• BMB Reports
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• v.31 no.6
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• pp.565-571
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• 1998

The expression of the endogenous human apolipoprotein(apo)E gene was significantly induced when HepG2 cells were treated with exogenous 25-hydroxy-cholesterol. This sterol-mediated apoE gene upregulation appears to require the participation of a positive element for the apoE gene transcription (PET) ( -169/ -140), a core sequence of upstream regulatory element (URE)1 enhancer of the human apoE gene. This PET was renamed as sterol regulatory element (SRE)4 based on its new role as a sensor for the level of intracellular sterol. Furthermore, a gel mobility shift analysis showed that binding activity of the SRE4 binding protein (BP) obtained from HepG2 cells was induced by sterol treatment, while that from either MCF7 or BT20 cells remained unchanged. Binding activity of SRE4BP was also induced in mouse macrophage cells, J774A.1, by sterol treatment, but it was drastically reduced when cells were subjected to treatment of AY-9944, a potent inhibitor for sterol synthesis. However, binding activity of Spl, which is a co-binding protein to the SRE4 region, remained the same in either condition, suggesting that SRE4BP (formally known as PETBP) may be mainly responsible for the sterol-mediated regulation of the apoE gene expression. Deletion analysis of the core binding site of SRE4BP by gel mobility shift assays showed that the minimal sequence of the SRE4BP binding appears to reside between -157 and -140, confirming the identity of SRE4 with the previously determined core sequence of URE1.

• Journal of Microbiology and Biotechnology
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• v.8 no.4
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• pp.310-317
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• 1998

Peptide synthetases are large multifunctional enzyme complexes that catalyze the nonribosomal synthesis of a structurally diverse family of peptide antibiotics. These enzymes are composed of functionally independent domains with independent enzymatic activities. Their specific linkage order of domains forms the protein template that defines the sequence of the incorporated amino acids. Within each domain, several motifs of highly conserved sequences have been identified from the sequence alignment of the various peptide synthetases ［30］. Taking advantage of the conserved nucleotide sequence of Core 1 and Core 2, we designed PCR primers to amplify the peptide synthetase genes from three different gram-positive bacterial strains. Nucleotide sequence analysis of the amplified PCR products from those three strains showed significant homology to various peptide synthetase genes, suggesting that the PCR products are parts of peptide synthetase genes. Therefore, this rapid and efficient PCR technique can be used for the isolation of peptide synthetase genes from various strains.

• Ocean and Polar Research
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• v.29 no.4
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• pp.411-418
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• 2007

We studied the bottom morphology and sedimentary environments of the Masan Bay using high-resolution Chirp seismic profiles and sediments data. According to deep-drilled core samples (up to 20 m thick) penetrated into the weathered rock basement, the sediments consist largely of three sediment types: the lower sandy gravel facies (Unit I) of 1-4 m in thickness, the middle sandy mud and/or muddy sand facies(Unit II) of 1-2 m thick and the upper mudfacies (Unit III) of over 10 m in thickness. The sedimentary column above the acoustic basement can be divided into two major sequences by a relatively strong mid-reflector, which show the lower sedimentary sequenc e(T) with parallel to subparallel internal reflectors and the upper sedimentary sequence(H) with free acoustic patterns. Acoustic basement, the lower sedimentary sequence (T), and the upper sequence (H) are well correlated with poorly sorted massive sandy gravels (Unit I), the sand/mud-mixed sediment (Unit II), and the muddy facies(Unit III), respectively. The acoustic facies and sediment data suggest that the Masan bay is one of the most typical semi-enclosed coastal embayments developed during the Holocene sea-level changes. The area of the Masan Bay reduced from about $19\;km^2$ in 1964 to about $13\;km^2$ in 2005 by reclamation, and its bottom morphology changed as a result of dredging of about $2{\times}10^7\;m^3$.

• Bioinformatics and Biosystems
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• v.2 no.2
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• pp.46-51
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• 2007

In the proteomics research using mass spectrometry, the protein database search gives the protein information from the peptide sequences that show the best match with the tandem mass spectra. The protein sequence database has been a powerful knowledgebase for this protein identification. However, as we accumulate the protein sequence information in the database, the database size gets to be huge. Now it becomes hard to consider all the protein sequences in the database search because it consumes much computing time. For the high-throughput analysis of the proteome, usually we have used the non-redundant refined database such as IPI human database of European Bioinformatics Institute. While the non-redundant database can supply the search result in high speed, it misses the variation of the protein sequences. In this study, we have concerned the proteomics data in the point of protein similarities and used the network analysis tool to build a new analysis method. This method will be able to save the computing time for the database search and keep the sequence variation to catch the modified peptides.

• Korean Journal of Microbiology
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• v.28 no.1
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• pp.1-5
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• 1990

The coding sequence of hepatitis B viral core antigen (HBcAg) (subtype adr) contains two in-phase initiation codons, one for precore and the other for core antigen gene. To study the expression of core antigen and the role of precore region, the coding sequence of HBcAg with or without precore (pre-C) region were subcloned into yeast expression vector containing phosphoglycerate kinase (PGK) promoter. To study the role of upstream region in the expression of the core antigen, a series of 5' deletion mutants were also subcloned into the vector. After transformation into various host strains, the expression of HBcAg were analysed by radio-immunoassat. Under optimal condition of core antigen gene expression in yeast, the highest amount of antigen was detected in the cell line SHY4 containing pGKHBc plasmid composed of the yeast PGK gene promoter, terminator and C-gene. Regardless of the presence of precore region, core antigen was not detected in the medium but in cell extract. These results suggest that precore region cannot affect the secretion of core antigen in Saccharomyces cerevisiae.

• International Journal of Industrial Entomology and Biomaterials
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• v.2 no.1
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• pp.87-89
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• 2001

The nucleotide sequence of the domestic silkworm (Bombyx mori) mitochondrial (mt) control region and its flanking genes was determined from PCR clones. The control region of the silkworm mt genome was located between the small ribosomal RNA gene and transfer RN $A^{Met}$. This 499 bp control region hale 95.4% A+T content. Extensive comparative analysis studies performed with similar control region of other insect genomes could not reveal a highly conserved region containing conserved motifs of animal mito-chondrial genome. The remarkable feature that found in this control region was the presence of tandem motifs containing nine repetitive sequences. The potential usefulness of this motif sequences for Bombyx species or their taxonomically related species is enhanced by its unique localization in the maternally inheritance mitochondrial molecule.e.

• Korean Journal of Computational Design and Engineering
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• v.20 no.4
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• pp.367-374
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• 2015

Sandwich panels consisting of various materials have widely been applied for mitigating dynamic impacts such as ballistic and blast impacts. Especially, the selection of materials for different core set-ups can directly influence its performance. In this study, we design the sandwich panels for alleviating ballistic and blast impacts by controlling the stacking sequence of core materials and their thicknesses. FEM studies are performed to simulate the dynamic behavior of sandwich panels subjected to ballistic and blast impacts. Delamination between the core layers is also considered in the FEM studies for feasible design. Based on the FEM data, kriging models are generated for approximating design space and quickly predicting the FEM outputs. Finally, design optimizations are implemented to find the optimum stacking sequence of core materials and thicknesses with given impact situations.

• BMB Reports
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• v.34 no.1
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• pp.51-58
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• 2001

Attempts using in vitro and in vivo selection procedures have been made to search for hammerhead ribozymes that have higher activities than the wild-type ribozyme and also to determine whether other sequences might be possible in the catalytic core of the hammerhead ribozyme. Active sequences selected in the past conformed broadly to the consensus core sequence except at A9, and no sequences were associated with higher activity than that of the hammerhead with the consensus core, an indication that the consensus sequence derived from viruses and virusoids is probably the optimal sequence [Vaish et al. (1997) Biochemistry 36, 6495-6501]. Recently, during construction of ribozyme expression vectors, we isolated a mutant hammerhead ribozyme, with an insertion of G between A9 and G10.1, that appeared to show significant activity [Kawasaki et al. (1996) Nucleic Acids Res. 24, 3010-3016; Kawasaki et al. (1998) Nature 393, 284-289]. We, therefore, characterized kinetic properties of the G-inserted mutant ribozymes in terms of the NUX rule. We demonstrate that the NUX rule is basically applicable to the G-inserted ribozymes and, more importantly, one type of G-inserted ribozyme was very active with $k_{cat}$, value of $6.4\;min^{-1}$ in 50 mM Tris-HCl (pH 8.0) and 10 mM $MgCl_2$ at $37^{\circ}C$.

• Journal of Microbiology and Biotechnology
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• v.8 no.6
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• pp.650-655
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• 1998

The chromosomal DNA fragment from Phaffia rhodozyma CBS 6938 which is able to autonomously replicate in the yeast Saccharomyces cerevisiae was cloned on an integrative URA3 plasmid. Its minimal fragment exhibiting autonomously replicating activiy in the S. cerevisiae gave a higher frequency transformation efficiency than that found for centromere-based plasmid, and enabled extrachromosoma1ly stable transmission of the plasmids in one copy per yeast cell under non-selective culture condition. The 836-bp DNA element lacked an ORF and did not contain any acceptable match to an ARS core consensus. Sequence analysis, however, displayed a cluster of three hairpin-Ioop-sequences with individual $\triangle {G_{25}}^{\circ}C$ free energy value of -10.0, -17.5, and -17.0 kcal. $mor^{-l}$as well as a 9-bp sequence with two base pair mismatches to the S. cerevisiae/E. coli gyrase-binding site. This 836-bp sequence also included one 7-bp sequence analogous to the core consensus of centromeric DNA element III (CDEIII) of S. cerevisiae, but CDEIII-like 7 bp sequence alone did not give a replicative function in this yeast.

• Structural Engineering and Mechanics
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• v.52 no.2
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• pp.323-349
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• 2014

In this paper, linear buckling analysis of a curved sandwich beam with a flexible core is investigated. Derivation of equations for face sheets is accomplished via the classical theory of curved beam, whereas for the flexible core, the elasticity equations in polar coordinates are implemented. Employing the von-Karman type geometrical non-linearity in strain-displacement relations, nonlinear governing equations are resulted. Linear pre-buckling analysis is performed neglecting the rotation effects in pre-buckling state. Stability equations are concluded based on the adjacent equilibrium criterion. Considering the movable simply supported type of boundary conditions, suitable trigonometric solutions are adopted which satisfy the assumed edge conditions. The critical uniform load of the beam is obtained as a closed-form expression. Numerical results cover the effects of various parameters on the critical buckling load of the curved beam. It is shown that, face thickness, core thickness, core module, fiber angle of faces, stacking sequence of faces and openin angle of the beam all affect greatly on the buckling pressure of the beam and its buckled shape.