Sphingomonas ginsenosidivorax sp. nov., with the ability to transform ginsenosides.

A Gram-negative, strictly aerobic, non-motile, non-spore-forming and rod-shaped bacterial strain designated KHI67(T) was isolated from sediment of the Gapcheon River in South Korea and its taxonomic position was investigated by using a polyphasic approach. Strain KHI67(T) was observed to grow optimally at 25-30 °C and at pH 7.0 on nutrient and R2A agar.

Nocardioides panaciterrulae sp. nov., isolated from soil of a ginseng field, with ginsenoside converting activity.

A Gram-positive, coccoid to rod-shaped, non-spore-forming bacterium, designated Gsoil 958(T), was isolated from soil of a ginseng field located in Pocheon province in South Korea. This bacterium was characterized in order to determine its taxonomic position by using a polyphasic approach. Strain Gsoil 958(T) was observed to grow well at 25-30 °C and at pH 7.

Restricted N-glycan conformational space in the PDB and its implication in glycan structure modeling.

Understanding glycan structure and dynamics is central to understanding protein-carbohydrate recognition and its role in protein-protein interactions. Given the difficulties in obtaining the glycan's crystal structure in glycoconjugates due to its flexibility and heterogeneity, computational modeling could play an important role in providing glycosylated protein structure models. To address if glycan structures available in the PDB can be used as templates or fragments for glycan modeling, we present a survey of the N-glycan structures of 35 different sequences in the PDB.

Two Dimensional Window Exchange Umbrella Sampling for Transmembrane Helix Assembly.

The method of window exchange umbrella sampling molecular dynamics (WEUSMD) with a pre-optimized parameter set was recently used to obtain the most probable conformations and the energetics of transmembrane (TM) helix assembly of a generic TM sequence. When applied to glycophorin A TM domain (GpA-TM) using the restraint potentials along the helix-helix distance, however, tight interfacial packing of GpA-TM resulted in insufficient conformational sampling at short helix-helix separation. This sampling issue is addressed by extending the WEUSMD into two dimensions with the restraint potentials along the helix-helix distance and crossing angle.

Tunable emission from blue to white light in single-phase Na(0.34)Ca(0.66-x-y)Al(1.66)Si(2.34)O8:xEu2+,yMn2+ (x = 0.07) phosphor for white-light UV LEDs.

A series of single-phased emission-tunable Na(0.34)Ca(0.66)Al(1.

Assessing smectic liquid-crystal continuum models for elastic bilayer deformations.

For four decades, since W. Helfrich's pioneering study of smectic A liquid crystals in 1973, continuum elastic models (CEMs) have been employed as tools to understand the energetics of protein-induced lipid bilayer deformations. Among the assumptions underlying this use is that all relevant protein-lipid interactions can be included in the continuum representation of the protein-bilayer interactions through the physical parameters determined for protein-free bilayers and the choice of boundary conditions at the protein/bilayer interface.

Dry anaerobic digestion of food waste under mesophilic conditions: performance and methanogenic community analysis.

The performance of dry anaerobic digestion (AD) of food waste was investigated under mesophilic conditions and the methanogenic community was investigated using 454 pyrosequencing. Stable dry AD was achieved by hydraulic retention time (HRT) control without the addition of alkali agents. The average CH4 production rate, CH4 content, and volatile solid reduction rate were 2.

Lactobacillus ginsenosidimutans sp. nov., isolated from kimchi with the ability to transform ginsenosides.

Biotransformation of ginsenosides was examined using lactic acid bacteria isolated from several kinds of kimchi. A Gram-positive, facultatively anaerobic, non-motile, non-spore-forming, and rod-shaped lactic acid bacterial strain, designated EMML 3041(T), was determined to have ginsenoside-converting activity and its taxonomic position was investigated using a polyphasic approach. Strain EMML 3041(T) displayed β-glucosidase activity that was responsible for its ability to transform ginsenoside Rb1 (one of the dominant active components of ginseng) to F2 via gypenoside XVII, ginsenoside Rb2 to compound Y via compound O, ginsenoside Rc to compound Mc via compound Mc1, and ginsenoside Rd to ginsenoside F2.

Suitability of autologous serum for expanding rabbit adipose-derived stem cell populations.

Adipose-derived stem cells (ASCs) are believed to have potential use for treating many illnesses. Most cells, including ASCs, are generally cultured in medium containing fetal bovine serum (FBS). However, FBS, which could induce an immune response or infection, is not recommended for clinical applications.

Bioconversion of ginsenoside Rc into Rd by a novel α-L-arabinofuranosidase, Abf22-3 from Leuconostoc sp. 22-3: cloning, expression, and enzyme characterization.

A novel α-L-arabinofuranosidase (Abf22-3) that could biotransform ginsenoside Rc into Rd was obtained from the ginsenoside converting Leuconostoc sp. strain 22-3, isolated from the Korean fermented food kimchi. The gene, termed abf22-3, consisting of 1,527 bp and encoding a protein with a predicted molecular mass of 58,486 Da was cloned into the pMAL-c2x (TEV) vector.

CHARMM-GUI Ligand Binder for absolute binding free energy calculations and its application.

Advanced free energy perturbation molecular dynamics (FEP/MD) simulation methods are available to accurately calculate absolute binding free energies of protein-ligand complexes. However, these methods rely on several sophisticated command scripts implementing various biasing energy restraints to enhance the convergence of the FEP/MD calculations, which must all be handled properly to yield correct results. Here, we present a user-friendly Web interface, CHARMM-GUI Ligand Binder ( http://www.

Protein dynamics and ion traffic in bacterioferritin.

Bacterioferritin (Bfr) is a spherical protein composed of 24 subunits and 12 heme molecules. Bfrs contribute to regulate iron homeostasis in bacteria by capturing soluble but potentially toxic Fe(2+) and by compartmentalizing it in the form of a bioavailable ferric mineral inside the protein's hollow cavity. When iron is needed, Fe(3+) is reduced and mobilized into the cytosol as Fe(2+).

Glycan fragment database: a database of PDB-based glycan 3D structures.

The glycan fragment database (GFDB), freely available at http://www.glycanstructure.org, is a database of the glycosidic torsion angles derived from the glycan structures in the Protein Data Bank (PDB).

Tumor size as a prognostic factor in gastric cancer patient.

Purpose: The purpose of this study is to investigate the prognostic significance of tumor size for 5-year survival rate in patients with gastric cancer.

Materials And Methods: A total of 1,697 patients with gastric cancer, who underwent potentially curative gastrectomy, were evaluated. Patients were divided into 4 groups as follows, according to the median size of early and advanced gastric cancer, respectively: small early gastric cancer (tumor size ≤3 cm), large early gastric cancer (tumor size >3 cm), small advanced gastric cancer (tumor size ≤6 cm), and large advanced gastric cancer (tumor size >6 cm).

Novel blue-emitting Na(x)Ca(1-x)Al(2-x)Si(2+x)O8:Eu2+ (x = 0.34) phosphor with high luminescent efficiency for UV-pumped light-emitting diodes.

A novel blue-emitting phosphor, Na(0.34)Ca(0.66)Al(1.

Identification of ligand templates using local structure alignment for structure-based drug design.

With a rapid increase in the number of high-resolution protein-ligand structures, the known protein-ligand structures can be used to gain insight into ligand-binding modes in a target protein. On the basis of the fact that the structurally similar binding sites share information about their ligands, we have developed a local structure alignment tool, G-LoSA (graph-based local structure alignment). The known protein-ligand binding-site structure library is searched by G-LoSA to detect binding-site structures with similar geometry and physicochemical properties to a query binding-site structure regardless of sequence continuity and protein fold.

Characterization of the ginsenoside-transforming recombinant β-glucosidase from Actinosynnema mirum and bioconversion of major ginsenosides into minor ginsenosides.

This study focused on the cloning, expression, and characterization of ginsenoside-transforming recombinant β-glucosidase from Actinosynnema mirum KACC 20028(T) in order to biotransform ginsenosides efficiently. The gene, termed as bglAm, encoding a β-glucosidase (BglAm) belonging to the glycoside hydrolase family 3 was cloned. bglAm consisted of 1,830 bp (609 amino acid residues) with a predicted molecular mass of 65,277 Da.

Promoting Li2O2 oxidation by an La(1.7)Ca(0.3)Ni(0.75)Cu(0.25)O4 layered perovskite in lithium-oxygen batteries.

We demonstrate for the first time that La(1.7)Ca(0.3)Ni(0.

Phosphor in glasses with Pb-free silicate glass powders as robust color-converting materials for white LED applications.

Phosphor-in-glass (PiG) typed robust color converters were fabricated using Pb-free silicate glasses for high-power white LED applications. SiO2-B2O3-RO(R=Ba,Zn) glass powder showed good sintering behavior and high visible transparency under the sintering condition of 750 °C for 30 min without noticeable interaction with phosphors. By simply changing the thickness of the PiG plate or mixing ratio of glass to Y3Al5O12:Ce3+ phosphor, CIE chromaticity coordinates of the LED can be easily controlled.

Bioconversion of major ginsenosides Rg1 to minor ginsenoside F1 using novel recombinant ginsenoside hydrolyzing glycosidase cloned from Sanguibacter keddieii and enzyme characterization.

This study focuses on the cloning, expression, and characterization of recombinant ginsenoside hydrolyzing glycosidase from Sanguibacter keddieii in order to biotransform ginsenosides efficiently. The gene, termed bglSk, consists of 1857 bp and revealed significant homology to that of glycoside hydrolase family 3. The enzyme was over-expressed in Escherichia coli BL21 (DE3) using a GST-fused pGEX 4T-1 vector system.

Application of binding free energy calculations to prediction of binding modes and affinities of MDM2 and MDMX inhibitors.

Molecular docking is widely used to obtain binding modes and binding affinities of a molecule to a given target protein. Despite considerable efforts, however, prediction of both properties by docking remains challenging mainly due to protein's structural flexibility and inaccuracy of scoring functions. Here, an integrated approach has been developed to improve the accuracy of binding mode and affinity prediction and tested for small molecule MDM2 and MDMX antagonists.

Electroacupuncture enhances motor recovery performance with brain-derived neurotrophic factor expression in rats with cerebral infarction.

Objective: Electroacupuncture (EA) is a traditional medicine in patients with post-stroke rehabilitation. Brain-derived neurotrophic factor (BDNF) is a potent growth factor involved in recovery following cerebral injury. The aim of the present study was to investigate whether EA increases BDNF levels and facilitates functional recovery.

Activity of tedizolid phosphate (TR-701) in murine models of infection with penicillin-resistant and penicillin-sensitive Streptococcus pneumoniae.

The in vitro activity of tedizolid (previously known as torezolid, TR-700) against penicillin-resistant Streptococcus pneumoniae (PRSP) clinical isolates and the in vivo efficacy of tedizolid phosphate (torezolid phosphate, TR-701) in murine models of PRSP systemic infection and penicillin-susceptible S. pneumoniae (PSSP) pneumonia were examined using linezolid as a comparator. The MIC(90) against 28 PRSP isolates was 0.

Improving the CHARMM force field for polyunsaturated fatty acid chains.

CHARMM36 (C36) is the most up-to-date pairwise additive all-atom lipid force field and is able to accurately represent bilayer properties of saturated and monounsaturated lipid molecules in the natural constant particle, pressure, and temperature (NPT) ensemble. However, molecular dynamics (MD) simulations on 1-stearoyl-2-docosahexaenoyl-sn-glycerco-3-phosphocholine (SDPC) bilayers of the polyunsaturated fatty acid (PUFA) chains result in inaccuracies of the surface area per lipid (SA), deuterium order parameters (S(CD)), and X-ray form factors. Therefore, in this study, high-level quantum mechanical calculations are used to improve the dihedral potential of neighboring double bonds, and the corresponding force field is referred to as C36p.

Circulating CD62E+ microparticles and cardiovascular outcomes.

Background: Activated endothelial cells release plasma membrane submicron vesicles expressing CD62E (E-selectin) into blood, known as endothelial microparticles (EMPs). We studied whether the levels of endothelial microparticles expressing CD62E(+), CD31(+)/Annexin-V(+), or CD31(+)/CD42(-) predict cardiovascular outcomes in patients with stroke history.

Methods/principal Findings: Patients with stroke history at least 3 months prior to enrolment were recruited.