Sequence- and site-specific photodissociation at 266 nm of protonated synthetic polypeptides containing a tryptophanyl residue

Oh, Joo Yeon,Moon, Jeong Hee,Kim, Myung Soo John Wiley Sons, Ltd. 2004 Rapid communications in mass spectrometry Vol.18 No.22

<P>Photodissociation at 266 nm of protonated synthetic polypeptides containing a tryptophanyl residue was investigated using a homebuilt tandem time-of-flight mass spectrometer equipped with a matrix-assisted laser desorption/ionization source. Efficient photodissociation of the protonated peptides was demonstrated. Most of the intense peaks in the laser-induced tandem mass spectra were sequence ions. Furthermore, sequence ions due to cleavages at all the peptide bonds were observed; this is a feature of the technique that is particularly useful for peptide sequencing. Fragmentations at both ends of the tryptophanyl residue were especially prevalent, which can be useful for location of the tryptophanyl chromophore in a peptide. Copyright © 2004 John Wiley & Sons, Ltd.</P>

Dexamethasone-conjugated polyethylenimine as an efficient gene carrier with an anti-apoptotic effect to cardiomyocytes

Kim, Hyunjung,Kim, Hyun Ah,Bae, Yun Mi,Choi, Joon Sig,Lee, Minhyung John Wiley Sons, Ltd. 2009 The journal of gene medicine Vol.11 No.6

<B>Background</B><P>Dexamethasone is a potent glucocorticoid with anti-inflammatory effects. Dexamethasone can protect ischemic cardiomyocytes from apoptosis. To apply the anti-apoptotic effect of dexamethasone to ischemic disease gene therapy, dexamethasone-conjugated polyethylenimine (PEI-Dexa) was synthesized and evaluated as an anti-apoptotic gene carrier.</P><B>Methods</B><P>PEI-Dexa was synthesized with low molecular weight polyethylenimine (PEI2K, 2 kDa). The transfection efficiency and cytotoxicity of PEI-Dexa were evaluated by luciferase assay and the MTT assay. To evaluate the anti-apoptotic effect, PEI-Dexa/DNA complex was transfected into cells and the cells were treated with H<SUB>2</SUB>O<SUB>2</SUB>. Cell viability and apoptosis level were measured by the MTT assay and caspase-3 assay, respectively.</P><B>Results</B><P>A transfection assay into H9C2 rat cardiomyocytes showed that PEI-Dexa had the highest transfection efficiency at an 8 : 1 weight ratio (PEI-Dexa/DNA). At this ratio, PEI-Dexa had higher transfection efficiency than high molecular polyethylenimine (PEI25K, 25 kDa) and PEI2K. In addition, the cytotoxicity of PEI-Dexa was lower than that of PEI25K. To evaluate the anti-apoptotic effect, PEI-Dexa/pSV-Luc or PEI2K/pSV-Luc was transfected into H9C2 cells and the cells were treated with H<SUB>2</SUB>O<SUB>2</SUB>. PEI-Dexa was found to reduce caspase-3 activity and increase cell viability compared to PEI2K. Heme oxygenase-1 (HO-1) can protect ischemic cardiomyocytes from apoptosis. Therefore, pSV-HO-1 was cloned and transfected into H9C2 cells using PEI-Dexa. The cells transfected with PEI-Dexa/pSV-HO-1 complex had lower caspase-3 activity and higher viability than the cells transfected with PEI-Dexa/pSV-Luc complex after the H<SUB>2</SUB>O<SUB>2</SUB> treatment.</P><B>Conclusions</B><P>PEI-Dexa is an efficient gene carrier with an anti-apoptotic effect and may be useful for anti-apoptotic gene therapy in combination with pSV-HO-1. Copyright © 2009 John Wiley & Sons, Ltd.</P>

Identification of a naturally-occurring 8-[α-D-glucopyranosyl-(1→6)-β-D-glucopyranosyl]daidzein from cultivated kudzu root

Nguyen, Van Dao,Min, Byoung-Cheol,Kyung, Myung-Ok,Park, Jong-Tae,Lee, Byong Hoon,Choi, Chung-Hyo,Seo, Nam-Seok,Kim, Yong-Ro,Ahn, Dong Uk,Lee, Sung-Joon,Park, Cheon-Seok,Kim, Jung-Wan,Park, Kwan-Hwa John Wiley Sons, Ltd. 2009 Phytochemical analysis Vol.20 No.6

<P>Introduction – Kudzu root (Radix puerariae) is a rich source of isoflavones that are effective in preventing osteoporosis, heart disease and symptoms associated with menopause. The major isoflavonoids in kudzu root extracts were reported as puerarin, daidzin and daidzein. Recently, an unknown isoflavonoid (compound 1) was detected from one-year-old kudzu root cultivated in Vietnam.</P><P>Objective – To identify a novel compound 1 in kudzu root extract and determine the structure of the compound by ESI<SUP>+</SUP> TOF MS-MS, <SUP>1</SUP>H-, <SUP>13</SUP>C-NMR and enzymatic hydrolysis.</P><P>Methodology – Samples were prepared by extraction of one-year-old kudzu root with 50% ethanol and the isoflavonoids were purified using recycling preparative HPLC. Unknown compound 1 was detected using UV-light at 254 nm in TLC and HPLC analyses. The molecular weight of 1 was determined using a TOF mass spectrometer equipped with an electrospray ion source. The structure of 1 was determined from the <SUP>13</SUP>C and <SUP>1</SUP>H NMR spectra recorded at 100.40 and 400.0 MHz, respectively.</P><P>Results – ESI<SUP>+</SUP> TOF MS-MS analysis shows that 1 is a puerarin diglycoside. The interglycosidic linkage of diglycoside determined by <SUP>1</SUP>H-, <SUP>13</SUP>C-NMR, and enzymatic hydrolysis suggests that 1 has a glucosyl residue linked to puerarin by an α-1,6-glycosidic bond. This compound is the first naturally-occurring 8-[α-D-glucopyranosyl-(1→6)-β-D-glucopyranosyl]daidzein in kudzu root. The concentration of glucosyl-α-1,6-puerarin in kudzu root was 2.3 mg/g as determined by HPLC.</P><P>Conclusion – The results indicate that puerarin diglycoside is one of the major isoflavonoids in kudzu root and has a significant impact on the preparation of highly water-soluble glycosylated puerarin. Copyright © 2009 John Wiley & Sons, Ltd.</P>

Preparative isolation of six major saponins from Platycodi Radix by high-speed counter-current chromatography

Ha, Young Wan,Kim, Yeong Shik John Wiley Sons, Ltd. 2009 Phytochemical analysis Vol.20 No.3

<B>Introduction</B><P>Platycosides, the primary constituents of Platycodi Radix, are known to have numerous and varied biological activities, exerting anti-inflammation, anti-allergy, anti-tumour, anti-obesity and anti-hyperlipidemia effects. However, effective methods for isolating and purifying platycosides from Platycodi Radix are not currently available.</P><B>Objective</B><P>To develop an efficient method for the preparative separation of six platycosides from Platycodi Radix by high-speed counter-current chromatography (HSCCC) coupled with an evaporative light scattering detection (ELSD) system.</P><B>Methodology</B><P>Preparative separation was performed by water extraction using reversed-phase C<SUB>18</SUB> column chromatography on an HSCCC-ELSD system. A two-phase solvent system comprised hexane–n-butanol–water (1:40:20, v/v) and (1:10:5, v/v) was employed. Two other key parameters, revolution speed of the separation column and flow-rate of the mobile phase, were also investigated for optimum HSCCC performance. Each peak fraction obtained from separation of the platycosides was collected according to the ELSD elution profile and determined by HPLC.</P><B>Results</B><P>Using the described method, six platycosides, all with purities of over 94%, could be isolated from 300 mg of the platycoside-enriched fraction. Their structures were characterized by electrospray ionisation mass spectrometry (ESI-MS), <SUP>1</SUP>H-NMR and <SUP>13</SUP>C-NMR.</P><B>Conclusion</B><P>Six of the main bioactive platycosides in Platycodi Radix could be isolated and purified systematically by HSCCC. Copyright © 2009 John Wiley & Sons, Ltd.</P>

A hybrid interface method for three-dimensional multiphase flows based on front tracking and level set techniques

Shin, Seungwon,Juric, Damir John Wiley Sons, Ltd. 2009 International journal for numerical methods in flu Vol.60 No.7

<P>Successful interface methods for multiphase flows need to be designed to operate well in the opposite extremes of strongly surface tension-dominant flows on the one hand and strongly deforming flows on the other. To this end, recent advances in direct numerical simulation of multiphase flows have involved the hybridization of popular methods. One hybrid approach developed by the authors is the level contour reconstruction method (LCRM), which combines the characteristics of both the front tracking and the level set method. It was designed specifically for general 3D multiphase flow problems where very dynamic and deformable interfaces interact and where accuracy, reliability, and simplicity are essential features. In this paper, we carry the hybridization of the LCRM with the level set technique to a further level in that the explicit calculation of a distance function is introduced and plays a crucial role in the interface reconstruction procedure as well as in the calculation of the surface tension force. An accurate method of computing the distance function directly from the tracked interface is presented whereby a vector distance function is found, i.e. the minimum distance to the interface as well as the corresponding minimum distance point location on the interface itself. This information allows us to calculate a compact curvature field for the computation of the surface tension force, which decreases the level of parasitic currents to a negligible level. Various benchmark test cases to demonstrate the accuracy of the new schemes compared with other existing methods are provided. Copyright © 2008 John Wiley & Sons, Ltd.</P>

Intracellular small interfering RNA delivery using genetically engineered double-stranded RNA binding protein domain

Kim, Juwon,Lee, Soo Hyeon,Choe, Joonho,Park, Tae Gwan John Wiley Sons, Ltd. 2009 The journal of gene medicine Vol.11 No.9

<B>Background</B><P>A variety of synthetic carriers, such as cationic polymers and lipids, have been used as nonviral carriers for small interfering RNA (siRNA) delivery. Although siRNA polyplexes and lipoplexes exhibited good gene silencing efficiencies, they often showed serious cytotoxicities, which are not useful for clinical applications. A double-stranded RNA binding cellular protein with highly specific siRNA binding property and noncytotoxicity was used for siRNA delivery.</P><B>Methods</B><P>A double-stranded RNA binding domain (dsRBD) of human double-stranded RNA activated protein kinase R was genetically produced and utilized to complex siRNA for intracellular delivery. For characterization of the siRNA/dsRBD complexes, decomplexation assay and RNase protection assay were performed. Cytotoxicity and target gene inhibition ability were also examined using human carcinoma cell lines.</P><B>Results</B><P>The recombinantly produced polypeptide dsRBD exhibited its inherent binding activity for siRNA without sequence specificity, and the siRNA/dsRBD complexes protected siRNA from degradation by ribonucleases. Green fluorescent protein (GFP) siRNA/dsRBD complexes showed prominent down-regulation of a target GFP gene, when an endosomal escape function was supplemented by addition of a fusogenic peptide, KALA, in the formulation.</P><B>Conclusions</B><P>The results suggest that dsRBD-based protein carriers could be successfully applied for a wide range of therapeutic siRNAs for intracellular gene inhibition without showing any cytotoxicity. Copyright © 2009 John Wiley & Sons, Ltd.</P>

A discontinuous Galerkin method for elliptic interface problems with application to electroporation

Guyomarc'h, Gré,gory,Lee, Chang-Ock,Jeon, Kiwan John Wiley Sons, Ltd. 2009 Communications in numerical methods in engineering Vol.25 No.10

<P>We solve elliptic interface problems using a discontinuous Galerkin (DG) method, for which discontinuities in the solution and in its normal derivatives are prescribed on an interface inside the domain. Standard ways to solve interface problems with finite element methods consist in enforcing the prescribed discontinuity of the solution in the finite element space. Here, we show that the DG method provides a natural framework to enforce both discontinuities weakly in the DG formulation, provided the triangulation of the domain is fitted to the interface. The resulting discretization leads to a symmetric system that can be efficiently solved with standard algorithms. The method is shown to be optimally convergent in the L<SUP>2</SUP>-norm. We apply our method to the numerical study of electroporation, a widely used medical technique with applications to gene therapy and cancer treatment. Mathematical models of electroporation involve elliptic problems with dynamic interface conditions. We discretize such problems into a sequence of elliptic interface problems that can be solved by our method. We obtain numerical results that agree with known exact solutions. Copyright © 2008 John Wiley & Sons, Ltd.</P>

Qualitative and quantitative comparison of N-glycans between pig endothelial and islet cells by high-performance liquid chromatography and mass spectrometry-based strategy

Kim, Yun-Gon,Gil, Geun-Cheol,Jang, Kyung-Soon,Lee, Sukmook,Kim, Hyoung-Il,Kim, Jung-Sik,Chung, Junho,Park, Chung-Gyu,Harvey, David J.,Kim, Byung-Gee John Wiley Sons, Ltd. 2009 Journal of mass spectrometry Vol.44 No.7

<P>N-glycan structures released from miniature pig endothelial and islet cells were determined by matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF), negative ion electrospray ionization (ESI) MS/MS and normal-phase high performance liquid chromatography (NP-HPLC) combined with exoglycosidase digestion. Totally, the identified structures were 181 N-glycans including 129 sialylated and 18 α-galactosylated glycans from pig endothelial cells and 80 N-glycans including 41 sialylated and one α-galactosylated glycans from pig islet cells. The quantity of the α-galactosylated glycans from pig islet cells was certainly neglectable compared to pig endothelial cells. A number of NeuGc-terminated N-glycans (80 from pig endothelial cells and 13 from pig islet cells) are newly detected by our mass spectrometric strategies. The detailed structural information will be a matter of great interest in organ or cell xenotransplantation using α 1,3-galactosyltransferase gene-knockout (GalT-KO) pig. Copyright © 2009 John Wiley & Sons, Ltd.</P>

Client ahead-of-time compiler for embedded Java platforms

Hong, Sunghyun,Kim, Jin-Chul,Moon, Soo-Mook,Shin, Jin Woo,Lee, Jaemok,Oh, Hyeong-Seok,Choi, Hyung-Kyu John Wiley Sons, Ltd. 2009 SOFTWARE-PRACTICE & EXPERIENCE Vol.39 No.3

<P>Many embedded Java platforms execute two types of Java classes: those installed statically on the client device and those downloaded dynamically from service providers at run time. For achieving higher performance, the static Java classes can be compiled into machine code by ahead-of-time compiler (AOTC) in the server, and the translated machine code can be installed on the client device. Unfortunately, AOTC cannot be applicable to the dynamically downloaded classes. This paper proposes client-AOTC (c-AOTC), which performs AOTC on the client device using the just-in-time compiler (JITC) module installed on the device, obviating the JITC overhead and complementing the server-AOTC. The machine code of a method translated by JITC is cached on a persistent memory of the device, and when the method is invoked again in a later run of the program, the machine code is loaded and executed directly without any translation overhead. A major issue in c-AOTC is relocation because some of the address constants embedded in the cached machine code are not correct when the machine code is loaded and used in a different run; those addresses should be corrected before they are used. Constant pool resolution and inlining complicate the relocation problem, and we propose our solutions. The persistent memory overhead for saving the relocation information is also an issue, and we propose a technique to encode the relocation information and compress the machine code efficiently. We developed a c-AOTC on Sun's CDC VM reference implementation, and our evaluation results indicate that c-AOTC can improve the performance significantly, as much as an average of 12% for EEMBC and 4% for SpecJVM98, with a persistent memory overhead of 1% on average. Copyright © 2008 John Wiley & Sons, Ltd.</P>

Performance analysis of APSK modulation for DVB-S2 transmission over nonlinear channels

Sung, Wonjin,Kang, Seokheon,Kim, Pansoo,Chang, Dae-Ig,Shin, Dong-Joon John Wiley Sons, Ltd. 2009 International journal of satellite communications Vol.27 No.6

<P>For increased bandwidth efficiency and receiver performance, standards for satellite broadcasting systems are evolving by utilizing efficient transmission techniques. The second-generation digital video broadcasting for satellites (DVB-S2) adopts the amplitude phase shift keying (APSK) modulation for enhanced performance over nonlinear channels. In this paper, we derive error rate bounds for APSK modulated symbols and generalize the bounds to the case of distorted constellation, which occurs when the maximum transmission amplitude is saturated by the soft-limiter type channel. The derived bound is shown to significantly improve the previously known result, to accurately predict both the symbol error rate and bit error rate in the entire signal-to-noise ratio (SNR) region of interest. Using the derived formula, the optimal input power level for the soft-limiter channel is determined, and the corresponding minimal error rates for 16- and 32-APSK are quantified. The result is also interpreted in terms of optimal input back-off (IBO) for nonlinear power amplifiers by evaluating the performance degradation as a function of IBO. Copyright © 2009 John Wiley & Sons, Ltd.</P>