, however, statistically significant relationships between the diversity indices and sampling time. The analysis pointed to a different distribution of the two markers. The ITS marker exhibited more unique sequences in time and space, whereas a greater role for common and ubiquitous sequences was indicated by the cpcBA-IGS data. Examination of the Pcy community structure demonstrated that communities were grouped in highly similar clusters according to sampling season/time rather than to the trophic status of the lake. Our results suggest that time is more important than trophic status in shaping the diversity and structure of Pcy communities. The seasonal changes in picocyanobacteria and differences in diversity and community structures are discussed in the context of well-established ecological hypotheses: the PEG model, intermediate disturbance hypothesis (IDH), and horizontal gene transfer (HGT).

• Journal of the Korean Society of Groundwater Environment
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• v.4 no.2
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• pp.103-108
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• 1997

A series of batch tests were conducted to evaluate the design parameters for the application of soil washing techniques to the hydrophobic organic compounds (HOCs)-contaminated soil using mixed surfactants. Because the mixed surfactants form different structures of molecular aggregates from single surfactant, they were applied to improve the washing efficiency. Kinds of surfactants added, mixing ratio, and total concentration of mixed surfactants were evaluated. The uncontaminated soil was obtained from a country hill near Nock-Chun Station in Seoul. The portion of soil passing #4 (4.75 mm) sieve was used. The pH, organic contents and cation exchange capacity were 4.4, 1.6% and 4.08 meq/100 g, respectively The soil was artificially contaminated by n-dodecane. The 5% solution of OA-5 and OA-14 (1:1) showed 86% washing efficency. The 4% solution of SDS and OA-5 (1:1) showed 95% washing efficiency.

• Molecules and Cells
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• v.28 no.4
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• pp.347-363
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• 2009

The 15,389-bp long complete mitogenome of the endangered red-spotted apollo butterfly, Parnassius bremeri (Lepidoptera: Papilionidae) was determined in this study. The start codon for the COI gene in insects has been extensively discussed, and has long remained a matter of some controversy. Herein, we propose that the CGA (arginine) sequence functions as the start codon for the COI gene in lepidopteran insects, on the basis of complete mitogenome sequences of lepidopteran insects, including P. bremeri, as well as additional sequences of the COI start region from a diverse taxonomic range of lepidopteran species (a total of 53 species from 15 families). In our extensive search for a tRNA-like structure in the A+T-rich region, one $tRNA^{Trp}$-like sequence and one $tRNA^{Leu}(UUR)$-like sequence were detected in the P. bremeri A+T-rich region, and one or more tRNA-like structures were detected in the A+T-rich region of the majority of other sequenced lepidopteran insects, thereby indicating that such features occur frequently in the lepidopteran mitogenomes. Phylogenetic analysis using the concatenated 13 amino acid sequences and nucleotide sequences of PCGs of the four macrolepidopteran superfamilies together with the Tortricoidea and Pyraloidea resulted in the successful recovery of a monophyly of Papilionoidea and a monophyly of Bombycoidea. However, the Geometroidea were unexpectedly identified as a sister group of the Bombycoidea, rather than the Papilionoidea.