• BMB Reports
• /
• v.40 no.3
• /
• pp.419-425
• /
• 2007

In vitro directed evolution through DNA shuffling is a powerful molecular tool for creation of new biological phenotypes. E. coli $\beta$-galactosidase and $\beta$-glucuronidase are widely used, and their biological function, catalytic mechanism, and molecular structures are well characterized. We applied an in vitro directed evolution strategy through DNA shuffling and obtained five mutants named YG6764, YG6768, YG6769, YG6770 and YG6771 after two rounds of DNA shuffling and screening, which exhibited more $\beta$-glucuronidase activity than wild-type $\beta$-galactosidase. These variants had mutations at fourteen nucleic acid sites, resulting in changes in ten amino acids: S193N, T266A, Q267R, V411A, D448G, G466A, L527I, M543I, Q626R and Q951R. We expressed and purified those mutant proteins. Compared to the wild-type protein, five mutant proteins exhibited high $\beta$-glucuronidase activity. The comparison of molecular models of the mutated and wildtype enzymes revealed the relationship between protein function and structural modification.

• Parasites, Hosts and Diseases
• /
• v.54 no.6
• /
• pp.777-786
• /
• 2016

Raillietina species are prevalent in domestic chickens (Gallus gallus domesticus) in Phayao province, northern Thailand. Their infection may cause disease and death, which affects the public health and economic situation in chicken farms. The identification of Raillietina has been based on morphology and molecular analysis. In this study, morphological observations using light (LM) and scanning electron microscopies (SEM) coupled with molecular analysis of the internal transcribed spacer 2 (ITS2) region and the nicotinamide adenine dinucleotide dehydrogenase subunit 1 (ND1) gene were employed for precise identification and phylogenetic relationship studies of Raillietina spp. Four Raillietina species, including R. echinobothrida, R. tetragona, R. cesticillus, and Raillietina sp., were recovered in domestic chickens from 4 districts in Phayao province, Thailand. LM and SEM observations revealed differences in the morphology of the scolex, position of the genital pore, number of eggs per egg capsule, and rostellar opening surface structures in all 4 species. Phylogenetic relationships were found among the phylogenetic trees obtained by the maximum likelihood and distance-based neighbor-joining methods. ITS2 and ND1 sequence data recorded from Raillietina sp. appeared to be monophyletic. The query sequences of R. echinobothrida, R. tetragona, R. cesticillus, and Raillietina sp. were separated according to the different morphological characters. This study confirmed that morphological studies combined with molecular analyses can differentiate related species within the genus Raillietina in Thailand.

• Proceedings of the Korean Society for Bioinformatics Conference
• /
• 2000.11a
• /
• pp.56-58
• /
• 2000

Post-genomics may be defined in different ways depending on how one views the challenges after the genome. A popular view is to follow the concept of the central dogma in molecular biology, namely from genome to transcriptome to proteome. Projects are going on to analyze gene expression profiles both at the mRNA and protein levels and to catalog protein 3D structure families, which will no doubt help the understanding of information in the genome. However complete, such catalogs of genes, RNAs, and proteins only tell us about the building blocks of life. They do not tell us much about the wiring (interaction) of building blocks, which is essential for uncovering systemic functional behaviors of the cell or the organism. Thus, an alternative view of post-genomics is to go up from the molecular level to the cellular level, and to understand, what I call, the "interactome"or a complete picture of molecular interactions in the cell. KEGG (http://www.genome.ad.jp/kegg/) is our attempt to computerize current knowledge on various cellular processes as a collection of "generalized"protein-protein interaction networks, to develop new graph-based algorithms for predicting such networks from the genome information, and to actually reconstruct the interactomes for all the completely sequenced genomes and some partial genomes. During the reconstruction process, it becomes readily apparent that certain pathways and molecular complexes are present or absent in each organism, indicating modular structures of the interactome. In addition, the reconstruction uncovers missing components in an otherwise complete pathway or complex, which may result from misannotation of the genome or misrepresentation of the KEGG pathway. When combined with additional experimental data on protein-protein interactions, such as by yeast two-hybrid systems, the reconstruction possibly uncovers unknown partners for a particular pathway or complex. Thus, the reconstruction is tightly coupled with the annotation of individual genes, which is maintained in the GENES database in KEGG. We are also trying to expand our literature surrey to include in the GENES database most up-to-date information about gene functions.

• Composites Research
• /
• v.30 no.6
• /
• pp.371-378
• /
• 2017

In this study, hygroelastic behavior of thermosetting epoxy is predicted by molecular dynamics simulations. Since consistent exposures to humid environments lead to macroscopic degradation of polymer composite, computational simulation study of the hygroscopically aged epoxy cell is essential for long-time durability. Therefore, we modeled amorphous epoxy molecular unit cell structures at a crosslinking ratio of 30, 90% and with the moisture weight fraction of 0, 4 wt% respectively. Diglycidyl ether of bisphenol F (EPON862) and triethylenetetramine (TETA) are chosen as resin and curing agent respectively. Incorporating equilibrium and non-equilibrium ensemble simulation with a classical interatomic potential, various hygroelastic properties including diffusion coefficient of water, coefficient of moisture expansion (CME), stress-strain curve and elastic modulus are predicted. To establish the structural property relationship of pure epoxy, free volume and internal non-bond potential energy of epoxy are examined.

• Journal of Microbiology and Biotechnology
• /
• v.27 no.11
• /
• pp.1999-2009
• /
• 2017

The secretion efficiency of a protein in a Sec-type secretion system is mainly determined by an N-terminal signal peptide and its combination with its cognate protein. Five signal peptides, namely, two synthetic Sec-type and three Bacillus licheniformis alpha-amylase-derived signal peptides, were compared for periplasmic expression of the human growth hormone (hGH) in E. coli. Based on in silico predictions on the signal peptides' cleavage efficiencies and their corresponding mRNA secondary structures, a number of amino acid substitutions and silent mutations were considered in the modified signal sequences. The two synthetic signal peptides, specifically designed for hGH secretion in E. coli, differ in their N-terminal positively charged residues and hydrophobic region lengths. According to the mRNA secondary structure predictions, combinations of the protein and each of the five signal sequences could lead to different outcomes, especially when accessibility of the initiator ATG and ribosome binding sites were considered. In the experimental stage, the two synthetic signal peptides displayed complete processing and resulted in efficient secretion of the mature hGH in periplasmic regions, as was demonstrated by protein analysis. The three alpha-amylase-derived signal peptides, however, were processed partially from their precursors. Therefore, to achieve efficient secretion of a protein in a heterologous system, designing a specific signal peptide by using a combined approach of optimizations of the mRNA secondary structure and the signal peptide H-domain and cleavage site is recommended.

• Korean Journal of Veterinary Research
• /
• v.46 no.4
• /
• pp.371-379
• /
• 2006

Newcastle disease virus (NDV) is a single-stranded negative sense RNA virus, which has been classified as a member of the Avulavirus genus of the Paramyxoviridae family. It is also one of the most important pathogens in the poultry industry. The glycoproteins, fusion (F) and hemagglutinin-neuraminidase (HN), determine the virulence of NDV, and the relevant molecular structures have already been determined. NDV isolates differ in terms of virulence, and at least 2 of 9 genotypes (I-IX) have been shown to co-circulate. Therefore, it is clearly important to differentiate between vaccine strains and field isolates. In vivo pathogenicity tests have been the standard protocol for some time, but molecular methods appear preferable in terms of the rapidity of diagnosis, as well as animal welfare concerns. In this study, we have designed primer sets from HN gene for phylogenetic analysis and restriction enzyme analysis, and from F gene for pathotype-specific RT-PCR. Via the combination of 2 methods, 106 Korean NDV isolates obtained from 1980 to 2005 were differentiated into vaccine strains, and virulent genotypes VI and VII. The genotype VI viruses were only rarely isolated after 1999, and genotype VII, after it was initially isolated from poultry in 1995, recurred in 2000, and then became the main NDV constituting a threat to the Korean poultry industry.

• Applied Biological Chemistry
• /
• v.34 no.2
• /
• pp.110-116
• /
• 1991

As the model compounds, citral and n-octanol which possess similar characteristics and structures of low molecular weight insect pheromones and $({\pm})-5-hydroxy-4-methyl-heptan-3-one$ which shows the aggregation pheromones activity of the rice weevil and the maize weevil were microencapsulated with low molecular weight polyethylene(LMPE) and urea-formaldehyde resin as wall materials. The core materials were microencapsulated as small particles in LMPE and urea-formaldehyde resin polymers and the microencapsulated polymers were white powders. And the polymer made from urea-formaldehyde resin was better than that from LMPE as wall material. The slow releasing effect and the releasing patten of the microencapsulated core materials were examined by solvent extraction method and headspace sampling method. Citral and n-octanol and $({\pm})-5-hydroxy-4-methyl-heptan-3-one$ were release more than 40 days and 15 days, respectively. The releasing pattern of urea-formaldehyde resin microcapsules showed rather smooth decrease than that of LMPE and was maintained at steady level longer.

• Molecules and Cells
• /
• v.23 no.2
• /
• pp.228-238
• /
• 2007

Since molecular structure of hnRNP is not available in foreseeable future, it is best to construct a working model for hnRNP structure. A geometric problem, assembly of $700{\pm}20$ nucleotides with 48 proteins, is visualized by a frame work in which all the proteins participate in primary binding, followed by secondary, tertiary and quaternary binding with neighboring proteins without additional import. Thus, 40S hnRNP contains crown-like secondary structure (48 stemloops) and appearance of 6 petal (octamers) rose-like architectures. The proteins are wrapped by RNA. Co-transcriptional folding for RNP fibril of FMR1 gene can produce 2,571 stem-loops with frequency of 1 stem-loop/15.3 nucleotides and 53 40S hnRNP beaded structure. By spliceosome driven reactions, there occurs removal of 16 separate lariated RNPs, joining 17 separate beaded exonic structures and anchoring EJC on each exon junction. Skipping exon 12 has 5'GU, 3'AG and very compact folding pattern with frequency of 1 stem-loop per 12 nucleotides in short exon length (63 nucleotides). 5' end of exon 12 contains SS (Splicing Silencer) element of UAGGU. In exons 10, 15 and 17 where both regular and alternative splice sites exist, SS (hnRNP A1 binding site) is observed at the regular splicing site. End products are mature FMR-1 mRNP, 4 species of Pri-microRNAs derived from introns 7,9,15 and 3'UTR of exon17, respectively. There may also be some other regulatory RNAs containing ALU/Line elements as well.

• Journal of Adhesion and Interface
• /
• v.5 no.4
• /
• pp.17-23
• /
• 2004

In this study, we prepared the polycarbonates with various molecular weights by melt polymerization and investigated the crystallization by solvent induced crystallization. Effects of the types and compositions of solvents, crystallizing temperatures and molecular weights on crystallinity and melt temperatures of polycarbonates were evaluated by DSC, XRD and SEM. In case of low molecular weight polycarbonates and high crystallization temperature, the crystallinity of the polycarbonate was increased. As the increase of the crystallization temperature and the solution concentration, relatively uniform crystalline structures were obtained. Also, by treating with mixed solvents, the control of desired surface areas and crystallinity could be possible.

• The Bulletin of The Korean Astronomical Society
• /
• v.38 no.1
• /
• pp.51.1-51.1
• /
• 2013

We present molecular line observations of a small group of Young Stellar Objects (YSOs), L1251C. Observations by Spitzer Space Telescope legacy program "From Molecular Cores to Planet Forming Disks"(c2d; Evans et al. 2003) revealed that there are three YSOs within ~15" in L1251C: IRS1 (Class I), IRS2 (Class II), and IRS3 (Class II). In order to understand the molecular environment around these YSOs, we carried out the KVN single-dish observations in $HCO^+$ J=1-0, $H^{13}CO^+$ J=1-0, $N_2H^+$ J=1-0 and HCN J=1-0. CO J=1-0 was also mapped in L1251C with the TRAO 14m telescope. Integrated intensity maps of high density tracers such as $H^{13}CO^+$ J=1-0, $N_2H^+$ J=1-0 and HCN J=1-0 show similar emission distributions, whose peaks are off from the positions of YSOs. However, $HCO^+$ J=1-0, which is believed to trace both infall and outflow, presents its emission distribution different from those of other molecular transitions. The line profile of $HCO^+$ J=1-0 is superimposed by two velocity (narrow and broad) components. The $HCO^+$ outflow map reveals multiple structures while the CO outflow map elongates mainly along the EW direction. With the KVN single dish, the 22 GHz $H_2O$ maser emission has been also monitored toward L1251C to find variations of the systemic velocity and intensity with time.