• Bulletin of the Korean Chemical Society
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• v.33 no.12
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• pp.4041-4046
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• 2012

The recombinant expression of proteins has been the method of choice to meet the demands from proteomics and structural genomics studies. Despite its successful production of many heterologous proteins, Escherichia coli failed to produce many other proteins in their native forms. This may be related to the fact that the stresses resulting from the overproduction interfere with cellular processes. To better understand the physiological change during the overproduction phase, we profiled the metabolites along the time course of the recombinant protein expression. We identified 32 metabolites collected from different time points in the protein production phase. The stress induced by protein production can be characterized by (A) the increased usage of aspartic acid, choline, glycerol, and N-acetyllysine; and (B) the accumulation of adenosine, alanine, oxidized glutathione, glycine, N-acetylputrescine, and uracil. We envision that this work can be used to create a strategy for the production of usable proteins in large quantities.

• Genomics & Informatics
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• v.8 no.4
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• pp.170-176
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• 2010

The Ribonucleotide reductases (RNR) are essential enzymes that catalyze the conversion of nucleotides to deoxynucleotides in DNA replication and repair in all living organisms. The RNRs operate by a free radical mechanism but differ in the composition of subunit, cofactor required and regulation by allostery. Based on these differences the RNRs are classified into three classesclass I, class II and class III which depend on oxygen, adenosylcobalamin and S-adenosylmethionine with an iron sulfur cluster respectively for radical generation. In this article thirty seven sequences belonging to each of the three classes of RNR were analyzed by using various tools of bioinformatics. Phylogenetic analysis, dot-plot comparisons and motif analysis was done to identify a number of differences in the three classes of RNRs. In this research article, we have attempted to decipher evolutionary relationship between the three classes of RNR by using bioinformatics approach.

• Genomics & Informatics
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• v.5 no.1
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• pp.24-29
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• 2007

Computational virtual screening has become an essential platform of drug discovery for the efficient identification of active candidates. Moleculardocking, a key technology of receptor-centric virtual screening, is commonly used to predict the binding affinities of chemical compounds on target receptors. Despite the advancement and extensive application of these methods, substantial improvement is still required to increase their accuracy and time-efficiency. Here, we evaluate several advanced structure-based virtual screening approaches for elucidating the rank-order activity of chemical libraries, and the quantitative structureactivity relationship (QSAR). Our results show that the ensemble-average free energy estimation, including implicit solvation energy terms, significantly improves the hit enrichment of the virtual screening. We also demonstrate that the assignment of quantum mechanical-polarized (QM-polarized) partial charges to docked ligands contributes to the reproduction of the crystal pose of ligands in the docking and scoring procedure.

• Biotechnology and Bioprocess Engineering:BBE
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• v.5 no.5
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• pp.327-331
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• 2000

The application of LFH-PCR(long flanking homology region-PCR) for Bacillus subtilis gene disruption is presented. Without plasmid- or phage-vector construction, only by PCR, based on a DNA sequence retrieved from B. subtilis genome data base, kanamycin resistance gene was inserted into two genes of B. subtilis involved in sporulation, spoIIIE and spoIIIG. The effect of gene disruption on subtilisin expression was examined and the sporulation frequency of two mutants was compared to that of the host strain. For this purpose, only 2 or 3 rounds of PCR were required with 4 primers. We first demonstrated the possibility of LFH-PCR for rapid gene disruption to characterize an unknown functional gene of B. subtilis or other prokaryote in the genomic era.

• Genomics & Informatics
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• v.7 no.2
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• pp.111-121
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• 2009

Cell membrane proteins play crucial roles in the cell's molecular interaction with its environment and within itself. They consist of membrane-bound proteins and many types of transmembrane (TM) proteins such as receptors, transporters, channel proteins, and enzymes. Membrane proteomes of cellular organisms reveal some characteristics in their global topological distribution according to their evolutionary positions, and show their own information transfer complexity. Predicted transmembrane segments (TMSs) in membrane proteomes with HMMTOP showed near power-law distribution and frequency characteristics in 6-TMS and 7-TMS proteins in prokaryotes and eukaryotes, respectively. This reaffirms the important roles of membrane receptors in cellular communication and biological evolutionary history.

• Genomics & Informatics
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• v.4 no.3
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• pp.129-132
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• 2006

Toxicogenomics has recently emerged in the field of toxicology and the DNA microarray technique has become common strategy for predictive toxicology which studies molecular mechanism caused by exposure of chemical or environmental stress. Although microarray experiment offers extensive genomic information to the researchers, yet high dimensional characteristic of the data often makes it hard to extract meaningful result. Therefore we developed toxicant enrichment analysis similar to the common enrichment approach. We also developed web-based system graPT to enable considerable prediction of toxic endpoints of experimental chemical.

• Genomics & Informatics
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• v.7 no.1
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• pp.26-31
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• 2009

Heat shock proteins are a class of molecular chaperones that can be found in nearly all organisms from Bacteria, Archaea and Eukarya domains. Heat shock proteins experience increased transcription during periods of heat induced osmotic stress and are involved in protein disaggregation and refolding as part of a cell's danger signaling cascade. Heat shock protein, Hsp20 is a small molecular chaperone that is approximately 20kDa in weight and is hypothesized to prevent aggregation and denaturation. Hsp20 can be found in several strains of Proteobacteria, which comprises the largest phyla of the Bacteria domain and also contains several medically significant bacterial strains. Genomic analyses were performed to determine a common evolutionary pattern among Hsp20 sequences in Proteobacteria. It was found that Hsp20 shared a common ancestor within and among the five subclasses of Proteobacteria. This is readily apparent from the amount of sequence similarities within and between Hsp20 protein sequences as well as phylogenetic analysis of sequences from proteobacterial and non-proteobacterial species.

• Journal of Plant Biotechnology
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• v.37 no.4
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• pp.562-566
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• 2010

SOD2-transgenic $T_3$ petunia line (A2-36-2-1-1-35) was treated with different levels of methyl viologen (MV) to determine its resistance to oxidative stress. Four (4) levels of MV (0, 100, 200, and $400\;{\mu}M$) were applied. The SOD2-transgenic $T_3$ petunia line exhibited a very significant oxidative stress resistance at the highest MV concentration ($400\;{\mu}M$) treatment compared to non-transgenic plant. RNA and protein expression of SOD2 transgene and higher parenchyma cell density in the transgenic petunias exhibiting resistance to oxidative stress proves its contribution to the expression of its resistance to oxidative stress.

• Animal Bioscience
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• v.35 no.7
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• pp.1069-1079
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• 2022

Objective: The objective of this study was to investigate the effect of 4-month intensive feeding on the meat quality, fatty acid profile, flavor, and growth performance of grazing Hulunbuir sheep (HBS). Methods: The HBS were selected 4-months after birth in a pasture rearing system as the experimental animals (n = 44, female, average body weight 23.8±2.2 kg) then divided equally into pasture-based grazing fattening (PAS) and concentrate-included intensive fattening (CON) groups for another 4-month finishing. When finished fattening, all animals were slaughtered to collect musculus longissimus dorsi subcutaneous adipose tissue and to investigate the influences on meat quality, fatty acid profile, flavor and growth performance. Results: The results showed lambs in CON group got significantly higher live weight, hot carcass weight, and dressing percentage. The CON group had significantly higher value of redness (a^*), lightness (L^*) and water holding capacity (p<0.05), significantly lower value of Warner-Bratzler shear force than the PAS group (p<0.05). The subcutaneous fat from CON group lambs demonstrated a significantly higher content of C18:1 and C18:2 (p<0.05), but lower C14:0 and C16:0, indicating an increased degree of unsaturated fatty acid. The content of 4-methyloctanoic acid, 4-ethyloctanoic acid and 4-methylnonanoic acid had increased 2 to 4 times, representing a more intense odor in the CON group. However, the values were still lower than most sheep breeds reported, indicating the indoor feeding system could not fundamentally deteriorate the excellent meat characteristic of HBS. Conclusion: It was evident that lambs in CON group exhibited a better meat production performance, improved in meat color, texture and healthier fatty acid profile through pasture-weaned concentrate included intensive fattening system, which offers a good alternative regimen for lamb finishing and has a wide prospection in the HBS meat industry.

• Journal of Microbiology and Biotechnology
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• v.18 no.4
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• pp.658-662
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• 2008

Effects of pH shock on the secretion system of S. coelicolor A3(2) have been investigated at a transcriptional level by using DNA microarrays. Actinorhodin secretion was observed to be highly enhanced when an acidic-pH shock was applied to surface grown cultures of S. coelicolor A3(2). In this culture, a gene of actVA-orf1 encoding a putative efflux pump or transporter protein for actinorhodin was strongly upregulated. A major number of efflux pumps for other metabolites and a major number of secretion proteins for protein secretion were also observed to be upregulated with pH shock. The secretion of actinorhodin was observed to be remarkably enhanced in liquid culture as well.