• BMB Reports
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• v.40 no.2
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• pp.172-179
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• 2007

PCR-mediated recombination describes the process of in vitro chimera formation from related template sequences present in a single PCR amplification. The high levels of genetic redundancy in eukaryotic genomes should make recombination artifacts occur readily. However, few evolutionary biologists adequately consider this phenomenon when studying gene lineages. The cytosolic glyceraldehyde-3-phosphate dehydrogenase gene (GapC), which encodes a NADP-dependent nonphosphorylating glyceraldehyde-3-phosphate dehydrogenase in the cytosol, is a classical lowcopy nuclear gene marker and is commonly used in molecular evolutionary studies. Here, we report on the occurrence of PCR-mediated recombination in the GapC gene family of Hibiscus tiliaceus. The study suggests that recombinant areas appear to be correlated with DNA template secondary structures. Our observations highlight that recombination artifacts should be considered when studying specific and allelic phylogenies. The authors suggest that nested PCR be used to suppress PCRmediated recombination.

• BMB Reports
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• v.48 no.12
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• pp.691-695
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• 2015

We report that phytosphingosine, a sphingolipid found in many organisms and implicated in cellular signaling, promotes megakaryocytic differentiation of myeloid leukemia cells. Specifically, phytosphingosine induced several hallmark changes associated with megakaryopoiesis from K562 and HEL cells including cell cycle arrest, cell size increase and polyploidization. We also confirmed that cell type specific markers of megakaryocytes, CD41a and CD42b are induced by phytosphingosine. Phospholipids with highly similar structures were unable to induce similar changes, indicating that the activity of phytosphingosine is highly specific. Although phytosphingosine is known to activate p38 mitogen-activated protein kinase (MAPK)-mediated apoptosis, the signaling mechanisms involved in megakaryopoiesis appear to be distinct. In sum, we present another model for dissecting molecular details of megakaryocytic differentiation which in large part remains obscure.

• Composites Research
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• v.24 no.2
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• pp.9-13
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• 2011

,In this paper, the symmetric axis parameter method, which was proposed to identify defects, dislocations and stacking fault, with perfect structures in the zinc-blende materials, was introduced as a way to distinguish between elastic and plastic deformation. LAMMPS, a molecular dynamics programme of Sandia National Laboratories, was used to perform nanoindentation simulation on silicon, a zinc-blende material. Defects in silicon (111) under spherical indentation showed the threefold pattern and the slip system in the form of ring crack. Also simulation results show good agreement with experimental results and existing theoretical analyses.

• Molecules and Cells
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• v.27 no.1
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• pp.89-97
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• 2009

We investigate the molecular and cellular etiologies that underlie the deletion of the six amino acid residues (${\Delta}F323-Y328$; ${\Delta}FY$) in human torsin A (HtorA). The most common and severe mutation involved with early-onset torsion dystonia is a glutamic acid deletion (${\Delta}E$ 302/303; ${\Delta}E$) in HtorA which induces protein aggregates in neurons and cells. Even though ${\Delta}FY$ HtorA forms no protein clusters, flies expressing ${\Delta}FY$ HtorA in neurons or muscles manifested a similar but delayed onset of adult locomotor disability compared with flies expressing ${\Delta}E$ in HtorA. In addition, flies expressing ${\Delta}FY$ HtorA had fewer aberrant ultrastructures at synapses compared with flies expressing ${\Delta}E$ HtorA. Taken together, the ${\Delta}FY$ mutation in HtorA may be responsible for behavioral and anatomical aberrations in Drosophila.

• The Plant Pathology Journal
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• v.33 no.6
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• pp.529-542
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• 2017

Control of plant diseases is largely dependent on use of agrochemicals. However, there are widening gaps between our knowledge on plant diseases gained from genetic/mechanistic studies and rapid translation of the knowledge into target-oriented development of effective agrochemicals. Here we propose that the time is ripe for computer-aided drug discovery/design (CADD) in molecular plant pathology. CADD has played a pivotal role in development of medically important molecules over the last three decades. Now, explosive increase in information on genome sequences and three dimensional structures of biological molecules, in combination with advances in computational and informational technologies, opens up exciting possibilities for application of CADD in discovery and development of agrochemicals. In this review, we outline two categories of the drug discovery strategies: structure- and ligand-based CADD, and relevant computational approaches that are being employed in modern drug discovery. In order to help readers to dive into CADD, we explain concepts of homology modelling, molecular docking, virtual screening, and de novo ligand design in structure-based CADD, and pharmacophore modelling, ligand-based virtual screening, quantitative structure activity relationship modelling and de novo ligand design for ligand-based CADD. We also provide the important resources available to carry out CADD. Finally, we present a case study showing how CADD approach can be implemented in reality for identification of potent chemical compounds against the important plant pathogens, Pseudomonas syringae and Colletotrichum gloeosporioides.

• The Korean Journal of Physiology and Pharmacology
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• v.3 no.6
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• pp.597-603
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• 1999

Caldesmon (CaD), one of microfilament-associated proteins, plays a key role in microfilament assembly in mitosis. We have investigated the effects of overexpression of the high molecular weight isoform of CaD (h-CaD) on the physiology of vascular smooth muscle cells (VSMCs). Rat aortic VSMCs were stably transfected with plasmids carrying a full length human h-CaD cDNA under control of cytomegalovirus promoter. The majority of the overexpressed h-CaD appears to be localized predominantly on cytoskeleton structures as determined by detergent lysis. The overexpression of h-CaD, however, does not decrease the level of endogenous low molecular weight isoform of CaD. h-CaD overexpressing VSMCs (h-CaD/VSMCs) show a decreased growth rate than that of vector-only transfected cells when determined by $[^3H]thymidine$ uptake and cell counting after fetal bovine serum (FBS) stimulation. h-CaD/VSMCs were smaller than vector-transfected cells by 18% in cell diameter. These data suggest that overexpression of h-CaD can inhibit the poliferation and the cell volume of VSMCs stimulated by growth factors and that the gene therapy with h-CaD may be helpful to prevent the conditions associated with hypertrophy and/or hyperplasia of VSMCs after arterial injuries.

• Journal of Microbiology and Biotechnology
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• v.20 no.1
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• pp.138-145
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• 2010

A bacterial strain isolated from soil for its potential to control the anthracnose disease caused by Colletotrichum gloeosporioides was identified as a Bacillus subtilis. Bacillus subtilis CMB32 produced antifungal agents on M9 broth at $30^{\circ}C$. Biosurfactant lipopeptides produced by Bacillus subtilis CMB32 were precipitated by adjusting to pH 2 and extracting using chloroform/methanol, and then were purified using column chromatography and reverse-phase HPLC. The molecular masses of the lipopeptides were estimated by MALDI-TOF mass spectrometry as (a) 1,080, (b) 1,486, and (c) 1,044 Da, respectively. They had cyclic structures and amino acid compositions of (a) Pro, Asx, Ser, Tyr, Glx, (b) Glx, Tyr, Thr, Ala, Pro, lie, and (c) Glx, Leu, Val, Asx, respectively. Further analysis revealed that Bacillus subtilis CMB32 produced three antifungal lipopeptides: (a) iturin A, (b) fengycin, and (c) surfactin A.

• Journal of Biomedical Engineering Research
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• v.22 no.6
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• pp.519-526
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• 2001

At present. about 0.3 million and more THRs (Total Hip Replacement) in a rear are being done worldwide. The increase in mechanical failure with the increase in THR, required more revisions. Revisions compensate mainly the wear of the artificial joint frictional surface and the loosening of the cup and stem. According to recent researches, loosening is mainly due to wear debris UHMWPE (Ultra High Molecular Weight Polyethylene) from frictional surfaces . To overcome the wear problems associated with artificial joint materials , new surface structures with regular Patterns were designed and fabricated The lubrication Properties were examined to evaluate the wear of the frictional surfaces. The surface structure manifested a Pattern of "dents" with a 0.2-1.0 mm of diameter and 0.6-2.0 mm of Pitch. From the friction test of the SUS316L vs UHMWPE using the frictional tester, we found that the lubrication Performance was improved due to of drastically reduced amount of abrasion. There were optimum sizes for the diameter and the pitch of the Pattern. The results demonstrated that the lubrication properties could be improved by Patterning of the frictional surfaces. The surface Patterning was effective in preventing wear of the frictional surfaces, and the life of an artificial joint could be extended with such Patterning.

• Journal of the Korean Magnetic Resonance Society
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• v.2 no.2
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• pp.85-105
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• 1998

Prions cause neurodegenerative diseases in animals and humans. The scrapie prion protein (PrPSc) is the major-possibly only-component of the infectious prion and is generated from the cellular isoform (PrPC) by a conformational change. Limited proteolysis of PrPSc produces an polypeptide comprised primarily of residues 90 to 231, which retains infectivity. The three-dimensional structure of rPrP(90-231), a recombinant protein resembling PrPC with the Syrian hamster (SHa) sequence, was solved using multidimensional NMR. Low-resolution structures of rPrP(90-231), synthetic peptides up to 56 residues, a longer (29-231, full-length) protein with SHa sequence, and a short here further structure refinement of rPrP(90-231) and dynamic features of the protein. Consideration of these features in the context of published data suggests regions of conformational heterogeneity, structural elements involved in the PrPC\longrightarrowPrPSc transformation, and possible structural features related to a species barrier to transmission of prion diseases.

• Journal of the Korean Magnetic Resonance Society
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• v.14 no.2
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• pp.117-126
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• 2010

Hsp33 is a molecular chaperone achieving a holdase activity upon response to a dual stress by heat and oxidation. Despite several crystal structures available, the activation process is not clearly understood, because the structure inactive Hsp33 as its reduced, zinc-bound, monomeric form has not been solved yet. Thus, we initiated structural investigation of the reduced Hsp33 monomer by NMR. In this study, to overcome the high molecular weight (33 kDa), the protein was triply isotope-[$^{13}C$, $^{15}N$, $^2H$]-labeled and its inactive, monomeric state was ensured. 2D-[$^1H$, $^{15}N$]-TROSY and a series of triple resonance spectra could be successfully obtained on a high-field (900 MHz) NMR machine with a cryoprobe. However, under all of the different conditions tested, the number of resonances observed was significantly less than that expected from the amino acid sequence. Thus, a possible contribution of dynamic conformational exchange leading to a line broadening is suggested that might be important for activation process of Hsp33.