Wyniki wyszukiwania - Biblioteka Nauki

1

Towards Efficient Searching on the Secondary Structure of Protein Sequences

100%

Seo M. , Park S. , Won J.-I.

Fundamenta Informaticae

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2007

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tom Vol. 78, nr 4

525-542

EN

Approximate searching on the primary structure (i.e., amino acid arrangement) of protein sequences is an essential part in predicting the functions and evolutionary histories of proteins. However, because proteins distant in an evolutionary history do not conserve amino acid residue arrangements, approximate searching on proteins' secondary structure is quite important in finding out distant homology. In this paper, we propose an indexing scheme for efficient approximate searching on the secondary structure of protein sequences which can be easily implemented in RDBMS. Exploiting the concept of clustering and lookahead , the proposed indexing scheme processes three types of secondary structure queries (i.e., exact match, range match, and wildcard match) very quickly. To evaluate the performance of the proposed method, we conducted extensive experiments using a set of actual protein sequences. According to the experimental results, the proposed method was proved to be faster than the existing indexing methods up to 6.3 times in exact match, 3.3 times in range match, and 1.5 times in wildcard match, respectively.

2

Re-evaluation of the effects of growth regulators on callus induction and shoot regeneration in Agrobacterium-mediated transformation of lettuce

100%

Lim W. , Park J. , Park S.

Acta Physiologiae Plantarum

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2011

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tom 33

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nr 5

EN

Lettuce (Lactuca sativa) transformation varies by genotype. Various culture parameters have been studied in order to improve the transformation efficiency of lettuce cultivars. However, no improved transformation procedure for recalcitrant lettuce cultivars has yet been established. Here, we demonstrate the effects of varying concentrations and distinct combinations of growth regulators on recalcitrant lettuce transformation efficiency. More precisely, we assessed differences in the effects of several growth regulator combinations, including N-6(2-isopentenyl)-adenine (2ip), on induction of callus and regeneration of shoots after co-cultivation with Agrobacterium. When two commercial recalcitrant cultivars, Red Romaine and Bibb, were cultured on a medium with 2ip 1 mg l⁻¹, IAA 0.1 mg l⁻¹, and subsequently transferred to a second medium with BA 0.4 mg l⁻¹, NAA 0.05 mg l⁻¹ for selection and shoot regeneration, transformation efficiencies reached 8 and 9%, respectively. Stable integration and transmission of the transgene in T1 generation plants were confirmed by molecular analysis. This procedure represents a simple, efficient, and general means of transforming various lettuce cultivars, including recalcitrant commercial cultivars.

3

Superoxide is a potential culprit of caspase-3 dependent endothelial cell death induced by lysophosphatidylcholine

100%

Park S. , Kim J. A. , Choi S. , Suh S. A.

Journal of Physiology and Pharmacology

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2010

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tom 61

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nr 4

375-381

EN

Oxidative stress in the vascular wall has intimately been implicated in the apoptosis of human umbilical vein endothelial cells (HUVECs) by lysophosphatidylcholine (LPC). However, the major type of reactive oxygen species (ROS) in this apoptotic signaling pathway remains to be clarified. In this study, we report that superoxide mediate LPC-induced caspase-3 dependent apoptosis in cultured HUVECs. The stimulation of HUVECs with LPC evoked apoptosis and ROS generation, and inhibited nitric oxide (NO) production in a dose-dependent manner. The classical caspase-3 dependent apoptosis was determined after 16 hours treatment by Western blotting using an antibody against cleaved caspase-3. The caspase-3 activation induced by LPC was prominently inhibited by antioxidants or NO donors and enhanced by NO inhibitors. Especially, LPC-induced caspase-3 activation was inhibited by superoxide dismutase (SOD) and enhanced by ammonium tetrathiomolybdate, SOD inhibitor. Additionally, xanthine/xanthine oxidase mixture increased the caspase-3 activation but catalase failed to reduce this superoxide-induced caspase-3 activation. These findings indicate that the superoxide generation caused by LPC activates the caspase-3 which results in HUVECs death. This study reveals some evidences linking superoxide with caspase-3 activation and provides a new dimension to superoxide-mediated caspase-3 activation in developing the endothelial dysfunction and atherosclerosis.

4

Gas chromatographic determination of phenol in fish tissues as a phenyl acetate derivative following solvent extraction of acidified samples

88%

Kim H. , Kim Y. , Park S. , Lee J. , Choi J.

Acta Chromatographica

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2020

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tom Vol. 32, no. 1

64--67

EN

This study aimed to develop a chromatographic method to quantitatively determine phenol in fish tissues. This method involves solvent extraction of acidified samples, followed by derivatization to phenyl acetate and analysis with gas chromatography coupled with mass spectrometry (GC–MS). Phenol in a representative tissue sample (belly, gill, or renal tubules), which was homogenized with 2 N sulfuric acid, was extracted with ethyl acetate and derivatized to phenyl acetate using acetic anhydride and K2CO3 in water. An n-butyl acetate extract was injected into the GC–MS. The linearity (r2) of the calibration curve was greater than 0.996. The analytical repeatability, which is expressed as the relative standard deviation, was less than 6.14%, and the recovery was greater than 96.3%. The method detection limit and the limit of quantitation were 8.0 μg/kg and 26 μg/kg, respectively. The proposed method is also applicable to the analysis of other biological tissues for phenol and its analogs, such as pentachlorophenol.

5

Attempted rescue of circling mice by hair cell-specific expression (Myo7a promoter) of tmie transgene

88%

Park S. , Jang S. , Lee J.-H. , Kim S. H. , Ryoo Z. Y.

Medycyna Weterynaryjna

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2017

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tom 73

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nr 07

EN

The spontaneous mutant circling mouse (cir/cir) is deaf and displays abnormal behavior, particularly circling and head tossing. To rescue the circling mouse phenotype, we produced transgenic mice with hair cell-specific expression of the transmembrane inner ear (tmie) gene, using the Myo7a promoter, and generated cir/cir homozygous mice carrying the transgene (cir/cir-tgMyo7a) by breeding with circling mice. The cir/cir-tgMyo7a mice still exhibited circling behavior and were unable to swim in water unlike cir/ cir-tgCMV mice and wild-type mice. An auditory brainstem response (ABR) test demonstrated that the cir/cir-tgMyo7a mice could not respond to sound. Immunohistochemical analysis showed enhanced green fluorescent protein, a marker of tmie expression, in the inner and outer hair cells of the cir/cir-tgMyo7a mice. Hair cells and spiral ganglion neurons in the cir/cir-tgMyo7a mice were recovered, but not completely. This study demonstrates that tmie transgene expression in hair cells alone could not restore wild-type hearing and behavior in circling mice.

6

Isotopic water separation using AGMD and VEMD

88%

Kim J. , Park S. , Kim T.-S. , Jeong D.-Y. , Ko K.-H.

Nukleonika

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2004

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tom Vol. 49, nr 4

137-142

EN

The 18O isotopic water permeation and separation characteristics of a hydrophobic PTFE membrane using Air Gap Membrane Distillation (AGMD) and Vacuum Enhanced Membrane Distillation (VEMD) were investigated. Permeation fluxes were measured by weighing the collected membrane-permeated water vapor. 18O/16O of each water sample was analyzed by the Tunable Diode Laser Absorption Spectroscopy (TDLAS). We observed the effects of the air filled membrane pores and the temperature gradient applied to the membrane surfaces on the vapor permeation flux and the oxygen isotope separation for the first time. For both AGMD and VEMD, the permeation flux and the degree of 18O separation increased as the membrane interfacial temperature gradient increased. Even though, oxygen isotope separation and the permeation flux for VEMD is slightly higher than AGMD, the latter may be more efficient from the system's operational point of view.

7

Stimulation of large-conductance Ca2plus-activated Kplus channels by the Naplus-Ca2plus exchanger inhibitor dichlorobenzamil in cultured human umbilical vein endothelial cells and mouse aortic smooth muscle cells

88%

Liang G. H. , Park S. , Kim J. A. , Choi S. , Suh S. H.

Journal of Physiology and Pharmacology

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2009

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tom 60

|

nr 1

43-50

EN

We investigated the effects of the selective inhibitor of Na+/Ca2+ exchanger (NCX), 2',4'- and 3',4'-dichlorobenzamil (DCB), on large-conductance Ca2+-activated K+ (BKCa) channels in cultured human umbilical vein endothelial cells (HUVECs) and fresh isolated mouse aortic smooth muscle cells (MASMCs) using the patch clamp techniques. Both kinds of DCB reversibly activated BKCa currents in whole-cell clamped HUVECs or MASMCs. The EC50 of 2',4'-DCB for BKCa current activation in HUVECs was 2.64 ± 0.10 µM. In inside-out and outside-out patches, 2',4'-DCB remarkably increased BKCa channels activity. 2',4'-DCB increased open frequency, but had no significant effect on mean open time. In inside-out patches, 2',4'-DCB shifted the relationship curve between [Ca2+]i and open probability (NPo) to the left; the [Ca2+]i required to evoke half-maximal activation changed from 1087.45 ± 142.91 nM to 500.24 ± 66.83 nM by 10 µM 2',4'-DCB. In addition, 2',4'-DCB shifted the relationship curve between membrane potential and NPo to the left; the membrane potential to evoke half-maximal activation changed from 81.1 ± 2.4 to 64.7 ± 3.1 mV by 10 µM 2',4'-DCB. 3',4'-DCB also increased BKCa channels activity. There was no significant difference in the effect of DCB on BKCa channels between both excised patches. These results suggested that 2',4'- and 3',4'-DCB activate BKCa channels activity in HUVECs and MASMCs by increasing the sensitivity of BKCa channels to cytosolic free Ca2+ and membrane potential. Our report would provide a consideration if they are used as NCX blocker in vascular endothelial cells or smooth muscle cells.

8

Development of single-filter Doppler signal discrimination method for incoherent Doppler lidar system

75%

Choi S. , Baik S. , Park S. , Song I. , Kim D. , Jung J.

Optica Applicata

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2012

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tom Vol. 42, nr 3

545-553

EN

In this paper, we present a single-filter Doppler signal discrimination method for an incoherent Doppler lidar system that has been developed by the Korea Atomic Energy Research Institute. For the incoherent Doppler system, we use an injection-seeded pulsed Nd:YAG laser as a transmitter and an iodine filter as a Doppler frequency discriminator. To reduce the temperature-dependence error, a single iodine filter is used to lock the laser frequency and to detect the Doppler frequency shift. The mean squared error of the frequency locking process is 3.87 MHz, which corresponds to a wind velocity detection limit of approximately 1.04 m/s. The range and velocity measurements are performed using a tunable rotating disc. The results are consistent with those of previous studies in terms of the correlation between the signal ratio (signal/reference) and the actual speed of the rotating disc.

9

Proteomic analysis of tumor tissue in CT-26 implanted BALB/C mouse after treatment with ascorbic acid

75%

Lee J. , Lee G. , Park J. H. , Lee S. , Yeom C.-H. , Na B. , Park S.

Cellular and Molecular Biology Letters

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2012

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tom 17

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nr 1

EN

Tumor establishment and penetration consists of a series of complex processes involving multiple changes in gene expression and protein modification. Proteome changes of tumor tissue were investigated after intraperitoneal administration of a high concentration of ascorbic acid in BALB/C mice implanted with CT-26 cancer cells using two-dimensional gel electrophoresis and mass spectrometry. Eighteen protein spots were identified whose expression was different between control and ascorbic acid treatment groups. In particular, eukaryotic translation initiation factor 3 subunit 1, nucleophosmin, latexin, actin-related protein 2/3 complex subunit 5, M2-type pyruvate kinase, vimentin, tumor protein translationally-controlled 1, RAS oncogene family Ran, plastin 3 precursor, ATPase, Rho GDT dissociation inhibitor β, and proteasome activator subunit 2 expression were quantitatively up-regulated. The increase in the level of these proteins was accompanied by an increase in mRNA level. The cytoskeleton protein actin, vimentin, and tumor protein translationally-controlled 1 showed quantitative expression profile differences. A change in actin cytoskeleton distribution, functionally relevant to the proteome result, was observed after treatment with ascorbic acid. These results suggest a previously undefined role of ascorbic acid in the regulation of cytoskeleton remodeling in tumor tissues.

10

Studies of the erythrocyte spectrin tetramerization region

75%

Park S. , Mehboob S. , Luo B.-H. , Hurtuk M. , Johnson M. E. , Fung L. W.-M.

Cellular and Molecular Biology Letters

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2001

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tom 06

|

nr 3

571-585

11

Molecular studies of the erythrocyte spectrin tetramerization region

75%

Park S. , Mehboob S. , Luo B. H. , Hurtuk M. G. , Johnson M. E. , Fung L. W. M.

Cellular and Molecular Biology Letters

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2001

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tom 06

|

nr 2

12

Regulatory genes that control embryo development

63%

Harada J. J. , Le B. , Bui A. , Kwong L. , Pelletier J. , Stone S. L. , Braybrook S. A. , Park S. , Fischer R. L. , Goldberg R. B.

Acta Biologica Cracoviensia. Series Botanica. Supplement

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2005

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tom 47

|

nr 1

13

Seasonal variation of aflatoxin B1 content in dairy feed

63%

Ismail A. , Riaz M. , Akhtar S. , Yoo S. H. , Park S. , Abid M. , Aziz M. , Ahmad Z.

Journal of Animal and Feed Sciences

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2017

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tom 26

|

nr 1

EN

Aflatoxin B1 (AFB1 ) is a fungal metabolite and highly carcinogenic compound of category 1 according to the International Agency for Research on Cancer. In the liver AFB1 from contaminated feed is bioconverted into aflatoxin M1 and can be easily diffused to the animal milk. Provision of healthy milk for humans, particularly infants and adults, therefore, entails monitoring of AFB1 level in the feed for dairy animals. In the present study, AFB1 level was monitored in three different types of animal feed comprising commercially available animal feed, fresh fodder and leftover bread fed to dairy animals between October 2014 and September 2015. AFB1 was found in all collected feed samples at the amounts: 30.5%, 2.8% and 88.9% in commercial feed, fresh fodder and leftover bread samples, respectively. All these levels were over the EU permissible limits (5 μg · kg−1). Mean maximum levels of AFB1 were observed in all samples collected in the winter season, whereas the mean minimum levels – in the summer months. The results of the present study indicated that the leftover bread samples and commercial feed contain high levels of AFB1 , and so strict measures should be adopted to prevent dairy animal feed and at the same time the animal milk from aflatoxin contamination.