Next Issue
Previous Issue

E-Mail Alert

Add your e-mail address to receive forthcoming issues of this journal:

Journal Browser

Journal Browser

Table of Contents

Int. J. Mol. Sci., Volume 13, Issue 7 (July 2012), Pages 7872-9399

  • Issues are regarded as officially published after their release is announced to the table of contents alert mailing list.
  • You may sign up for e-mail alerts to receive table of contents of newly released issues.
  • PDF is the official format for papers published in both, html and pdf forms. To view the papers in pdf format, click on the "PDF Full-text" link, and use the free Adobe Readerexternal link to open them.
View options order results:
result details:
Displaying articles 1-94
Export citation of selected articles as:

Research

Jump to: Review, Other

Open AccessArticle Synthesis and Electrochemical Proprieties of Novel Unsymmetrical Bis-Tetrathiafulvalenes and Electrical Conductivity of Their Charge Transfer Complexes with Tetracyanoquinodimethane (TCNQ)
Int. J. Mol. Sci. 2012, 13(7), 7872-7885; doi:10.3390/ijms13077872
Received: 18 May 2012 / Revised: 13 June 2012 / Accepted: 14 June 2012 / Published: 25 June 2012
Cited by 4 | PDF Full-text (225 KB) | HTML Full-text | XML Full-text
Abstract
The synthesis and properties of a series of bis-tetrathiafulvalenes (bis-TTFs) containing nitrophenyl, aminophenyl or dimethylaminophenyl is reported. The synthesis was carried out by using routes involving Wittig-type, cross-coupling, reduction and alkylation reactions. The electron donor ability of these new compounds has been measured
[...] Read more.
The synthesis and properties of a series of bis-tetrathiafulvalenes (bis-TTFs) containing nitrophenyl, aminophenyl or dimethylaminophenyl is reported. The synthesis was carried out by using routes involving Wittig-type, cross-coupling, reduction and alkylation reactions. The electron donor ability of these new compounds has been measured by cyclic voltammetry (CV). Charge transfer complexes with tetracyanoquinodimethane (TCNQ) were prepared by chemical redox reactions. The complexes have been proven to give conducting materials. Full article
Figures

Open AccessArticle A Specific Oligodeoxynucleotide Promotes the Differentiation of Osteoblasts via ERK and p38 MAPK Pathways
Int. J. Mol. Sci. 2012, 13(7), 7902-7914; doi:10.3390/ijms13077902
Received: 10 May 2012 / Revised: 11 May 2012 / Accepted: 15 June 2012 / Published: 25 June 2012
Cited by 8 | PDF Full-text (413 KB) | HTML Full-text | XML Full-text
Abstract
A specific oligodeoxynucleotide (ODN), ODN MT01, was found to have positive effects on the proliferation and activation of the osteoblast-like cell line MG 63. In this study, the detailed signaling pathways in which ODN MT01 promoted the differentiation of osteoblasts were systematically examined.
[...] Read more.
A specific oligodeoxynucleotide (ODN), ODN MT01, was found to have positive effects on the proliferation and activation of the osteoblast-like cell line MG 63. In this study, the detailed signaling pathways in which ODN MT01 promoted the differentiation of osteoblasts were systematically examined. ODN MT01 enhanced the expression of osteogenic marker genes, such as osteocalcin and type I collagen. Furthermore, ODN MT01 activated Runx2 phosphorylation via ERK1/2 mitogen-activated protein kinase (MAPK) and p38 MAPK. Consistently, ODN MT01 induced up-regulation of osteocalcin, alkaline phosphatase (ALP) and type I collagen, which was inhibited by pre-treatment with the ERK1/2 inhibitor U0126 and the p38 inhibitor SB203580. These results suggest that the ERK1/2 and p38 MAPK pathways, as well as Runx2 activation, are involved in ODN MT01-induced up-regulation of osteocalcin, type I collagen and the activity of ALP in MG 63 cells. Full article
Open AccessArticle l-2-Oxothiazolidine-4-Carboxylic Acid or α-Lipoic Acid Attenuates Airway Remodeling: Involvement of Nuclear Factor-κB (NF-κB), Nuclear Factor Erythroid 2p45-Related Factor-2 (Nrf2), and Hypoxia-Inducible Factor (HIF)
Int. J. Mol. Sci. 2012, 13(7), 7915-7937; doi:10.3390/ijms13077915
Received: 30 March 2012 / Revised: 9 June 2012 / Accepted: 18 June 2012 / Published: 25 June 2012
Cited by 9 | PDF Full-text (2101 KB) | HTML Full-text | XML Full-text
Abstract
Reactive oxygen species (ROS) play a crucial role in the pathogenesis of acute and chronic respiratory diseases. Antioxidants have been found to ameliorate airway inflammation and hyperresponsiveness in animal models employing short-term exposure to allergen. However, little data are available on the effect
[...] Read more.
Reactive oxygen species (ROS) play a crucial role in the pathogenesis of acute and chronic respiratory diseases. Antioxidants have been found to ameliorate airway inflammation and hyperresponsiveness in animal models employing short-term exposure to allergen. However, little data are available on the effect of antioxidants on airway remodeling and signaling pathways in chronic asthma. In the present study, we used a long-term exposure murine model of allergic airway disease to evaluate the effects of an antioxidant, l-2-oxothiazolidine-4-carboxylic acid (OTC) or α-lipoic acid (LA) on airway remodeling, focusing on the ROS-related hypoxia-inducible signaling. Long-term challenge of ovalbumin (OVA) increased ROS production, airway inflammation, and airway hyperresponsiveness, and developed features of airway remodeling such as excessive mucus secretion, subepithelial fibrosis, and thickening of the peribronchial smooth muscle layer. Administration of OTC or LA reduced these features of asthma, including airway remodeling, which was accompanied by suppression of transforming growth factor-β1, vascular endothelial growth factor, and T-helper 2 cytokines. In addition, OVA-induced activation of nuclear factor-κB (NF-κB), nuclear factor erythroid 2p45-related factor-2 (Nrf2), hypoxia-inducible factor (HIF)-1α, and HIF-2α was reduced by OTC or LA. Our results also showed that OTC or LA down-regulated phosphoinositide 3-kinase activity and decreased phosphorylation of p38 mitogen-activated protein kinase but not extracellular signal-regulated kinase 1/2 or c-Jun N-terminal kinase. These findings demonstrate that OTC and LA can inhibit activation of NF-κB, Nrf2, and HIF, leading to attenuate allergen-induced airway remodeling. Full article
Open AccessArticle Degradability Enhancement of Poly(Lactic Acid) by Stearate-Zn3Al LDH Nanolayers
Int. J. Mol. Sci. 2012, 13(7), 7938-7951; doi:10.3390/ijms13077938
Received: 10 April 2012 / Revised: 23 May 2012 / Accepted: 13 June 2012 / Published: 26 June 2012
Cited by 23 | PDF Full-text (868 KB) | HTML Full-text | XML Full-text
Abstract
Recent environmental problems and societal concerns associated with the disposal of petroleum based plastics throughout the world have triggered renewed efforts to develop new biodegradable products compatible with our environment. This article describes the preparation, characterization and biodegradation study of poly(lactic acid)/layered double
[...] Read more.
Recent environmental problems and societal concerns associated with the disposal of petroleum based plastics throughout the world have triggered renewed efforts to develop new biodegradable products compatible with our environment. This article describes the preparation, characterization and biodegradation study of poly(lactic acid)/layered double hydroxide (PLA/LDH) nanocomposites from PLA and stearate-Zn3Al LDH. A solution casting method was used to prepare PLA/stearate-Zn3Al LDH nanocomposites. The anionic clay Zn3Al LDH was firstly prepared by co-precipitation method from a nitrate salt solution at pH 7.0 and then modified by stearate anions through an ion exchange reaction. This modification increased the basal spacing of the synthetic clay from 8.83 Å to 40.10 Å. The morphology and properties of the prepared PLA/stearate-Zn3Al LDH nanocomposites were studied by X-ray diffraction (XRD), transmission electron microscope (TEM), scanning electron microscope (SEM), thermogravimetric analysis (TGA), tensile tests as well as biodegradation studies. From the XRD analysis and TEM observation, the stearate-Zn3Al LDH lost its ordered stacking-structure and was greatly exfoliated in the PLA matrix. Tensile test results of PLA/stearate-Zn3Al LDH nanocomposites showed that the presence of around 1.0–3.0 wt % of the stearate-Zn3Al LDH in the PLA drastically improved its elongation at break. The biodegradation studies demonstrated a significant biodegradation rate improvement of PLA in the presence of stearate-Zn3Al LDH nanolayers. This effect can be caused by the catalytic role of the stearate groups in the biodegradation mechanism leading to much faster disintegration of nanocomposites than pure PLA. Full article
Open AccessArticle Artificial Intelligence Techniques to Optimize the EDC/NHS-Mediated Immobilization of Cellulase on Eudragit L-100
Int. J. Mol. Sci. 2012, 13(7), 7952-7962; doi:10.3390/ijms13077952
Received: 9 April 2012 / Revised: 21 May 2012 / Accepted: 19 June 2012 / Published: 26 June 2012
Cited by 6 | PDF Full-text (228 KB) | HTML Full-text | XML Full-text
Abstract
Two artificial intelligence techniques, namely artificial neural network (ANN) and genetic algorithm (GA) were combined to be used as a tool for optimizing the covalent immobilization of cellulase on a smart polymer, Eudragit L-100. 1-Ethyl-3-(3-dimethyllaminopropyl) carbodiimide (EDC) concentration, N-hydroxysuccinimide (NHS) concentration and
[...] Read more.
Two artificial intelligence techniques, namely artificial neural network (ANN) and genetic algorithm (GA) were combined to be used as a tool for optimizing the covalent immobilization of cellulase on a smart polymer, Eudragit L-100. 1-Ethyl-3-(3-dimethyllaminopropyl) carbodiimide (EDC) concentration, N-hydroxysuccinimide (NHS) concentration and coupling time were taken as independent variables, and immobilization efficiency was taken as the response. The data of the central composite design were used to train ANN by back-propagation algorithm, and the result showed that the trained ANN fitted the data accurately (correlation coefficient R2 = 0.99). Then a maximum immobilization efficiency of 88.76% was searched by genetic algorithm at a EDC concentration of 0.44%, NHS concentration of 0.37% and a coupling time of 2.22 h, where the experimental value was 87.97 ± 6.45%. The application of ANN based optimization by GA is quite successful. Full article
Open AccessArticle DsHsp90 Is Involved in the Early Response of Dunaliella salina to Environmental Stress
Int. J. Mol. Sci. 2012, 13(7), 7963-7979; doi:10.3390/ijms13077963
Received: 7 May 2012 / Revised: 20 June 2012 / Accepted: 20 June 2012 / Published: 27 June 2012
Cited by 6 | PDF Full-text (870 KB) | HTML Full-text | XML Full-text | Supplementary Files
Abstract
Heat shock protein 90 (Hsp90) is a molecular chaperone highly conserved across the species from prokaryotes to eukaryotes. Hsp90 is essential for cell viability under all growth conditions and is proposed to act as a hub of the signaling network and protein homeostasis
[...] Read more.
Heat shock protein 90 (Hsp90) is a molecular chaperone highly conserved across the species from prokaryotes to eukaryotes. Hsp90 is essential for cell viability under all growth conditions and is proposed to act as a hub of the signaling network and protein homeostasis of the eukaryotic cells. By interacting with various client proteins, Hsp90 is involved in diverse physiological processes such as signal transduction, cell mobility, heat shock response and osmotic stress response. In this research, we cloned the dshsp90 gene encoding a polypeptide composed of 696 amino acids from the halotolerant unicellular green algae Dunaliella salina. Sequence alignment indicated that DsHsp90 belonged to the cytosolic Hsp90A family. Further biophysical and biochemical studies of the recombinant protein revealed that DsHsp90 possessed ATPase activity and existed as a dimer with similar percentages of secondary structures to those well-studied Hsp90As. Analysis of the nucleotide sequence of the cloned genomic DNA fragment indicated that dshsp90 contained 21 exons interrupted by 20 introns, which is much more complicated than the other plant hsp90 genes. The promoter region of dshsp90 contained putative cis-acting stress responsive elements and binding sites of transcriptional factors that respond to heat shock and salt stress. Further experimental research confirmed that dshsp90 was upregulated quickly by heat and salt shock in the D. salina cells. These findings suggested that dshsp90 might serve as a component of the early response system of the D. salina cells against environmental stresses. Full article
(This article belongs to the Special Issue Advances in Molecular Plant Biology)
Figures

Open AccessArticle Adsorption of Sodium Dodecyl Sulfate on Ge Substrate: The Effect of a Low-Polarity Solvent
Int. J. Mol. Sci. 2012, 13(7), 7980-7993; doi:10.3390/ijms13077980
Received: 7 February 2012 / Revised: 16 May 2012 / Accepted: 15 June 2012 / Published: 28 June 2012
Cited by 7 | PDF Full-text (436 KB) | HTML Full-text | XML Full-text
Abstract
This paper describes the adsorption of sodium dodecyl sulfate (SDS) molecules in a low polar solvent on Ge substrate by using Fourier transform infrared-attenuated total reflection (FTIR-ATR) spectroscopy and atomic force microscopy (AFM). The maximum SDS amount adsorbed is (5.0 ± 0.3) ×
[...] Read more.
This paper describes the adsorption of sodium dodecyl sulfate (SDS) molecules in a low polar solvent on Ge substrate by using Fourier transform infrared-attenuated total reflection (FTIR-ATR) spectroscopy and atomic force microscopy (AFM). The maximum SDS amount adsorbed is (5.0 ± 0.3) × 1014 molecules cm−2 in CHCl3, while with the use of CCl4 as subphase the ability of SDS adsorbed is 48% lower. AFM images show that depositions are highly disordered over the interface, and it was possible to establish that the size of the SDS deposition is around 30–40 nm over the Ge surface. A complete description of the infrared spectroscopic bands for the head and tail groups in the SDS molecule is also provided. Full article
Open AccessArticle High Resolution Crystal Structures of the Cerebratulus lacteus Mini-Hb in the Unligated and Carbomonoxy States
Int. J. Mol. Sci. 2012, 13(7), 8025-8037; doi:10.3390/ijms13078025
Received: 31 May 2012 / Revised: 14 June 2012 / Accepted: 15 June 2012 / Published: 28 June 2012
Cited by 2 | PDF Full-text (746 KB) | HTML Full-text | XML Full-text
Abstract
The nerve tissue mini-hemoglobin from Cerebratulus lacteus (CerHb) displays an essential globinfold hosting a protein matrix tunnel held to allow traffic of small ligands to and from the heme. CerHb heme pocket hosts the distal TyrB10/GlnE7 pair, normally linked to low rates
[...] Read more.
The nerve tissue mini-hemoglobin from Cerebratulus lacteus (CerHb) displays an essential globin fold hosting a protein matrix tunnel held to allow traffic of small ligands to and from the heme. CerHb heme pocket hosts the distal TyrB10/GlnE7 pair, normally linked to low rates of O2 dissociation and ultra-high O2 affinity. However, CerHb affinity for O2 is similar to that of mammalian myoglobins, due to a dynamic equilibrium between high and low affinity states driven by the ability of ThrE11 to orient the TyrB10 OH group relative to the heme ligand. We present here the high resolution crystal structures of CerHb in the unligated and carbomonoxy states. Although CO binds to the heme with an orientation different from the O2 ligand, the overall binding schemes for CO and O2 are essentially the same, both ligands being stabilized through a network of hydrogen bonds based on TyrB10, GlnE7, and ThrE11. No dramatic protein structural changes are needed to support binding of the ligands, which can freely reach the heme distal site through the apolar tunnel. A lack of main conformational changes between the heme-unligated and -ligated states grants stability to the folded mini-Hb and is a prerequisite for fast ligand diffusion to/from the heme. Full article
(This article belongs to the Special Issue Protein Crystallography in Molecular Biology)
Figures

Open AccessArticle A Promising Tool to Achieve Chemical Accuracy for Density Functional Theory Calculations on Y-NO Homolysis Bond Dissociation Energies
Int. J. Mol. Sci. 2012, 13(7), 8051-8070; doi:10.3390/ijms13078051
Received: 25 May 2012 / Revised: 19 June 2012 / Accepted: 25 June 2012 / Published: 28 June 2012
Cited by 2 | PDF Full-text (608 KB) | HTML Full-text | XML Full-text | Supplementary Files
Abstract
A DFT-SOFM-RBFNN method is proposed to improve the accuracy of DFT calculations on Y-NO (Y = C, N, O, S) homolysis bond dissociation energies (BDE) by combining density functional theory (DFT) and artificial intelligence/machine learning methods, which consist of self-organizing feature mapping neural
[...] Read more.
A DFT-SOFM-RBFNN method is proposed to improve the accuracy of DFT calculations on Y-NO (Y = C, N, O, S) homolysis bond dissociation energies (BDE) by combining density functional theory (DFT) and artificial intelligence/machine learning methods, which consist of self-organizing feature mapping neural networks (SOFMNN) and radial basis function neural networks (RBFNN). A descriptor refinement step including SOFMNN clustering analysis and correlation analysis is implemented. The SOFMNN clustering analysis is applied to classify descriptors, and the representative descriptors in the groups are selected as neural network inputs according to their closeness to the experimental values through correlation analysis. Redundant descriptors and intuitively biased choices of descriptors can be avoided by this newly introduced step. Using RBFNN calculation with the selected descriptors, chemical accuracy (≤1 kcal·mol−1) is achieved for all 92 calculated organic Y-NO homolysis BDE calculated by DFT-B3LYP, and the mean absolute deviations (MADs) of the B3LYP/6-31G(d) and B3LYP/STO-3G methods are reduced from 4.45 and 10.53 kcal·mol−1 to 0.15 and 0.18 kcal·mol−1, respectively. The improved results for the minimal basis set STO-3G reach the same accuracy as those of 6-31G(d), and thus B3LYP calculation with the minimal basis set is recommended to be used for minimizing the computational cost and to expand the applications to large molecular systems. Further extrapolation tests are performed with six molecules (two containing Si-NO bonds and two containing fluorine), and the accuracy of the tests was within 1 kcal·mol−1. This study shows that DFT-SOFM-RBFNN is an efficient and highly accurate method for Y-NO homolysis BDE. The method may be used as a tool to design new NO carrier molecules. Full article
(This article belongs to the Special Issue Advances in Density Functional Theory)
Open AccessArticle Cancer Cell Cytotoxicities of 1-(4-Substitutedbenzoyl)-4-(4-chlorobenzhydryl)piperazine Derivatives
Int. J. Mol. Sci. 2012, 13(7), 8071-8085; doi:10.3390/ijms13078071
Received: 18 May 2012 / Revised: 7 June 2012 / Accepted: 13 June 2012 / Published: 28 June 2012
Cited by 13 | PDF Full-text (505 KB) | HTML Full-text | XML Full-text
Abstract
A series of novel 1-(4-substitutedbenzoyl)-4-(4-chlorobenzhydryl)piperazine derivatives 5ag was designed by a nucleophilic substitution reaction of 1-(4-chlorobenzhydryl)piperazine with various benzoyl chlorides and characterized by elemental analyses, IR and 1H nuclear magnetic resonance spectra. Cytotoxicity of the compounds was demonstrated on cancer
[...] Read more.
A series of novel 1-(4-substitutedbenzoyl)-4-(4-chlorobenzhydryl)piperazine derivatives 5ag was designed by a nucleophilic substitution reaction of 1-(4-chlorobenzhydryl)piperazine with various benzoyl chlorides and characterized by elemental analyses, IR and 1H nuclear magnetic resonance spectra. Cytotoxicity of the compounds was demonstrated on cancer cell lines from liver (HUH7, FOCUS, MAHLAVU, HEPG2, HEP3B), breast (MCF7, BT20, T47D, CAMA-1), colon (HCT-116), gastric (KATO-3) and endometrial (MFE-296) cancer cell lines. Time-dependent cytotoxicity analysis of compound 5a indicated the long-term in situ stability of this compound. All compounds showed significant cell growth inhibitory activity on the selected cancer cell lines. Full article
Open AccessArticle Green Formation of Spherical and Dendritic Silver Nanostructures under Microwave Irradiation without Reducing Agent
Int. J. Mol. Sci. 2012, 13(7), 8086-8096; doi:10.3390/ijms13078086
Received: 5 April 2012 / Revised: 4 June 2012 / Accepted: 11 June 2012 / Published: 28 June 2012
Cited by 11 | PDF Full-text (625 KB) | HTML Full-text | XML Full-text
Abstract
The rapid and green formation of spherical and dendritic silver nanostructures based on microwave irradiation time was investigated. Silver nanoparticles were successfully fabricated by reduction of Ag+ in a water medium and using polyvinylpyrrolidone (PVP) as the stabilizing agent and without the
[...] Read more.
The rapid and green formation of spherical and dendritic silver nanostructures based on microwave irradiation time was investigated. Silver nanoparticles were successfully fabricated by reduction of Ag+ in a water medium and using polyvinylpyrrolidone (PVP) as the stabilizing agent and without the use of any other reducing agent, and were compared with those synthesized by conventional heating method. UV–vis absorption spectrometry, transmission electron microscopy (TEM), atomic absorption spectroscopy (AAS) and photon correlation spectroscopy (PCS) measurements, indicated that increasing the irradiation time enhanced the concentration of silver nanoparticles and slightly increased the particle size. There was a lack of large silver nanoparticles at a high concentration, but interestingly, the formation and growth of silver dendrite nanostructures appeared. Compared to conventional heating methods, the silver nanoparticle suspension produced by irradiated microwaves was more stable over a six-month period in aqueous solution without any signs of precipitation. Full article
(This article belongs to the Section Material Sciences and Nanotechnology)
Open AccessArticle Production of Defatted Palm Kernel Cake Protein Hydrolysate as a Valuable Source of Natural Antioxidants
Int. J. Mol. Sci. 2012, 13(7), 8097-8111; doi:10.3390/ijms13078097
Received: 24 April 2012 / Revised: 4 June 2012 / Accepted: 14 June 2012 / Published: 29 June 2012
Cited by 11 | PDF Full-text (239 KB) | HTML Full-text | XML Full-text
Abstract
The aim of this study was to produce a valuable protein hydrolysate from palm kernel cake (PKC) for the development of natural antioxidants. Extracted PKC protein was hydrolyzed using different proteases (alcalase, chymotrypsin, papain, pepsin, trypsin, flavourzyme, and bromelain). Subsequently, antioxidant activity and
[...] Read more.
The aim of this study was to produce a valuable protein hydrolysate from palm kernel cake (PKC) for the development of natural antioxidants. Extracted PKC protein was hydrolyzed using different proteases (alcalase, chymotrypsin, papain, pepsin, trypsin, flavourzyme, and bromelain). Subsequently, antioxidant activity and degree of hydrolysis (DH) of each hydrolysate were evaluated using DPPH• radical scavenging activity and O-phthaldialdehyde spectrophotometric assay, respectively. The results revealed a strong correlation between DH and radical scavenging activity of the hydrolysates, where among these, protein hydrolysates produced by papain after 38 h hydrolysis exhibited the highest DH (91 ± 0.1%) and DPPH• radical scavenging activity (73.5 ± 0.25%) compared to the other hydrolysates. In addition, fractionation of the most effective (potent) hydrolysate by reverse phase high performance liquid chromatography indicated a direct association between hydrophobicity and radical scavenging activity of the hydrolysates. Isoelectric focusing tests also revealed that protein hydrolysates with basic and neutral isoelectric point (pI) have the highest radical scavenging activity, although few fractions in the acidic range also exhibited good antioxidant potential. Full article
(This article belongs to the Section Biochemistry, Molecular Biology and Biophysics)
Open AccessArticle Synthesis and Spectral Evaluation of Some Unsymmetrical Mesoporphyrinic Complexes
Int. J. Mol. Sci. 2012, 13(7), 8112-8125; doi:10.3390/ijms13078112
Received: 15 February 2012 / Revised: 13 June 2012 / Accepted: 21 June 2012 / Published: 29 June 2012
Cited by 4 | PDF Full-text (317 KB) | HTML Full-text | XML Full-text
Abstract
Synthesis and spectral evaluation of new zinc and copper unsymmetrical mesoporphyrinic complexes are reported. Zn(II)-5-(4-acetoxy-3-methoxyphenyl)-10,15,20-tris-(4-carboxymethylphenyl)porphyrin, Zn(II)-5-[(3,4-methylenedioxy)phenyl]-10,15,20-tris-(4-carboxymethylphenyl)porphyrin, Cu(II)-5-(4-acetoxy-3-methoxyphenyl)-10,15,20-tris-(4-carboxymethylphenyl)porphyrin and Cu(II)-5-[(3,4-methylenedioxy)phenyl]-10,15,20-tris-(4-carboxymethylphenyl)porphyrin were synthesized using microwave-assisted synthesis. The complexes were characterized by elemental analysis, FT-IR, UV-Vis, EPR and
[...] Read more.
Synthesis and spectral evaluation of new zinc and copper unsymmetrical mesoporphyrinic complexes are reported. Zn(II)-5-(4-acetoxy-3-methoxyphenyl)-10,15,20-tris-(4-carboxymethylphenyl)porphyrin, Zn(II)-5-[(3,4-methylenedioxy)phenyl]-10,15,20-tris-(4-carboxymethylphenyl)porphyrin, Cu(II)-5-(4-acetoxy-3-methoxyphenyl)-10,15,20-tris-(4-carboxymethylphenyl)porphyrin and Cu(II)-5-[(3,4-methylenedioxy)phenyl]-10,15,20-tris-(4-carboxymethylphenyl)porphyrin were synthesized using microwave-assisted synthesis. The complexes were characterized by elemental analysis, FT-IR, UV-Vis, EPR and NMR spectroscopy, which fully confirmed their structure. The spectral absorption properties of the porphyrinic complexes were studied in solvents with different polarities. Fluorescence emission and singlet oxygen formation quantum yields were evaluated for the compounds under study, revealing high yields for the zinc derivatives. The copper complexes are not emissive and only display residual capacity for singlet oxygen formation. Full article
Open AccessArticle Elongation Factor 1β' Gene from Spodoptera exigua: Characterization and Function Identification through RNA Interference
Int. J. Mol. Sci. 2012, 13(7), 8126-8141; doi:10.3390/ijms13078126
Received: 29 April 2012 / Revised: 13 June 2012 / Accepted: 18 June 2012 / Published: 29 June 2012
Cited by 2 | PDF Full-text (693 KB) | HTML Full-text | XML Full-text
Abstract
Elongation factor (EF) is a key regulation factor for translation in many organisms, including plants, bacteria, fungi, animals and insects. To investigate the nature and function of elongation factor 1β' from Spodoptera exigua (SeEF-1β'), its cDNA was cloned. This contained an open reading
[...] Read more.
Elongation factor (EF) is a key regulation factor for translation in many organisms, including plants, bacteria, fungi, animals and insects. To investigate the nature and function of elongation factor 1β' from Spodoptera exigua (SeEF-1β'), its cDNA was cloned. This contained an open reading frame of 672 nucleotides encoding a protein of 223 amino acids with a predicted molecular weight of 24.04 kDa and pI of 4.53. Northern blotting revealed that SeEF-1β' mRNA is expressed in brain, epidermis, fat body, midgut, Malpighian tubules, ovary and tracheae. RT-PCR revealed that SeEF-1β' mRNA is expressed at different levels in fat body and whole body during different developmental stages. In RNAi experiments, the survival rate of insects injected with SeEF-1β' dsRNA was 58.7% at 36 h after injection, which was significantly lower than three control groups. Other elongation factors and transcription factors were also influenced when EF-1β' was suppressed. The results demonstrate that SeEF-1β' is a key gene in transcription in S. exigua. Full article
(This article belongs to the Section Biochemistry, Molecular Biology and Biophysics)
Open AccessArticle Effects of Purified Saccharomyces cerevisiae (1→3)-β-Glucan on Venous Ulcer Healing
Int. J. Mol. Sci. 2012, 13(7), 8142-8158; doi:10.3390/ijms13078142
Received: 3 May 2012 / Revised: 22 May 2012 / Accepted: 24 May 2012 / Published: 2 July 2012
Cited by 11 | PDF Full-text (1308 KB) | HTML Full-text | XML Full-text
Abstract
Water-insoluble glucan was isolated from the baker’s yeast Saccharomyces cerevisiae. The yeast cells were treated with alkali and the residue then with acid. Chemical and NMR (1D and 2D) analyses showed that a linear (1→3)-β-glucan was purified that was not contaminated with
[...] Read more.
Water-insoluble glucan was isolated from the baker’s yeast Saccharomyces cerevisiae. The yeast cells were treated with alkali and the residue then with acid. Chemical and NMR (1D and 2D) analyses showed that a linear (1→3)-β-glucan was purified that was not contaminated with other carbohydrates, proteins or phenolic compounds. The effects of the glucan on wound healing were assessed in human venous ulcers by histopathological analysis after 30 days of topical treatment. (1→3)-β-glucan enhanced ulcer healing and increased epithelial hyperplasia, as well as increased inflammatory cells, angiogenesis and fibroblast proliferation. In one patient who had an ulcer that would not heal for over 15 years, glucan treatment caused a 67.8% decrease in the area of the ulcer. This is the first study to investigate the effects of (1→3)-β-glucan on venous ulcer healing in humans; our findings suggest that this glucan is a potential natural biological response modifier in wound healing. Full article
Open AccessArticle Genetic Variation and Population Differentiation in a Medical Herb Houttuynia cordata in China Revealed by Inter-Simple Sequence Repeats (ISSRs)
Int. J. Mol. Sci. 2012, 13(7), 8159-8170; doi:10.3390/ijms13078159
Received: 16 April 2012 / Revised: 14 June 2012 / Accepted: 25 June 2012 / Published: 2 July 2012
Cited by 8 | PDF Full-text (285 KB) | HTML Full-text | XML Full-text
Abstract
Houttuynia cordata is an important traditional Chinese herb with unresolved genetics and taxonomy, which lead to potential problems in the conservation and utilization of the resource. Inter-simple sequence repeat (ISSR) markers were used to assess the level and distribution of genetic diversity in
[...] Read more.
Houttuynia cordata is an important traditional Chinese herb with unresolved genetics and taxonomy, which lead to potential problems in the conservation and utilization of the resource. Inter-simple sequence repeat (ISSR) markers were used to assess the level and distribution of genetic diversity in 226 individuals from 15 populations of H. cordata in China. ISSR analysis revealed low genetic variations within populations but high genetic differentiations among populations. This genetic structure probably mainly reflects the historical association among populations. Genetic cluster analysis showed that the basal clade is composed of populations from Southwest China, and the other populations have continuous and eastward distributions. The structure of genetic diversity in H. cordata demonstrated that this species might have survived in Southwest China during the glacial age, and subsequently experienced an eastern postglacial expansion. Based on the results of genetic analysis, it was proposed that as many as possible targeted populations for conservation be included. Full article
Open AccessArticle Proteomic Analysis of the Organ of Corti Using Nanoscale Liquid Chromatography Coupled with Tandem Mass Spectrometry
Int. J. Mol. Sci. 2012, 13(7), 8171-8188; doi:10.3390/ijms13078171
Received: 27 April 2012 / Revised: 5 June 2012 / Accepted: 25 June 2012 / Published: 2 July 2012
Cited by 3 | PDF Full-text (412 KB) | HTML Full-text | XML Full-text | Supplementary Files
Abstract
The organ of Corti (OC) in the cochlea plays an essential role in auditory signal transduction in the inner ear. For its minute size and trace amount of proteins, the identification of the molecules in pathophysiologic processes in the bone-encapsulated OC requires both
[...] Read more.
The organ of Corti (OC) in the cochlea plays an essential role in auditory signal transduction in the inner ear. For its minute size and trace amount of proteins, the identification of the molecules in pathophysiologic processes in the bone-encapsulated OC requires both delicate separation and a highly sensitive analytical tool. Previously, we reported the development of a high resolution metal-free nanoscale liquid chromatography system for highly sensitive phosphoproteomic analysis. Here this system was coupled with a LTQ-Orbitrap XL mass spectrometer to investigate the OC proteome from normal hearing FVB/N male mice. A total of 628 proteins were identified from six replicates of single LC-MS/MS analysis, with a false discovery rate of 1% using the decoy database approach by the OMSSA search engine. This is currently the largest proteome dataset for the OC. A total of 11 proteins, including cochlin, myosin VI, and myosin IX, were identified that when defective are associated with hearing impairment or loss. This study demonstrated the effectiveness of our nanoLC-MS/MS platform for sensitive identification of hearing loss-associated proteins from minute amount of tissue samples. Full article
(This article belongs to the collection Advances in Proteomic Research)
Open AccessArticle Investigation of Spectroscopic Properties and Spin-Orbit Splitting in the X2Π and A2Π Electronic States of the SO+ Cation
Int. J. Mol. Sci. 2012, 13(7), 8189-8209; doi:10.3390/ijms13078189
Received: 12 April 2012 / Revised: 6 June 2012 / Accepted: 7 June 2012 / Published: 3 July 2012
PDF Full-text (358 KB) | HTML Full-text | XML Full-text
Abstract
The potential energy curves (PECs) of the X2Π and A2Π electronic states of the SO+ ion are calculated using the complete active space self-consistent field method, which is followed by the internally contracted multireference configuration interaction (MRCI) approach
[...] Read more.
The potential energy curves (PECs) of the X2Π and A2Π electronic states of the SO+ ion are calculated using the complete active space self-consistent field method, which is followed by the internally contracted multireference configuration interaction (MRCI) approach for internuclear separations from 0.08 to 1.06 nm. The spin-orbit coupling effect on the spectroscopic parameters is included using the Breit-Pauli operator. To improve the quality of PECs and spin-orbit coupling constant (A0), core-valence correlation and scalar relativistic corrections are included. To obtain more reliable results, the PECs obtained by the MRCI calculations are corrected for size-extensivity errors by means of the Davidson modification (MRCI+Q). At the MRCI+Q/aug-cc-pV5Z+CV+DK level, the A0 values of the SO+(X2Π1/2, 3/2) and SO+(A2Π1/2, 3/2) are 362.13 and 58.16 cm−1 when the aug-cc-pCVTZ basis set is used to calculate the spin-orbit coupling splitting, and the A0 of the SO+(X2Π1/2, 3/2) and SO+(A2Π1/2, 3/2) are 344.36 and 52.90 cm−1 when the aug-cc-pVTZ basis set is used to calculate the spin-orbit coupling splitting. The conclusion is drawn that the core-valence correlations correction makes the A0 slightly larger. The spectroscopic results are obtained and compared with those reported in the literature. Excellent agreement exists between the present results and the measurements. The vibrational manifolds are calculated, and those of the first 30 vibrational states are reported for the J = 0 case. Comparison with the measurements shows that the present vibrational manifolds are both reliable and accurate. Full article
(This article belongs to the Section Physical Chemistry, Theoretical and Computational Chemistry)
Open AccessArticle Isojacareubin from the Chinese Herb Hypericum japonicum: Potent Antibacterial and Synergistic Effects on Clinical Methicillin-Resistant Staphylococcus aureus (MRSA)
Int. J. Mol. Sci. 2012, 13(7), 8210-8218; doi:10.3390/ijms13078210
Received: 7 May 2012 / Revised: 31 May 2012 / Accepted: 18 June 2012 / Published: 3 July 2012
Cited by 16 | PDF Full-text (250 KB) | HTML Full-text | XML Full-text
Abstract
Through bioassay-guided fractionation of the extracts from the aerial parts of the Chinese herb Hypericum japonicum Thunb. Murray, Isojacareubin (ISJ) was characterized as a potent antibacterial compound against the clinical methicillin-resistant Staphylococcus aureus (MRSA). The broth microdilution assay was used to determine
[...] Read more.
Through bioassay-guided fractionation of the extracts from the aerial parts of the Chinese herb Hypericum japonicum Thunb. Murray, Isojacareubin (ISJ) was characterized as a potent antibacterial compound against the clinical methicillin-resistant Staphylococcus aureus (MRSA). The broth microdilution assay was used to determine the minimal inhibitory concentrations (MICs) and minimal bactericidal concentrations (MBCs) of ISJ alone. The results showed that its MICs/MBCs ranged from 4/16 to 16/64 μg/mL, with the concentrations required to inhibit or kill 50% of the strains (MIC50/MBC50) at 8/16 μg/mL. Synergistic evaluations of this compound with four conventional antibacterial agents representing different types were performed by the chequerboard and time-kill tests. The chequerboard method showed significant synergy effects when ISJ was combined with Ceftazidime (CAZ), Levofloxacin (LEV) and Ampicillin (AMP), with the values of 50% of the fractional inhibitory concentration indices (FICI50) at 0.25, 0.37 and 0.37, respectively. Combined bactericidal activities were also observed in the time-kill dynamic assay. The results showed the ability of ISJ to reduce MRSA viable counts by log10CFU/mL at 24 h of incubation at a concentration of 1 × MIC were 1.5 (LEV, additivity), 0.92 (CAZ, indifference) and 0.82 (AMP, indifference), respectively. These in vitro anti-MRSA activities of ISJ alone and its synergy with conventional antibacterial agents demonstrated that ISJ enhanced their efficacy, which is of potential use for single and combinatory therapy of patients infected with MRSA. Full article
(This article belongs to the Section Biochemistry, Molecular Biology and Biophysics)
Open AccessArticle Genome-Wide Analysis of DNA Methylation and Expression of MicroRNAs in Breast Cancer Cells
Int. J. Mol. Sci. 2012, 13(7), 8259-8272; doi:10.3390/ijms13078259
Received: 30 May 2012 / Revised: 19 June 2012 / Accepted: 27 June 2012 / Published: 3 July 2012
Cited by 20 | PDF Full-text (389 KB) | HTML Full-text | XML Full-text
Abstract
DNA methylation of promoters is linked to transcriptional silencing of protein-coding genes, and its alteration plays important roles in cancer formation. For example, hypermethylation of tumor suppressor genes has been seen in some cancers. Alteration of methylation in the promoters of microRNAs (miRNAs)
[...] Read more.
DNA methylation of promoters is linked to transcriptional silencing of protein-coding genes, and its alteration plays important roles in cancer formation. For example, hypermethylation of tumor suppressor genes has been seen in some cancers. Alteration of methylation in the promoters of microRNAs (miRNAs) has also been linked to transcriptional changes in cancers; however, no systematic studies of methylation and transcription of miRNAs have been reported. In the present study, to clarify the relation between DNA methylation and transcription of miRNAs, next-generation sequencing and microarrays were used to analyze the methylation and expression of miRNAs, protein-coding genes, other non-coding RNAs (ncRNAs), and pseudogenes in the human breast cancer cell lines MCF7 and the adriamycin (ADR) resistant cell line MCF7/ADR. DNA methylation in the proximal promoter of miRNAs is tightly linked to transcriptional silencing, as it is with protein-coding genes. In protein-coding genes, highly expressed genes have CpG-rich proximal promoters whereas weakly expressed genes do not. This is only rarely observed in other gene categories, including miRNAs. The present study highlights the epigenetic similarities and differences between miRNA and protein-coding genes. Full article
(This article belongs to the Special Issue Advances in Molecular Oncology (special issue))
Open AccessArticle Fasudil, a Rho-Kinase Inhibitor, Attenuates Bleomycin-Induced Pulmonary Fibrosis in Mice
Int. J. Mol. Sci. 2012, 13(7), 8293-8307; doi:10.3390/ijms13078293
Received: 21 May 2012 / Revised: 19 June 2012 / Accepted: 28 June 2012 / Published: 4 July 2012
Cited by 29 | PDF Full-text (2727 KB) | HTML Full-text | XML Full-text
Abstract
The mechanisms underlying the pathogenesis of idiopathic pulmonary fibrosis (IPF) involve multiple pathways, such as inflammation, epithelial mesenchymal transition, coagulation, oxidative stress, and developmental processes. The small GTPase, RhoA, and its target protein, Rho-kinase (ROCK), may interact with other signaling pathways known to
[...] Read more.
The mechanisms underlying the pathogenesis of idiopathic pulmonary fibrosis (IPF) involve multiple pathways, such as inflammation, epithelial mesenchymal transition, coagulation, oxidative stress, and developmental processes. The small GTPase, RhoA, and its target protein, Rho-kinase (ROCK), may interact with other signaling pathways known to contribute to pulmonary fibrosis. This study aimed to determine the beneficial effects and mechanisms of fasudil, a selective ROCK inhibitor, on bleomycin-induced pulmonary fibrosis in mice. Our results showed that the Aschcroft score and hydroxyproline content of the bleomycin-treated mouse lung decreased in response to fasudil treatment. The number of infiltrated inflammatory cells in the bronchoalveolar lavage fluid (BALF) was attenuated by fasudil. In addition, fasudil reduced the production of transforming growth factor-β1 (TGF-β1), connective tissue growth factor (CTGF), alpha-smooth muscle actin (α-SMA), and plasminogen activator inhibitor-1 (PAI-1) mRNA and protein expression in bleomycin-induced pulmonary fibrosis. These findings suggest that fasudil may be a potential therapeutic candidate for the treatment of pulmonary fibrosis. Full article
Open AccessArticle Potential of Fruit Wastes as Natural Resources of Bioactive Compounds
Int. J. Mol. Sci. 2012, 13(7), 8308-8323; doi:10.3390/ijms13078308
Received: 27 April 2012 / Revised: 20 June 2012 / Accepted: 21 June 2012 / Published: 4 July 2012
Cited by 23 | PDF Full-text (208 KB) | HTML Full-text | XML Full-text
Abstract
Fruit wastes are one of the main sources of municipal waste. In order to explore the potential of fruit wastes as natural resources of bioactive compounds, the antioxidant potency and total phenolic contents (TPC) of lipophilic and hydrophilic components in wastes (peel and
[...] Read more.
Fruit wastes are one of the main sources of municipal waste. In order to explore the potential of fruit wastes as natural resources of bioactive compounds, the antioxidant potency and total phenolic contents (TPC) of lipophilic and hydrophilic components in wastes (peel and seed) of 50 fruits were systematically evaluated. The results showed that different fruit residues had diverse antioxidant potency and the variation was very large. Furthermore, the main bioactive compounds were identified and quantified, and catechin, cyanidin 3-glucoside, epicatechin, galangin, gallic acid, homogentisic acid, kaempferol, and chlorogenic acid were widely found in these residues. Especially, the values of ferric-reducing antioxidant power (FRAP), trolox equivalent antioxidant capacity (TEAC) and TPC in the residues were higher than in pulps. The results showed that fruit residues could be inexpensive and readily available resources of bioactive compounds for use in the food and pharmaceutical industries. Full article
(This article belongs to the Section Biochemistry, Molecular Biology and Biophysics)
Open AccessArticle Occurrence of Aflatoxins in Selected Processed Foods from Pakistan
Int. J. Mol. Sci. 2012, 13(7), 8324-8337; doi:10.3390/ijms13078324
Received: 20 April 2012 / Revised: 3 June 2012 / Accepted: 24 June 2012 / Published: 4 July 2012
Cited by 15 | PDF Full-text (411 KB) | HTML Full-text | XML Full-text
Abstract
A total of 125 (ready to eat) processed food samples (70 intended for infant and 55 for adult intake) belonging to 20 different food categories were analyzed for aflatoxins contamination using Reverse Phase High Performance Liquid Chromatography (RP-HPLC) with fluorescent detection. A solvent
[...] Read more.
A total of 125 (ready to eat) processed food samples (70 intended for infant and 55 for adult intake) belonging to 20 different food categories were analyzed for aflatoxins contamination using Reverse Phase High Performance Liquid Chromatography (RP-HPLC) with fluorescent detection. A solvent mixture of acetonitrile-water was used for the extraction followed by immunoaffinity clean-up to enhance sensitivity of the method. The limit of detection (LOD) (0.01–0.02 ng·g−1) and limit of quantification (LOQ) (0.02 ng·g−1) was established for aflatoxins based on signal to noise ratio of 3:1 and 10:1, respectively. Of the processed food samples tested, 38% were contaminated with four types of aflatoxins, i.e., AFB1 (0.02–1.24 μg·kg−1), AFB2 (0.02–0.37 μg·kg−1), AFG1 (0.25–2.7 μg·kg−1) and AFG2 (0.21–1.3 μg·kg−1). In addition, the results showed that 21% of the processed foods intended for infants contained AFB1 levels higher than the European Union permissible limits (0.1 μg·kg−1), while all of those intended for adult consumption had aflatoxin contamination levels within the permitted limits. Full article
Open AccessArticle Clinical Relevance of CDH1 and CDH13 DNA-Methylation in Serum of Cervical Cancer Patients
Int. J. Mol. Sci. 2012, 13(7), 8353-8363; doi:10.3390/ijms13078353
Received: 4 June 2012 / Revised: 28 June 2012 / Accepted: 29 June 2012 / Published: 5 July 2012
Cited by 12 | PDF Full-text (186 KB) | HTML Full-text | XML Full-text
Abstract
This study was designed to investigate the DNA-methylation status of E-cadherin (CDH1) and H-cadherin (CDH13) in serum samples of cervical cancer patients and control patients with no malignant diseases and to evaluate the clinical utility of these
[...] Read more.
This study was designed to investigate the DNA-methylation status of E-cadherin (CDH1) and H-cadherin (CDH13) in serum samples of cervical cancer patients and control patients with no malignant diseases and to evaluate the clinical utility of these markers. DNA-methylation status of CDH1 and CDH13 was analyzed by means of MethyLight-technology in serum samples from 49 cervical cancer patients and 40 patients with diseases other than cancer. To compare this methylation analysis with another technique, we analyzed the samples with a denaturing high performance liquid chromatography (DHPLC) PCR-method. The specificity and sensitivity of CDH1 DNA-methylation measured by MethyLight was 75% and 55%, and for CDH13 DNA-methylation 95% and 10%. We identified a specificity of 92.5% and a sensitivity of only 27% for the CDH1 DHPLC-PCR analysis. Multivariate analysis showed that serum CDH1 methylation-positive patients had a 7.8-fold risk for death (95% CI: 2.2–27.7; p = 0.001) and a 92.8-fold risk for relapse (95% CI: 3.9–2207.1; p = 0.005). We concluded that the serological detection of CDH1 and CDH13 DNA-hypermethylation is not an ideal diagnostic tool due to low diagnostic specificity and sensitivity. However, it was validated that CDH1 methylation analysis in serum samples may be of potential use as a prognostic marker for cervical cancer patients. Full article
(This article belongs to the Special Issue Advances in Molecular Oncology (special issue))
Open AccessArticle Risk-Association of DNA Methyltransferases Polymorphisms with Gastric Cancer in the Southern Chinese Population
Int. J. Mol. Sci. 2012, 13(7), 8364-8378; doi:10.3390/ijms13078364
Received: 22 April 2012 / Revised: 20 June 2012 / Accepted: 27 June 2012 / Published: 5 July 2012
Cited by 21 | PDF Full-text (148 KB) | HTML Full-text | XML Full-text | Supplementary Files
Abstract
DNA hypomethylation and/or hypermethylation are presumed to be early events in carcinogenesis, and one or more DNA methyltransferases (DNMTs) have been suggested to play roles in carcinogenesis of gastric cancer (GC). However, there have been no systematic studies regarding the association between DNMT
[...] Read more.
DNA hypomethylation and/or hypermethylation are presumed to be early events in carcinogenesis, and one or more DNA methyltransferases (DNMTs) have been suggested to play roles in carcinogenesis of gastric cancer (GC). However, there have been no systematic studies regarding the association between DNMT gene polymorphisms and GC risk. Here, we examined the associations of 16 single nucleotide polymorphisms (SNPs) from DNMT1 (rs2114724, rs2228611, rs2228612, rs8101866, rs16999593), DNMT2 (rs11695471, rs11254413), DNMT3A (rs1550117, rs11887120, rs13420827, rs13428812, rs6733301), DNMT3B (rs2424908, rs2424913, rs6087990) and DNMT3L (rs113593938) with GC in the Southern Chinese population. We assessed the associations of these 16 SNPs with GC in a case-control study that consisted of 242 GC cases and 294 controls, using the Sequenom MALDI-TOF-MS platform. Association analyses based on the χ2 test and binary logistic regression were performed to determine the odds ratio (OR) and 95% confidence interval (95%CI) for each SNP. We found that rs16999593 in DNMT1, rs11254413 in DNMT2 and rs13420827 in DNMT3A were significantly associated with GC susceptibility (OR 1.45, 0.15, 0.66, respectively; 95% CI 1.00–2.11, p = 0.047; 0.08–0.27, p < 0.01; 0.45–0.97, p = 0.034, respectively, overdominant model). These results suggested that DNMT1, DNMT2 and DNMT3A may play important roles in GC carcinogenesis. However, further studies are required to elucidate the mechanism. Full article
(This article belongs to the Section Biochemistry, Molecular Biology and Biophysics)
Open AccessArticle Astragalus membranaceus Inhibits Inflammation via Phospho-P38 Mitogen-Activated Protein Kinase (MAPK) and Nuclear Factor (NF)-κB Pathways in Advanced Glycation End Product-Stimulated Macrophages
Int. J. Mol. Sci. 2012, 13(7), 8379-8387; doi:10.3390/ijms13078379
Received: 25 April 2012 / Revised: 22 June 2012 / Accepted: 29 June 2012 / Published: 5 July 2012
Cited by 27 | PDF Full-text (376 KB) | HTML Full-text | XML Full-text
Abstract
Advanced glycation end products (AGEs) and inflammation contribute to the development of diabetic complications. Astragalus membranaceus has properties of immunological regulation in many diseases. The aim of this study was to determine the function of A. membranaceus extract (AME) on the AGE-induced inflammatory
[...] Read more.
Advanced glycation end products (AGEs) and inflammation contribute to the development of diabetic complications. Astragalus membranaceus has properties of immunological regulation in many diseases. The aim of this study was to determine the function of A. membranaceus extract (AME) on the AGE-induced inflammatory response in Ana-1 macrophages. The viability of cells treated with AME or AGEs was evaluated with the MTT [3-(4,5-dimethyl-2-thiazolyl)-2,5-diphenyl-2H-tetrazolium bromide] method. The secretion and mRNA levels of IL-1β and TNF-α were measured by ELISA and RT-PCR, respectively. The activity of NF-κB was assayed by EMSA. The phosphorylation of p38 MAPK was assessed by western blotting. The results showed that AME was not toxic to macrophages. The treatment of macrophages with AME effectively inhibited AGE-induced IL-1β and TNF-α secretion and mRNA expression in macrophages. These effects may be mediated by p38 MAPK and the NF-κB pathway. The results suggest that AME can inhibit AGE-induced inflammatory cytokine production to down-regulate macrophage-mediated inflammation via p38 MAPK and NF-κB signaling pathways and indicate that AME could be an immunoregulatory agent against AGE-induced inflammation in diabetes. Full article
Open AccessArticle CO2 Adsorption on Activated Carbon Honeycomb-Monoliths: A Comparison of Langmuir and Tóth Models
Int. J. Mol. Sci. 2012, 13(7), 8388-8397; doi:10.3390/ijms13078388
Received: 15 May 2012 / Revised: 15 June 2012 / Accepted: 18 June 2012 / Published: 5 July 2012
Cited by 15 | PDF Full-text (422 KB) | HTML Full-text | XML Full-text
Abstract
Activated carbon honeycomb-monoliths with different textural properties were prepared by chemical activation of African palm shells with H3PO4, ZnCl2 and CaCl2 aqueous solutions of various concentrations. The adsorbents obtained were characterized by N2 adsorption at 77
[...] Read more.
Activated carbon honeycomb-monoliths with different textural properties were prepared by chemical activation of African palm shells with H3PO4, ZnCl2 and CaCl2 aqueous solutions of various concentrations. The adsorbents obtained were characterized by N2 adsorption at 77 K, and their carbon dioxide adsorption capacities were measured at 273 K and 1 Bar in volumetric adsorption equipment. The experimental adsorption isotherms were fitted to Langmuir and Tóth models, and a better fit was observed to Tóth equation with a correlation coefficient of 0.999. The maximum experimental values for adsorption capacity at the highest pressure (2.627–5.756 mmol·g−1) are between the calculated data in the two models. Full article
(This article belongs to the Section Material Sciences and Nanotechnology)
Figures

Open AccessArticle Phylogenetic Relationships of the Mangalitsa Swine Breed Inferred from Mitochondrial DNA Variation
Int. J. Mol. Sci. 2012, 13(7), 8467-8481; doi:10.3390/ijms13078467
Received: 15 May 2012 / Revised: 25 June 2012 / Accepted: 26 June 2012 / Published: 9 July 2012
Cited by 2 | PDF Full-text (304 KB) | HTML Full-text | XML Full-text | Supplementary Files
Abstract
The Mangalitsa pig, a swine breed belonging to the protected gene fund of original and primitive animal breeds of the FAO (Food and Agriculture Organization), has been known to inhabit Romanian territories since the 19th century. The aim of this study was to
[...] Read more.
The Mangalitsa pig, a swine breed belonging to the protected gene fund of original and primitive animal breeds of the FAO (Food and Agriculture Organization), has been known to inhabit Romanian territories since the 19th century. The aim of this study was to compare the Mangalitsa breed with several European and Asiatic swine breeds in order to emphasize its uniqueness and to elucidate its origin. For this purpose, we analyzed a 613 bp mitochondrial DNA D-loop fragment and 1140 bp of the cytochrome b gene in a population of Mangalitsa pigs and the polymorphic sites were compared with sequences from GenBank originating from other swine breeds. Taking into account the total of 24 breeds and 5 different Wild Boar populations analyzed, 86 polymorphic sites representing 32 haplotypes were observed, with an average percentage of polymorphic sites of 4.9%. Three Neighbor-Joining phylogenetic trees were constructed based on Kimura 2-parameter distances, using D-loop, cytochrome b and mitochondrial reunited sequences. For the analyzed Mangalitsa population, four distinct haplotypes were identified, including one that was common to other breeds. Our study suggests that the Mangalitsa swine originate from primitive breeds which might be directly derived from the Wild Boar. Full article
(This article belongs to the Section Biochemistry, Molecular Biology and Biophysics)
Open AccessArticle Chemopreventive Efficacy of Atorvastatin against Nitrosamine-Induced Rat Bladder Cancer: Antioxidant, Anti-Proliferative and Anti-Inflammatory Properties
Int. J. Mol. Sci. 2012, 13(7), 8482-8499; doi:10.3390/ijms13078482
Received: 23 April 2012 / Revised: 14 June 2012 / Accepted: 2 July 2012 / Published: 9 July 2012
Cited by 7 | PDF Full-text (2305 KB) | HTML Full-text | XML Full-text
Abstract
To investigate the anti-carcinogenic effects of Atorvastatin (Atorva) on a rat bladder carcinogenesis model with N-butyl-N-(4-hydroxibutil)nitrosamine (BBN), four male Wistar rat groups were studied: (1) Control: vehicle; (2) Atorva: 3 mg/kg bw/day; (3) Carcinogen: BBN (0.05%); (4) Preventive Atorva:
[...] Read more.
To investigate the anti-carcinogenic effects of Atorvastatin (Atorva) on a rat bladder carcinogenesis model with N-butyl-N-(4-hydroxibutil)nitrosamine (BBN), four male Wistar rat groups were studied: (1) Control: vehicle; (2) Atorva: 3 mg/kg bw/day; (3) Carcinogen: BBN (0.05%); (4) Preventive Atorva: 3 mg/kg bw/day Atorva + BBN. A two phase protocol was used, in which the drug and the carcinogen were given between week 1 and 8 and tumor development or chemoprevention were expressed between week 9 and 20, when the bladders were collected for macroscopic, histological and immunohistochemical (p53, ki67, CD31) evaluation. Serum was assessed for markers of inflammation, proliferation and redox status. The incidence of bladder carcinoma was: control 0/8 (0%); Atorva 0/8 (0%); BBN 13/20 (65%) and Atorva + BBN 1/8 (12.5%). The number and volume of tumors were significantly lower in the Atorva + BBN group, with a marked reduction in hyperplasia, dysplasia and carcinoma in situ lesions. An anti-proliferative, anti-inflammatory and antioxidant profile was also observed in the preventive Atorva group. p53 and ki67 immunostaining were significantly increased in the BBN-treated rats, which was prevented in the Atorva + BBN group. No differences were found for CD31 expression. In conclusion, Atorvastatin had a clear inhibitory effect on bladder cancer development, probably due to its antioxidant, anti-proliferative and anti-inflammatory properties. Full article
(This article belongs to the Special Issue Advances in Molecular Oncology (special issue))
Open AccessArticle Structural Analysis of Cytochrome P450 105N1 Involved in the Biosynthesis of the Zincophore, Coelibactin
Int. J. Mol. Sci. 2012, 13(7), 8500-8513; doi:10.3390/ijms13078500
Received: 1 June 2012 / Revised: 22 June 2012 / Accepted: 28 June 2012 / Published: 9 July 2012
Cited by 11 | PDF Full-text (375 KB) | HTML Full-text | XML Full-text
Abstract
Coelibactin is a putative non-ribosomally synthesized peptide with predicted zincophore activity and which has been implicated in antibiotic regulation in Streptomyces coelicolor A3(2). The coelibactin biosynthetic pathway contains a stereo- and regio-specific monooxygenation step catalyzed by a cytochrome P450 enzyme (CYP105N1). We have
[...] Read more.
Coelibactin is a putative non-ribosomally synthesized peptide with predicted zincophore activity and which has been implicated in antibiotic regulation in Streptomyces coelicolor A3(2). The coelibactin biosynthetic pathway contains a stereo- and regio-specific monooxygenation step catalyzed by a cytochrome P450 enzyme (CYP105N1). We have determined the X-ray crystal structure of CYP105N1 at 2.9 Å and analyzed it in the context of the bacterial CYP105 family as a whole. The crystal structure reveals a channel between the α-helical domain and the β-sheet domain exposing the heme pocket and the long helix I to the solvent. This wide-open conformation of CYP105N1 may be related to the bulky substrate coelibactin. The ligand-free CYP105N1 structure has enough room in the substrate access channel to allow the coelibactin to enter into the active site. Analysis of typical siderophore ligands suggests that CYP105N1 may produce derivatives of coelibactin, which would then be able to chelate the zinc divalent cation. Full article
(This article belongs to the Special Issue Protein Crystallography in Molecular Biology)
Open AccessArticle miR-338-3p Is Down-Regulated by Hepatitis B Virus X and Inhibits Cell Proliferation by Targeting the 3′-UTR Region of CyclinD1
Int. J. Mol. Sci. 2012, 13(7), 8514-8539; doi:10.3390/ijms13078514
Received: 5 March 2012 / Revised: 26 May 2012 / Accepted: 28 June 2012 / Published: 9 July 2012
Cited by 22 | PDF Full-text (1653 KB) | HTML Full-text | XML Full-text | Supplementary Files
Abstract
Hepatitis B virus X protein (HBx) is recognized as an oncogene in hepatocellular carcinoma (HCC). HBx regulates microRNA expression, including down-regulating miR-338-3p in LO2 cells. Here, we investigated miR-338-3p function in HBx-mediated hepatocarcinogenesis. In 23 HBV-infected HCC clinical patient tumor and adjacent non-tumor
[...] Read more.
Hepatitis B virus X protein (HBx) is recognized as an oncogene in hepatocellular carcinoma (HCC). HBx regulates microRNA expression, including down-regulating miR-338-3p in LO2 cells. Here, we investigated miR-338-3p function in HBx-mediated hepatocarcinogenesis. In 23 HBV-infected HCC clinical patient tumor and adjacent non-tumor control tissues, 17 and 19 tumors expressed HBx mRNA and protein, respectively. When considered as a group, HBV-infected HCC tumors had lower miR-338-3p expression than controls; however, miR-338-3p was only significantly down-regulated in HBx-positive tumors, indicating that HBx inversely correlated with miR-338-3p. Functional characterization of miR-338-3p indicated that miR-338-3p mimics inhibited cell proliferation by inducing cell cycle arrest at the G1/S phase as assessed by EdU and cell cycle assays in HBx-expressing LO2 cells. CyclinD1, containing two putative miR-338-3p targets, was confirmed as a direct target using 3′-UTR luciferase reporter assays from cells transfected with mutated binding sites. Mutating the 2397–2403 nt binding site conferred the greatest resistance to miR-338-3p suppression of CyclinD1, indicating that miR-338-3p suppresses CyclinD1 at this site. Overall, this study demonstrates that miR-338-3p inhibits proliferation by regulating CyclinD1, and HBx down-regulates miR-338-3p in HCC. This newly identified miR-338-3p/CyclinD1 interaction provides novel insights into HBx-mediated hepatocarcinogenesis and may facilitate therapeutic development against HCC. Full article
Open AccessArticle Reflection and Transmission Coefficient of Yttrium Iron Garnet Filled Polyvinylidene Fluoride Composite Using Rectangular Waveguide at Microwave Frequencies
Int. J. Mol. Sci. 2012, 13(7), 8540-8548; doi:10.3390/ijms13078540
Received: 6 May 2012 / Revised: 20 June 2012 / Accepted: 1 July 2012 / Published: 9 July 2012
Cited by 8 | PDF Full-text (549 KB) | HTML Full-text | XML Full-text
Abstract
The sol-gel method was carried out to synthesize nanosized Yttrium Iron Garnet (YIG). The nanomaterials with ferrite structure were heat-treated at different temperatures from 500 to 1000 °C. The phase identification, morphology and functional groups of the prepared samples were characterized by powder
[...] Read more.
The sol-gel method was carried out to synthesize nanosized Yttrium Iron Garnet (YIG). The nanomaterials with ferrite structure were heat-treated at different temperatures from 500 to 1000 °C. The phase identification, morphology and functional groups of the prepared samples were characterized by powder X-ray diffraction (PXRD), scanning electron microscopy (SEM) and Fourier transform infrared spectroscopy (FT-IR), respectively. The YIG ferrite nanopowder was composited with polyvinylidene fluoride (PVDF) by a solution casting method. The magnitudes of reflection and transmission coefficients of PVDF/YIG containing 6, 10 and 13% YIG, respectively, were measured using rectangular waveguide in conjunction with a microwave vector network analyzer (VNA) in X-band frequencies. The results indicate that the presence of YIG in polymer composites causes an increase in reflection coefficient and decrease in transmission coefficient of the polymer. Full article
(This article belongs to the Section Physical Chemistry, Theoretical and Computational Chemistry)
Open AccessArticle Involvement of Disperse Repetitive Sequences in Wheat/Rye Genome Adjustment
Int. J. Mol. Sci. 2012, 13(7), 8549-8561; doi:10.3390/ijms13078549
Received: 1 June 2012 / Revised: 25 June 2012 / Accepted: 4 July 2012 / Published: 10 July 2012
PDF Full-text (184 KB) | HTML Full-text | XML Full-text | Supplementary Files
Abstract
The union of different genomes in the same nucleus frequently results in hybrid genotypes with improved genome plasticity related to both genome remodeling events and changes in gene expression. Most modern cereal crops are polyploid species. Triticale, synthesized by the cross between wheat
[...] Read more.
The union of different genomes in the same nucleus frequently results in hybrid genotypes with improved genome plasticity related to both genome remodeling events and changes in gene expression. Most modern cereal crops are polyploid species. Triticale, synthesized by the cross between wheat and rye, constitutes an excellent model to study polyploidization functional implications. We intend to attain a deeper knowledge of dispersed repetitive sequence involvement in parental genome reshuffle in triticale and in wheat-rye addition lines that have the entire wheat genome plus each rye chromosome pair. Through Random Amplified Polymorphic DNA (RAPD) analysis with OPH20 10-mer primer we unraveled clear alterations corresponding to the loss of specific bands from both parental genomes. Moreover, the sequential nature of those events was revealed by the increased absence of rye-origin bands in wheat-rye addition lines in comparison with triticale. Remodeled band sequencing revealed that both repetitive and coding genome domains are affected in wheat-rye hybrid genotypes. Additionally, the amplification and sequencing of pSc20H internal segments showed that the disappearance of parental bands may result from restricted sequence alterations and unraveled the involvement of wheat/rye related repetitive sequences in genome adjustment needed for hybrid plant stabilization. Full article
(This article belongs to the Special Issue Advances in Molecular Plant Biology)
Open AccessArticle Fraction from Wax Apple [Syzygium samarangense (Blume) Merrill and Perry] Fruit Extract Ameliorates Insulin Resistance via Modulating Insulin Signaling and Inflammation Pathway in Tumor Necrosis Factor α-Treated FL83B Mouse Hepatocytes
Int. J. Mol. Sci. 2012, 13(7), 8562-8577; doi:10.3390/ijms13078562
Received: 19 May 2012 / Revised: 5 June 2012 / Accepted: 3 July 2012 / Published: 10 July 2012
Cited by 4 | PDF Full-text (1187 KB) | HTML Full-text | XML Full-text
Abstract
Inflammation is associated with the development of insulin resistance in Type 2 diabetes mellitus. In the present study, mouse FL83B cells were treated with tumor necrosis factor-alpha (TNF-α) to induce insulin resistance, and then co-incubated with a fraction from wax apple fruit extract
[...] Read more.
Inflammation is associated with the development of insulin resistance in Type 2 diabetes mellitus. In the present study, mouse FL83B cells were treated with tumor necrosis factor-alpha (TNF-α) to induce insulin resistance, and then co-incubated with a fraction from wax apple fruit extract (FWFE). This fraction significantly increased the uptake of the nonradioactive fluorescent indicator 2-[N-(7-nitrobenz-2-oxa-1,3-diazol-4-yl) amino]-2-deoxy-d-glucose (2-NBDG) in insulin resistant cells. Western blot analysis revealed that, compared with the TNF-α-treated control group, FWFE increased the expression of the insulin receptor (IR), insulin receptor substrate-1 (IRS-1), protein kinase B (Akt/PKB), phosphatidylinositol-3 kinase (PI3K), and glucose transporter 2 (GLUT-2), and increased IR tyrosyl phosporylation, in insulin resistant FL83B cells. However, FWFE decreased phosphorylation of c-Jun N-terminal kinases (JNK), but not the expression of the intercellular signal-regulated kinases (ERK), in the same cells. These results suggest that FWFE might alleviate insulin resistance in TNF-α-treated FL83B cells by activating PI3K-Akt/PKB signaling and inhibiting inflammatory response via suppression of JNK, rather than ERK, activation. Full article
(This article belongs to the Section Biochemistry, Molecular Biology and Biophysics)
Open AccessArticle Molecular Cloning and 3D Structure Modeling of APEX1, DNA Base Excision Repair Enzyme from the Camel, Camelus dromedarius
Int. J. Mol. Sci. 2012, 13(7), 8578-8596; doi:10.3390/ijms13078578
Received: 28 March 2012 / Revised: 15 June 2012 / Accepted: 27 June 2012 / Published: 10 July 2012
Cited by 3 | PDF Full-text (1356 KB) | HTML Full-text | XML Full-text
Abstract
The domesticated one-humped camel, Camelus dromedarius, is one of the most important animals in the Arabian Desert. It is exposed most of its life to both intrinsic and extrinsic genotoxic factors that are known to cause gross DNA alterations in many organisms.
[...] Read more.
The domesticated one-humped camel, Camelus dromedarius, is one of the most important animals in the Arabian Desert. It is exposed most of its life to both intrinsic and extrinsic genotoxic factors that are known to cause gross DNA alterations in many organisms. Ionic radiation and sunlight are known producers of Reactive Oxygen Species (ROS), one of the causes for DNA lesions. The damaged DNA is repaired by many enzymes, among of them Base Excision Repair enzymes, producing the highly mutagenic apurinic/apyrimidinicsites (AP sites). Therefore, recognition of AP sites is fundamental to cell/organism survival. In the present work, the full coding sequence of a putative cAPEX1 gene was amplified for the first time from C. dromedarius by RT-PCR and cloned (NCBI accession number are HM209828 and ADJ96599 for nucleotides and amino acids, respectively). cDNA sequencing was deduced to be 1041 nucleotides, of which 954 nucleotides encode a protein of 318 amino acids, similar to the coding region of the APEX1 gene and the protein from many other species. The calculated molecular weight and isoelectric point of cAPEX1 using Bioinformatics tools was 35.5 kDa and 8.11, respectively. The relative expressions of cAPEX1 in camel kidney, spleen, lung and testis were examined using qPCR and compared with that of the liver using a 18S ribosomal subunit as endogenous control. The highest level of cAPEX1 transcript was found in the testis; 325% higher than the liver, followed by spleen (87%), kidney (20%) and lung (5%), respectively. The cAPEX1 is 94%–97% similar to their mammalian counterparts. Phylogenetic analysis revealed that cAPEX1 is grouped together with that of S. scrofa. The predicted 3D structure of cAPEX1 has similar folds and topology with the human (hAPEX1). The root-mean-square deviation (rmsd) between cAPEX1 and hAPEX1 was 0.582 and the Q-score was 0.939. Full article
(This article belongs to the Section Biochemistry, Molecular Biology and Biophysics)
Open AccessArticle Effects of Brown Rice and White Rice on Expression of Xenobiotic Metabolism Genes in Type 2 Diabetic Rats
Int. J. Mol. Sci. 2012, 13(7), 8597-8608; doi:10.3390/ijms13078597
Received: 6 June 2012 / Revised: 20 June 2012 / Accepted: 26 June 2012 / Published: 10 July 2012
Cited by 5 | PDF Full-text (159 KB) | HTML Full-text | XML Full-text
Abstract
Xenobiotics constantly influence biological systems through several means of interaction. These interactions are disturbed in type 2 diabetes, with implications for disease outcome. We aimed to study the implications of such disturbances on type 2 diabetes and rice consumption, the results of which
[...] Read more.
Xenobiotics constantly influence biological systems through several means of interaction. These interactions are disturbed in type 2 diabetes, with implications for disease outcome. We aimed to study the implications of such disturbances on type 2 diabetes and rice consumption, the results of which could affect management of the disease in developing countries. In a type 2 diabetic rat model induced through a combination of high fat diet and low dose streptozotocin injection, up-regulation of xenobiotic metabolism genes in the diabetic untreated group was observed. Xenobiotic metabolism genes were upregulated more in the white rice (WR) group than the diabetic untreated group while the brown rice (BR) group showed significantly lower expression values, though not as effective as metformin, which gave values closer to the normal non-diabetic group. The fold changes in expression in the WR group compared to the BR group for Cyp2D4, Cyp3A1, Cyp4A1, Cyp2B1, Cyp2E1, Cyp2C11, UGT2B1, ALDH1A1 and Cyp2C6 were 2.6, 2, 1.5, 4, 2.8, 1.5, 1.8, 3 and 5, respectively. Our results suggest that WR may upregulate these genes in type 2 diabetes more than BR, potentially causing faster drug metabolism, less drug efficacy and more toxicity. These results may have profound implications for rice eating populations, constituting half the world’s population. Full article
(This article belongs to the Section Molecular Toxicology)
Open AccessArticle Infrared Study of Er3+/Yb3+ Co-Doped GeO2-PbO-Bi2O3 Glass
Int. J. Mol. Sci. 2012, 13(7), 8609-8614; doi:10.3390/ijms13078609
Received: 21 May 2012 / Revised: 20 June 2012 / Accepted: 25 June 2012 / Published: 10 July 2012
Cited by 4 | PDF Full-text (308 KB) | HTML Full-text | XML Full-text
Abstract
Heavy metal oxide glasses, containing bismuth and/or lead in their glass structure are new alternatives for rare eart (RE) doped hosts. Hence, the study of the structure of these vitreous systems is of great interest for science and technology. In this research work,
[...] Read more.
Heavy metal oxide glasses, containing bismuth and/or lead in their glass structure are new alternatives for rare eart (RE) doped hosts. Hence, the study of the structure of these vitreous systems is of great interest for science and technology. In this research work, GeO2-PbO-Bi2O3 glass host doped with Er3+/Yb3+ ions was synthesized by a conventional melt quenching method. The Fourier transform infrared (FTIR) results showed that PbO and Bi2O3 participate with PbO4 tetragonal pyramids and strongly distort BiO6 octahedral units in the glass network, which subsequently act as modifiers in glass structure. These results also confirmed the existence of both four and six coordination of germanium oxide in glass matrix. Full article
(This article belongs to the Section Material Sciences and Nanotechnology)
Open AccessArticle Monocyte Chemotactic Protein-1 as a Potential Biomarker for Early Anti-Thrombotic Therapy after Ischemic Stroke
Int. J. Mol. Sci. 2012, 13(7), 8670-8678; doi:10.3390/ijms13078670
Received: 7 May 2012 / Revised: 21 June 2012 / Accepted: 3 July 2012 / Published: 12 July 2012
Cited by 4 | PDF Full-text (291 KB) | HTML Full-text | XML Full-text
Abstract
Inflammation following ischemic brain injury is correlated with adverse outcome. Preclinical studies indicate that treatment with acetylsalicylic acid + extended-release dipyridamole (ASA + ER-DP) has anti-inflammatory and thereby neuroprotective effects by inhibition of monocyte chemotactic protein-1 (MCP-1) expression. We hypothesized that early treatment
[...] Read more.
Inflammation following ischemic brain injury is correlated with adverse outcome. Preclinical studies indicate that treatment with acetylsalicylic acid + extended-release dipyridamole (ASA + ER-DP) has anti-inflammatory and thereby neuroprotective effects by inhibition of monocyte chemotactic protein-1 (MCP-1) expression. We hypothesized that early treatment with ASA + ER-DP will reduce levels of MCP-1 also in patients with ischemic stroke. The EARLY trial randomized patients with ischemic stroke or TIA to either ASA + ER-DP treatment or ASA monotherapy within 24 h following the event. After 7 days, all patients were treated for up to 90 days with ASA + ER-DP. MCP-1 was determined from blood samples taken from 425 patients on admission and day 8. The change in MCP-1 from admission to day 8 did not differ between patients treated with ASA + ER-DP and ASA monotherapy (p > 0.05). Comparisons within MCP-1 baseline quartiles indicated that patients in the highest quartile (>217–973 pg/mL) showed improved outcome at 90 days if treated with ASA + ER-DP in comparison to treatment with ASA alone (p = 0.004). Our data does not provide any evidence that treatment with ASA + ER-DP lowers MCP-1 in acute stroke patients. However, MCP-1 may be a useful biomarker for deciding on early stroke therapy, as patients with high MCP-1 at baseline appear to benefit from early treatment with ASA + ER-DP. Full article
(This article belongs to the Special Issue Neuroprotective Strategies 2012)
Open AccessArticle A Freshwater Streptomyces, Isolated from Tyume River, Produces a Predominantly Extracellular Glycoprotein Bioflocculant
Int. J. Mol. Sci. 2012, 13(7), 8679-8695; doi:10.3390/ijms13078679
Received: 15 May 2012 / Revised: 18 June 2012 / Accepted: 21 June 2012 / Published: 13 July 2012
Cited by 16 | PDF Full-text (779 KB) | HTML Full-text | XML Full-text
Abstract
We evaluated bioflocculant production by a freshwater actinobacteria whose 16S rDNA nucleotide sequence was deposited in GenBank as Streptomyces sp. Gansen (accession number HQ537129). Optimum culture conditions for bioflocculant production were an initial medium pH of 6.8, incubation temperature of 30 °C, agitation
[...] Read more.
We evaluated bioflocculant production by a freshwater actinobacteria whose 16S rDNA nucleotide sequence was deposited in GenBank as Streptomyces sp. Gansen (accession number HQ537129). Optimum culture conditions for bioflocculant production were an initial medium pH of 6.8, incubation temperature of 30 °C, agitation speed of 160 rpm and an inoculum size of 2% (v/v) of cell density 1.5 × 108 cfu/mL. The carbon, nitrogen and cation sources for optimum bioflocculant production were glucose (89% flocculating activity), ammonium sulfate (76% flocculating activity) and MgCl2. Bioflocculant pyrolysis showed three step decomposition indicative of three components while chemical analyses showed 78% carbohydrate and 22% protein (wt/wt). The mass ratio of neutral sugar, amino sugar and uronic acids was 4.6:2.4:3. FTIR spectrometry indicated the presence of carboxyl, hydroxyl and amino groups, typical for heteropolysaccharide. The bioflocculant showed a lattice structure as seen by SEM imaging. Its high flocculation activity suggests its suitability for industrial applicability. Full article
Open AccessArticle Mitochondrial Dysfunction and Oxidative Stress Promote Apoptotic Cell Death in the Striatum via Cytochrome c/ Caspase-3 Signaling Cascade Following Chronic Rotenone Intoxication in Rats
Int. J. Mol. Sci. 2012, 13(7), 8722-8739; doi:10.3390/ijms13078722
Received: 27 April 2012 / Revised: 4 July 2012 / Accepted: 5 July 2012 / Published: 13 July 2012
Cited by 19 | PDF Full-text (3489 KB) | HTML Full-text | XML Full-text
Abstract
Parkinson’s disease (PD) is a progressive neurological disorder marked by nigrostriatal dopaminergic degeneration. Evidence suggests that mitochondrial dysfunction may be linked to PD through a variety of different pathways, including free-radical generation and dysfunction of the mitochondrial Complex I activity. In Lewis rats,
[...] Read more.
Parkinson’s disease (PD) is a progressive neurological disorder marked by nigrostriatal dopaminergic degeneration. Evidence suggests that mitochondrial dysfunction may be linked to PD through a variety of different pathways, including free-radical generation and dysfunction of the mitochondrial Complex I activity. In Lewis rats, chronic systemic administration of a specific mitochondrial Complex I inhibitor, rotenone (3 mg/kg/day) produced parkinsonism-like symptoms. Increased oxidized proteins and peroxynitrite, and mitochondrial or cytosol translocation of Bim, Bax or cytochrome c in the striatum was observed after 2–4 weeks of rotenone infusion. After 28 days of systemic rotenone exposure, imunohistochemical staining for tyrosine hydroxylase indicated nigrostriatal dopaminergic neuronal cell degeneration. Characteristic histochemical (TUNEL or activated caspase-3 staining) or ultrastructural (electron microscopy) features of apoptotic cell death were present in the striatal neuronal cell after chronic rotenone intoxication. We conclude that chronic rotenone intoxication may enhance oxidative and nitrosative stress that induces mitochondrial dysfunction and ultrastructural damage, resulting in translocation of Bim and Bax from cytosol to mitochondria that contributes to apoptotic cell death in the striatum via cytochrome c/caspase-3 signaling cascade. Full article
(This article belongs to the Special Issue Molecular Mechanisms of Organ-Specific Toxicity)
Open AccessArticle Sampling Strategy and Potential Utility of Indels for DNA Barcoding of Closely Related Plant Species: A Case Study in Taxus
Int. J. Mol. Sci. 2012, 13(7), 8740-8751; doi:10.3390/ijms13078740
Received: 8 February 2012 / Revised: 23 June 2012 / Accepted: 27 June 2012 / Published: 13 July 2012
Cited by 11 | PDF Full-text (200 KB) | HTML Full-text | XML Full-text | Supplementary Files
Abstract
Although DNA barcoding has become a useful tool for species identification and biodiversity surveys in plant sciences, there remains little consensus concerning appropriate sampling strategies and the treatment of indels. To address these two issues, we sampled 39 populations for nine Taxus species
[...] Read more.
Although DNA barcoding has become a useful tool for species identification and biodiversity surveys in plant sciences, there remains little consensus concerning appropriate sampling strategies and the treatment of indels. To address these two issues, we sampled 39 populations for nine Taxus species across their entire ranges, with two to three individuals per population randomly sampled. We sequenced one core DNA barcode (matK) and three supplementary regions (trnH-psbA, trnL-trnF and ITS) for all samples to test the effects of sampling design and the utility of indels. Our results suggested that increasing sampling within-population did not change the clustering of individuals, and that meant within-population P-distances were zero for most populations in all regions. Based on the markers tested here, comparison of methods either including or excluding indels indicated that discrimination and nodal support of monophyletic groups were significantly increased when indels were included. Thus we concluded that one individual per population was adequate to represent the within-population variation in these species for DNA barcoding, and that intra-specific sampling was best focused on representing the entire ranges of certain taxa. We also found that indels occurring in the chloroplast trnL-trnF and trnH-psbA regions were informative to differentiate among for closely related taxa barcoding, and we proposed that indel-coding methods should be considered for use in future for closed related plant species DNA barcoding projects on or below generic level. Full article
(This article belongs to the Section Biochemistry, Molecular Biology and Biophysics)
Open AccessArticle Comparison of Different Ranking Methods in Protein-Ligand Binding Site Prediction
Int. J. Mol. Sci. 2012, 13(7), 8752-8761; doi:10.3390/ijms13078752
Received: 14 May 2012 / Revised: 19 June 2012 / Accepted: 2 July 2012 / Published: 16 July 2012
Cited by 2 | PDF Full-text (465 KB) | HTML Full-text | XML Full-text | Supplementary Files
Abstract
In recent years, although many ligand-binding site prediction methods have been developed, there has still been a great demand to improve the prediction accuracy and compare different prediction algorithms to evaluate their performances. In this work, in order to improve the performance of
[...] Read more.
In recent years, although many ligand-binding site prediction methods have been developed, there has still been a great demand to improve the prediction accuracy and compare different prediction algorithms to evaluate their performances. In this work, in order to improve the performance of the protein-ligand binding site prediction method presented in our former study, a comparison of different binding site ranking lists was studied. Four kinds of properties, i.e., pocket size, distance from the protein centroid, sequence conservation and the number of hydrophobic residues, have been chosen as the corresponding ranking criterion respectively. Our studies show that the sequence conservation information helps to rank the real pockets with the most successful accuracy compared to others. At the same time, the pocket size and the distance of binding site from the protein centroid are also found to be helpful. In addition, a multi-view ranking aggregation method, which combines the information among those four properties, was further applied in our study. The results show that a better performance can be achieved by the aggregation of the complementary properties in the prediction of ligand-binding sites. Full article
(This article belongs to the Section Physical Chemistry, Theoretical and Computational Chemistry)
Figures

Open AccessArticle MicroRNA-125b Functions as a Tumor Suppressor in Hepatocellular Carcinoma Cells
Int. J. Mol. Sci. 2012, 13(7), 8762-8774; doi:10.3390/ijms13078762
Received: 23 May 2012 / Revised: 19 June 2012 / Accepted: 6 July 2012 / Published: 16 July 2012
Cited by 31 | PDF Full-text (1240 KB) | HTML Full-text | XML Full-text | Supplementary Files
Abstract
MicroRNAs (miRNAs) are important regulators of multiple cellular processes, and the deregulation of miRNA is a common event in diverse human diseases, particularly cancer. However, the mechanisms underlying the relationship between disordered miRNA expression and tumorigenesis have remained largely unknown. In this study,
[...] Read more.
MicroRNAs (miRNAs) are important regulators of multiple cellular processes, and the deregulation of miRNA is a common event in diverse human diseases, particularly cancer. However, the mechanisms underlying the relationship between disordered miRNA expression and tumorigenesis have remained largely unknown. In this study, we demonstrated the down-regulation of miR-125b in hepatocellular carcinoma (HCC) tissues and HCC cell lines by Northern blot and quantitative RT-PCR analyses. The ectopic expression of miR-125b reduced the cellular proliferation and cell cycle progression of HCC cells by targeting Mcl-1 and IL6R. Furthermore, the miR-125b-induced inhibition of cell proliferation was rescued by the expression of Mcl-1 or IL6R variants that lacked 3' UTRs. Thus, this study revealed the differential expression of miR-125b in HCC cells and elucidated its potential as a tumor suppressor in HCC development. Full article
(This article belongs to the Special Issue Advances in Molecular Oncology (special issue))
Open AccessArticle Microwave-Assisted Method for Simultaneous Extraction and Hydrolysis for Determination of Flavonol Glycosides in Ginkgo Foliage Using Brönsted Acidic Ionic-Liquid [HO3S(CH2)4mim]HSO4 Aqueous Solutions
Int. J. Mol. Sci. 2012, 13(7), 8775-8788; doi:10.3390/ijms13078775
Received: 23 April 2012 / Revised: 5 July 2012 / Accepted: 6 July 2012 / Published: 16 July 2012
Cited by 11 | PDF Full-text (392 KB) | HTML Full-text | XML Full-text
Abstract
The Brönsted acidic ionic-liquid [HO3S(CH2)4mim] HSO4, a novel dual catalyst–solvent, has been successfully applied in simultaneous microwave-assisted extraction and hydrolysis for the determination of flavonol glycosides in Ginkgo foliage. The parameters, namely the [HO3
[...] Read more.
The Brönsted acidic ionic-liquid [HO3S(CH2)4mim] HSO4, a novel dual catalyst–solvent, has been successfully applied in simultaneous microwave-assisted extraction and hydrolysis for the determination of flavonol glycosides in Ginkgo foliage. The parameters, namely the [HO3S(CH2)4mim]HSO4 concentration, microwave-irradiation power, microwave-irradiation time, and solid–liquid ratio, were optimized. The optimum conditions were: an amount of 1.5 M [HO3S(CH2)4mim]HSO4, a microwave-irradiation power of 120 W, an irradiation time of 15 min, and a solid–liquid ratio of 1:30 g/mL. Compared with traditional methods the proposed approach demonstrates higher efficiency in a shorter operating time, and is an efficient, rapid, and simple sample preparation method. Full article
Open AccessArticle Extraction of Dihydroquercetin from Larix gmelinii with Ultrasound-Assisted and Microwave-Assisted Alternant Digestion
Int. J. Mol. Sci. 2012, 13(7), 8789-8804; doi:10.3390/ijms13078789
Received: 30 May 2012 / Revised: 1 July 2012 / Accepted: 3 July 2012 / Published: 16 July 2012
Cited by 8 | PDF Full-text (2019 KB) | HTML Full-text | XML Full-text
Abstract
An ultrasound and microwave assisted alternant extraction method (UMAE) was applied for extracting dihydroquercetin (DHQ) from Larix gmelinii wood. This investigation was conducted using 60% ethanol as solvent, 1:12 solid to liquid ratio, and 3 h soaking time. The optimum treatment time
[...] Read more.
An ultrasound and microwave assisted alternant extraction method (UMAE) was applied for extracting dihydroquercetin (DHQ) from Larix gmelinii wood. This investigation was conducted using 60% ethanol as solvent, 1:12 solid to liquid ratio, and 3 h soaking time. The optimum treatment time was ultrasound 40 min, microwave 20 min, respectively, and the extraction was performed once. Under the optimized conditions, satisfactory extraction yield of the target analyte was obtained. Relative to ultrasound-assisted or microwave-assisted method, the proposed approach provides higher extraction yield. The effect of DHQ of different concentrations and synthetic antioxidants on oxidative stability in soy bean oil stored for 20 days at different temperatures (25 °C and 60 °C) was compared. DHQ was more effective in restraining soy bean oil oxidation, and a dose-response relationship was observed. The antioxidant activity of DHQ was a little stronger than that of BHA and BHT. Soy bean oil supplemented with 0.08 mg/g DHQ exhibited favorable antioxidant effects and is preferable for effectively avoiding oxidation. The L. gmelinii wood samples before and after extraction were characterized by scanning electron microscopy. The results showed that the UMAE method is a simple and efficient technique for sample preparation. Full article
(This article belongs to the Section Biochemistry, Molecular Biology and Biophysics)
Open AccessArticle Isolation and Characterization of Cross-Amplification Microsatellite Panels for Species of Procapra (Bovidae; Antilopinae)
Int. J. Mol. Sci. 2012, 13(7), 8805-8818; doi:10.3390/ijms13078805
Received: 30 May 2012 / Revised: 4 July 2012 / Accepted: 9 July 2012 / Published: 16 July 2012
Cited by 1 | PDF Full-text (445 KB) | HTML Full-text | XML Full-text
Abstract
The three Procapra species, Tibetan gazelle (P. picticaudata), Mongolian gazelle (P. gutturosa) and Przewalski’s gazelle (P. przewalskii) are endemic to Asia. Several intraspecific genetic issues have been studied with species-specific microsatellite loci in these Asian gazelles. However,
[...] Read more.
The three Procapra species, Tibetan gazelle (P. picticaudata), Mongolian gazelle (P. gutturosa) and Przewalski’s gazelle (P. przewalskii) are endemic to Asia. Several intraspecific genetic issues have been studied with species-specific microsatellite loci in these Asian gazelles. However, cross-species microsatellite panels are absent, which inhibits comparative conservation and evolutionary studies of the Procapra. In this study, we isolated 20 cross-species microsatellite loci for Procapra from both related species and the genomic library of P. przewalskii. Fifty-three samples of the three gazelles were used to characterize the markers. Allele numbers ranged from three to 20, with a mean of 7.93 per locus. Observed heterozygosity (HO) averaged 0.680 and expected heterozygosity (HE) 0.767. The mean polymorphic information content (PIC) was 0.757 for P. picticaudata, 0.803 for P. gutturosa and 0.590 for P. przewalskii. Nine loci were significantly deviated from Hardy-Weinberg (H-W) equilibrium in the three species. Significant linkage disequilibrium was detected in four pairs of loci in P. przewalskii, five pairs in P. gutturosa and 51 pairs in P. picticaudata. Considering the abundance of published loci and their high success rates of cross-amplification, testing and utilization of loci from related species is efficient for wild species of Bovidae. The cross-species microsatellite loci we developed will facilitate further interspecies genetic studies in Procapra. Full article
(This article belongs to the Section Molecular Diagnostics)
Open AccessArticle Identification and Characterization of a Bursaphelenchus xylophilus (Aphelenchida: Aphelenchoididae) Thermotolerance-Related Gene: Bx-HSP90
Int. J. Mol. Sci. 2012, 13(7), 8819-8833; doi:10.3390/ijms13078819
Received: 18 May 2012 / Revised: 18 June 2012 / Accepted: 6 July 2012 / Published: 16 July 2012
Cited by 5 | PDF Full-text (1089 KB) | HTML Full-text | XML Full-text
Abstract
Temperatures directly influence the distribution and intensity of pine wilt disease caused by the pine wood nematode, Bursaphelenchus xylophilus. To date, however, little is known about the causation and mechanism of this influence. The molecular chaperone HSP90 is a key component that
[...] Read more.
Temperatures directly influence the distribution and intensity of pine wilt disease caused by the pine wood nematode, Bursaphelenchus xylophilus. To date, however, little is known about the causation and mechanism of this influence. The molecular chaperone HSP90 is a key component that contributes to survival in the abiotic stress response. In this study, we investigated the relationship between the survival of B. xylophilus and the functionality of the HSP90 gene. Bx-HSP90 was cloned from a suppression subtractive hybridization library. In situ mRNA hybridization showed that Bx-HSP90 was constitutively expressed in response to all of the temperatures tested, and RT-PCR indicated that all of the temperatures could induce Bx-HSP90 transcription, with the highest transcript level detected at 30 °C. The suppression of the Bx-HSP90 transcript by RNA interference led to a 25% reduction in the number of nematodes at 30 °C after 44 h. Sharp declines in the survival of the RNAi-treated nematodes were observed after 8 days at 25 °C, 48 h at 30 °C and 24 h at 35 °C. Both heat shock and the knockdown of Bx-HSP90 hindered the growth of the B. xylophilus populations. The results indicate that Bx-HSP90 is essential for the survival of B. xylophilus, confirming the thermoregulatory function of the gene, and delineate the timeframe and temperature range within which the gene function occurs. Full article
(This article belongs to the Section Biochemistry, Molecular Biology and Biophysics)
Open AccessArticle The Tricyclodecan-9-yl-xanthogenate D609 Triggers Ceramide Increase and Enhances FasL-Induced Caspase-Dependent and -Independent Cell Death in T Lymphocytes
Int. J. Mol. Sci. 2012, 13(7), 8834-8852; doi:10.3390/ijms13078834
Received: 1 June 2012 / Revised: 30 June 2012 / Accepted: 4 July 2012 / Published: 16 July 2012
Cited by 4 | PDF Full-text (552 KB) | HTML Full-text | XML Full-text
Abstract
D609 is known to modulate death receptor-induced ceramide generation and cell death. We show that in Jurkat cells, non-toxic D609 concentrations inhibit sphingomyelin synthase and, to a lesser extent, glucosylceramide synthase, and transiently increase the intracellular ceramide level. D609 significantly enhanced FasL-induced caspase
[...] Read more.
D609 is known to modulate death receptor-induced ceramide generation and cell death. We show that in Jurkat cells, non-toxic D609 concentrations inhibit sphingomyelin synthase and, to a lesser extent, glucosylceramide synthase, and transiently increase the intracellular ceramide level. D609 significantly enhanced FasL-induced caspase activation and apoptosis. D609 stimulated FasL-induced cell death in caspase-8-deficient Jurkat cells, indicating that D609 acts downstream of caspase-8. At high FasL concentration (500 ng/mL), cell death was significantly, but not completely, inhibited by zVAD-fmk, a broad-spectrum caspase inhibitor, indicating that FasL can activate both caspase-dependent and -independent cell death signaling pathways. FasL-induced caspase activation was abolished by zVAD-fmk, whereas ceramide production was only partially impaired. D609 enhanced caspase-independent ceramide increase and cell death in response to FasL. Also, D609 overcame zVAD-fmk-conferred resistance to a FasL concentration as low as 50 ng/mL and bypassed RIP deficiency. It is likely that mitochondrial events were involved, since Bcl-xL over-expression impaired D609 effects. In PHA-activated human T lymphocytes, D609 enhanced FasL-induced cell death in the presence or absence of zVAD-fmk. Altogether, our data strongly indicate that the inhibition of ceramide conversion to complex sphingolipids by D609 is accompanied by an enhancement of FasL-induced caspase-dependent and -independent cell death in T lymphocytes. Full article
(This article belongs to the collection Programmed Cell Death and Apoptosis)
Open AccessArticle Leukocyte Mitochondrial DNA Alteration in Systemic Lupus Erythematosus and Its Relevance to the Susceptibility to Lupus Nephritis
Int. J. Mol. Sci. 2012, 13(7), 8853-8868; doi:10.3390/ijms13078853
Received: 5 June 2012 / Revised: 28 June 2012 / Accepted: 9 July 2012 / Published: 16 July 2012
Cited by 11 | PDF Full-text (434 KB) | HTML Full-text | XML Full-text
Abstract
The role of mitochondrial DNA (mtDNA) alterations in the pathophysiology of systemic lupus erythematosus (SLE) remains unclear. We investigated sequence variations in the D310 region and copy number change of mtDNA in 85 SLE patients and 45 normal subjects. Leukocyte DNA and RNA
[...] Read more.
The role of mitochondrial DNA (mtDNA) alterations in the pathophysiology of systemic lupus erythematosus (SLE) remains unclear. We investigated sequence variations in the D310 region and copy number change of mtDNA in 85 SLE patients and 45 normal subjects. Leukocyte DNA and RNA were extracted from leukocytes of the peripheral venous blood. The D310 sequence variations and copy number of mtDNA, and mRNA expression levels of mtDNA-encoded genes in leukocytes were determined by quantitative real-time polymerase chain reaction (Q-PCR) and PCR-based direct sequencing, respectively. We found that leukocyte mtDNA in SLE patients exhibited higher frequency of D310 heteroplasmy (69.4% vs. 48.9%, p = 0.022) and more D310 variants (2.2 vs. 1.7, p = 0.014) than those found in controls. Among normal controls and patients with low, medium or high SLE disease activity index (SLEDAI), an ever-increasing frequency of D310 heteroplasmy was observed (p = 0.021). Leukocyte mtDNA copy number tended to be low in patients of high SLEDAI group (p = 0.068), especially in those harboring mtDNA with D310 heteroplasmy (p = 0.020). Moreover, the mtDNA copy number was positively correlated with the mRNA level of mtDNA-encoded ND1 (NADH dehydrogenase subunit 1) (p = 0.041) and ATPase 6 (ATP synthase subunit 6) (p = 0.030) genes. Patients with more D310 variants were more susceptible to lupus nephritis (p = 0.035). Taken together, our findings suggest that decrease in the mtDNA copy number and increase in D310 heteroplasmy of mtDNA are related to the development and progression of SLE, and that the patients harboring more D310 variants of mtDNA are more susceptible to lupus nephritis. Full article
(This article belongs to the Special Issue Advances in Free Radicals in Biology and Medicine)
Open AccessArticle Micronization of Taxifolin by Supercritical Antisolvent Process and Evaluation of Radical Scavenging Activity
Int. J. Mol. Sci. 2012, 13(7), 8869-8881; doi:10.3390/ijms13078869
Received: 4 June 2012 / Revised: 29 June 2012 / Accepted: 3 July 2012 / Published: 16 July 2012
Cited by 12 | PDF Full-text (574 KB) | HTML Full-text | XML Full-text
Abstract
The aim of this study was to prepare micronized taxifolin powder using the supercritical antisolvent precipitation process to improve the dissolution rate of taxifolin. Ethanol was used as solvent and carbon dioxide was used as an antisolvent. The effects of process parameters, such
[...] Read more.
The aim of this study was to prepare micronized taxifolin powder using the supercritical antisolvent precipitation process to improve the dissolution rate of taxifolin. Ethanol was used as solvent and carbon dioxide was used as an antisolvent. The effects of process parameters, such as temperature (35–65 °C), pressure (10–25 MPa), solution flow rate (3–6 mL/min) and concentration of the liquid solution (5–20 mg/mL) on the precipitate crystals were investigated. With a lower temperature, a stronger pressure and a lower concentration of the liquid solution, the size of crystals decreased. The precipitation temperature, pressure and concentration of taxifolin solution had a significant effect. However, the solution flow rate had a negligible effect. It was concluded that the physicochemical properties and dissolution rate of crystalline taxifolin could be improved by physical modification such as particle size reduction using the supercritical antisolvent (SAS) process. Further, the SAS process was a powerful methodology for improving the physicochemical properties and radical scavenging activity of taxifolin. Full article
(This article belongs to the Section Biochemistry, Molecular Biology and Biophysics)
Open AccessArticle Synergistic Interactions of Methanolic Extract of Acacia mearnsii De Wild. with Antibiotics against Bacteria of Clinical Relevance
Int. J. Mol. Sci. 2012, 13(7), 8915-8932; doi:10.3390/ijms13078915
Received: 27 March 2012 / Revised: 27 June 2012 / Accepted: 10 July 2012 / Published: 17 July 2012
Cited by 16 | PDF Full-text (148 KB) | HTML Full-text | XML Full-text
Abstract
With the emergence of multidrug-resistant organisms, combining medicinal plants with synthetic or orthodox medicines against resistant bacteria becomes necessary. In this study, interactions between methanolic extract of Acacia mearnsii and eight antibiotics were investigated by agar diffusion and checkerboard assays. The minimum inhibitory
[...] Read more.
With the emergence of multidrug-resistant organisms, combining medicinal plants with synthetic or orthodox medicines against resistant bacteria becomes necessary. In this study, interactions between methanolic extract of Acacia mearnsii and eight antibiotics were investigated by agar diffusion and checkerboard assays. The minimum inhibitory concentrations (MICs) of all the antibiotics ranged between 0.020 and 500 µg/mL while that of the crude extract varied between 0.156 and 1.25 mg/mL. The agar diffusion assay showed that extract-kanamycin combination had zones of inhibition ≥20 ± 1.0 mm in all the bacteria tested (100%), followed by extract-chloramphenicol (90%) > extract-ciprofloxacin = extract-tetracycline (70%) > extract-amoxicillin (60%) > extract-nalidixic acid (50%) > extract-erythromycin (40%) > extract-metronidazole (20%). The checkerboard showed synergistic interaction (61.25%), additivity/indifference (23.75%) and antagonistic (15%) effects. The synergistic interaction was most expressed by combining the extract with tetracycline, metronidazole, amoxicillin, ciprofloxacin, chloramphenicol and nalidixic acid against E. coli (ATCC 25922), erythromycin, metronidazole, amoxicillin, chloramphenicol and kanamycin against S. aureus (ATCC 6538), erythromycin, tetracycline, amoxicillin, nalidixic acid and chloramphenicol against B. subtilis KZN, erythromycin, metronidazole and amoxicillin against E. faecalis KZN, erythromycin, tetracycline, nalidixic acid and chloramphenicol against K. pneumoniae (ATCC 10031), erythromycin, tetracycline, metronidazole and chloramphenicol against P. vulgaris (ATCC 6830), erythromycin, tetracycline, amoxicillin and chloramphenicol against S. sonnei (ATCC 29930), metronidazole, amoxicillin and chloramphenicol against E. faecalis (ATCC 29212) and ciprofloxacin and chloramphenicol against Proteus vulgaris KZN. The synergistic interactions indicated that the bactericidal potentials of the antibacterial agents were improved and combining natural products with antibiotic could be potential sources for resistance-modifying agents useful against infectious multi-drug resistant bacteria. Full article
(This article belongs to the Section Biochemistry, Molecular Biology and Biophysics)
Open AccessArticle Exome Enrichment and SOLiD Sequencing of Formalin Fixed Paraffin Embedded (FFPE) Prostate Cancer Tissue
Int. J. Mol. Sci. 2012, 13(7), 8933-8942; doi:10.3390/ijms13078933
Received: 11 April 2012 / Revised: 29 May 2012 / Accepted: 9 July 2012 / Published: 17 July 2012
Cited by 16 | PDF Full-text (345 KB) | HTML Full-text | XML Full-text
Abstract
Next generation sequencing (NGS) technologies have revolutionized cancer research allowing the comprehensive study of cancer using high throughput deep sequencing methodologies. These methods detect genomic alterations, nucleotide substitutions, insertions, deletions and copy number alterations. SOLiD (Sequencing by Oligonucleotide Ligation and Detection, Life Technologies)
[...] Read more.
Next generation sequencing (NGS) technologies have revolutionized cancer research allowing the comprehensive study of cancer using high throughput deep sequencing methodologies. These methods detect genomic alterations, nucleotide substitutions, insertions, deletions and copy number alterations. SOLiD (Sequencing by Oligonucleotide Ligation and Detection, Life Technologies) is a promising technology generating billions of 50 bp sequencing reads. This robust technique, successfully applied in gene identification, might be helpful in detecting novel genes associated with cancer initiation and progression using formalin fixed paraffin embedded (FFPE) tissue. This study’s aim was to compare the validity of whole exome sequencing of fresh-frozen vs. FFPE tumor tissue by normalization to normal prostatic FFPE tissue, obtained from the same patient. One primary fresh-frozen sample, corresponding FFPE prostate cancer sample and matched adjacent normal prostatic tissue was subjected to exome sequencing. The sequenced reads were mapped and compared. Our study was the first to show comparable exome sequencing results between FFPE and corresponding fresh-frozen cancer tissues using SOLiD sequencing. A prior study has been conducted comparing the validity of sequencing of FFPE vs. fresh frozen samples using other NGS platforms. Our validation further proves that FFPE material is a reliable source of material for whole exome sequencing. Full article
Open AccessArticle Antioxidant Activity of Brazilian Vegetables and Its Relation with Phenolic Composition
Int. J. Mol. Sci. 2012, 13(7), 8943-8957; doi:10.3390/ijms13078943
Received: 21 February 2012 / Revised: 9 June 2012 / Accepted: 10 July 2012 / Published: 18 July 2012
Cited by 30 | PDF Full-text (254 KB) | HTML Full-text | XML Full-text
Abstract
Vegetables are widely consumed in Brazil and exported to several countries. This study was performed to evaluate the phenolic content and antioxidant activity of vegetables commonly consumed in Brazil using five different methods, namely DPPH and ABTS free radical, β-carotene bleaching, reduction of
[...] Read more.
Vegetables are widely consumed in Brazil and exported to several countries. This study was performed to evaluate the phenolic content and antioxidant activity of vegetables commonly consumed in Brazil using five different methods, namely DPPH and ABTS free radical, β-carotene bleaching, reduction of Fe3+ (FRAP), oxidative stability in Rancimat, and the chemical composition using gas chromatography-mass spectrometry (GC-MS). The content of phenolic compounds ranged from 1.2 mg GA/g (carrot) to 16.9 mg GA/g (lettuce). Vegetables presenting the highest antioxidant activity were lettuce (77.2 µmol Trolox/g DPPH; 447.1 µmol F2+/g FRAP), turmeric (118.6 µmol Trolox/g ABTS•+; 92.8% β-carotene), watercress and broccoli (protective factor 1.29—Rancimat method). Artichoke, spinach, broccoli, and asparagus also showed considerable antioxidant activity. The most frequent phenolic compounds identified by GC-MS were ferulic, caffeic, p-coumaric, 2-dihydroxybenzoic, 2,5-dihydroxybenzoic acids, and quercetin. We observed antioxidant activity in several vegetables and our results point out their importance in the diet. Full article
(This article belongs to the Section Biochemistry, Molecular Biology and Biophysics)
Open AccessArticle Binding Mode Prediction of Evodiamine within Vanilloid Receptor TRPV1
Int. J. Mol. Sci. 2012, 13(7), 8958-8969; doi:10.3390/ijms13078958
Received: 30 April 2012 / Revised: 18 June 2012 / Accepted: 26 June 2012 / Published: 18 July 2012
Cited by 12 | PDF Full-text (1088 KB) | HTML Full-text | XML Full-text | Supplementary Files
Abstract
Accurate assessment of the potential binding mode of drugs is crucial to computer-aided drug design paradigms. It has been reported that evodiamine acts as an agonist of the vanilloid receptor Transient receptor potential vanilloid-1 (TRPV1). However, the precise interaction between evodiamine and TRPV1
[...] Read more.
Accurate assessment of the potential binding mode of drugs is crucial to computer-aided drug design paradigms. It has been reported that evodiamine acts as an agonist of the vanilloid receptor Transient receptor potential vanilloid-1 (TRPV1). However, the precise interaction between evodiamine and TRPV1 was still not fully understood. In this perspective, the homology models of TRPV1 were generated using the crystal structure of the voltage-dependent shaker family K+ channel as a template. We then performed docking and molecular dynamics simulation to gain a better understanding of the probable binding modes of evodiamine within the TRPV1 binding pocket. There are no significant interspecies differences in evodiamine binding in rat, human and rabbit TRPV1 models. Pharmacophore modeling further provided confidence for the validity of the docking studies. This study is the first to shed light on the structural determinants required for the interaction between TRPV1 and evodiamine, and gives new suggestions for the rational design of novel TRPV1 ligands. Full article
Open AccessArticle Enrichment and Purification of Syringin, Eleutheroside E and Isofraxidin from Acanthopanax senticosus by Macroporous Resin
Int. J. Mol. Sci. 2012, 13(7), 8970-8986; doi:10.3390/ijms13078970
Received: 30 May 2012 / Revised: 29 June 2012 / Accepted: 6 July 2012 / Published: 18 July 2012
Cited by 6 | PDF Full-text (544 KB) | HTML Full-text | XML Full-text
Abstract
In order to screen a suitable resin for the preparative simultaneous separation and purification of syringin, eleutheroside E and isofraxidin from Acanthopanax senticosus, the adsorption and desorption properties of 17 widely used commercial macroporous resins were evaluated. According to our results, HPD100C,
[...] Read more.
In order to screen a suitable resin for the preparative simultaneous separation and purification of syringin, eleutheroside E and isofraxidin from Acanthopanax senticosus, the adsorption and desorption properties of 17 widely used commercial macroporous resins were evaluated. According to our results, HPD100C, which adsorbs by the molecular tiers model, was the best macroporous resin, offering higher adsorption and desorption capacities and higher adsorption speed for syringin, eleutheroside E and isofraxidin than other resins. Dynamic adsorption and desorption tests were carried out to optimize the process parameters. The optimal conditions were as follows: for adsorption, processing volume: 24 BV, flow rate: 2 BV/h; for desorption, ethanol–water solution: 60:40 (v/v), eluent volume: 4 BV, flow rate: 3 BV/h. Under the above conditions, the contents of syringin, eleutheroside E and isofraxidin increased 174-fold, 20-fold and 5-fold and their recoveries were 80.93%, 93.97% and 93.79%, respectively. Full article
(This article belongs to the Section Material Sciences and Nanotechnology)
Open AccessArticle Antioxidant Property Enhancement of Sweet Potato Flour under Simulated Gastrointestinal pH
Int. J. Mol. Sci. 2012, 13(7), 8987-8997; doi:10.3390/ijms13078987
Received: 30 May 2012 / Revised: 4 July 2012 / Accepted: 5 July 2012 / Published: 19 July 2012
Cited by 4 | PDF Full-text (265 KB) | HTML Full-text | XML Full-text
Abstract
Sweet potato is known to be rich in healthful antioxidants, but the stability of its antioxidant properties under gastrointestinal pH is very much unknown. Hence, this study aimed to evaluate the changes in antioxidant properties (total contents of phenolics and flavonoids as well
[...] Read more.
Sweet potato is known to be rich in healthful antioxidants, but the stability of its antioxidant properties under gastrointestinal pH is very much unknown. Hence, this study aimed to evaluate the changes in antioxidant properties (total contents of phenolics and flavonoids as well as antioxidant activity) of sweet potato flour (SPF) under simulated gastrointestinal pH conditions. It was found that the yield of SPF crude phenolic extract increased from 0.29 to 3.22 g/100 g SPF upon subjection to gastrointestinal pH conditions (p < 0.05). Also elevated significantly were the total phenolic content (TPC), total flavonoid content (TFC) and antioxidant activity of SPF (p < 0.05). In summary, the antioxidant properties of SPF were enhanced under gastrointestinal pH conditions, suggesting that SPF might possess a considerable amount of bound phenolic and other antioxidative compounds. The antioxidant properties of SPF are largely influenced by pH and thus might be enhanced during the in vivo digestive process. Full article
(This article belongs to the Section Biochemistry, Molecular Biology and Biophysics)
Open AccessArticle Homology Modeling and Analysis of Structure Predictions of the Bovine Rhinitis B Virus RNA Dependent RNA Polymerase (RdRp)
Int. J. Mol. Sci. 2012, 13(7), 8998-9013; doi:10.3390/ijms13078998
Received: 3 May 2012 / Revised: 3 July 2012 / Accepted: 11 July 2012 / Published: 19 July 2012
Cited by 3 | PDF Full-text (1437 KB) | HTML Full-text | XML Full-text | Supplementary Files
Abstract
Bovine Rhinitis B Virus (BRBV) is a picornavirus responsible for mild respiratory infection of cattle. It is probably the least characterized among the aphthoviruses. BRBV is the closest relative known to Foot and Mouth Disease virus (FMDV) with a ~43% identical polyprotein sequence
[...] Read more.
Bovine Rhinitis B Virus (BRBV) is a picornavirus responsible for mild respiratory infection of cattle. It is probably the least characterized among the aphthoviruses. BRBV is the closest relative known to Foot and Mouth Disease virus (FMDV) with a ~43% identical polyprotein sequence and as much as 67% identical sequence for the RNA dependent RNA polymerase (RdRp), which is also known as 3D polymerase (3Dpol). In the present study we carried out phylogenetic analysis, structure based sequence alignment and prediction of three-dimensional structure of BRBV 3Dpol using a combination of different computational tools. Model structures of BRBV 3Dpol were verified for their stereochemical quality and accuracy. The BRBV 3Dpol structure predicted by SWISS-MODEL exhibited highest scores in terms of stereochemical quality and accuracy, which were in the range of 2Å resolution crystal structures. The active site, nucleic acid binding site and overall structure were observed to be in agreement with the crystal structure of unliganded as well as template/primer (T/P), nucleotide tri-phosphate (NTP) and pyrophosphate (PPi) bound FMDV 3Dpol (PDB, 1U09 and 2E9Z). The closest proximity of BRBV and FMDV 3Dpol as compared to human rhinovirus type 16 (HRV-16) and rabbit hemorrhagic disease virus (RHDV) 3Dpols is also substantiated by phylogeny analysis and root-mean square deviation (RMSD) between C-α traces of the polymerase structures. The absence of positively charged α-helix at C terminal, significant differences in non-covalent interactions especially salt bridges and CH-pi interactions around T/P channel of BRBV 3Dpol compared to FMDV 3Dpol, indicate that despite a very high homology to FMDV 3Dpol, BRBV 3Dpol may adopt a different mechanism for handling its substrates and adapting to physiological requirements. Our findings will be valuable in the design of structure-function interventions and identification of molecular targets for drug design applicable to Aphthovirus RdRps. Full article
(This article belongs to the Special Issue Advances in Biomolecular Simulation)
Open AccessArticle Hepatoprotective Effects of Berberis vulgaris L. Extract/β Cyclodextrin on Carbon Tetrachloride–Induced Acute Toxicity in Mice
Int. J. Mol. Sci. 2012, 13(7), 9014-9034; doi:10.3390/ijms13079014
Received: 18 May 2012 / Revised: 25 June 2012 / Accepted: 5 July 2012 / Published: 19 July 2012
Cited by 11 | PDF Full-text (2775 KB) | HTML Full-text | XML Full-text
Abstract
The present study investigated the capacity of formulated Berberis vulgaris extract/β-cyclodextrin to protect liver against CCl4-induced hepatotoxicity in mice. Formulated and non-formulated extracts were given orally (50 mg/kg/day) to mice for 7 days and were then intra-peritoneally injected with 1.0 mL/kg
[...] Read more.
The present study investigated the capacity of formulated Berberis vulgaris extract/β-cyclodextrin to protect liver against CCl4-induced hepatotoxicity in mice. Formulated and non-formulated extracts were given orally (50 mg/kg/day) to mice for 7 days and were then intra-peritoneally injected with 1.0 mL/kg CCl4 on the 8th day. After 24 h of CCl4 administration, an increase in the levels of apartate-amino-transferase (AST), alanine-amino-transferase (ALT) and malondialdehyde (MDA) was found and a significant decrease in superoxide-dismutase (SOD), catalase (CAT), glutathione (GSH) and glutathione-peroxidase (GPx) levels could be detected. This was accompanied by extended centrilobular necrosis, steatosis, fibrosis and an altered ultrastructure of hepatocytes. Pre-treatment with formulated or non-formulated extract suppressed the increase in ALT, AST and MDA levels and restored the level of antioxidant enzymes at normal values. Histopathological and electron-microscopic examination showed milder liver damage in both pre-treated groups and the protective effect was more pronounced after the formulated extract was administered. Internucleosomal DNA fragmentation induced by CCl4 was reduced in the group which received non-formulated extract and absent in the group which received formulated extract. Taken together, our results suggest that Berberis vulgaris/β-cyclodextrin treatment prevents hepatic injury induced by CCl4 and can be considered for further nutraceutical studies. Full article
(This article belongs to the Section Biochemistry, Molecular Biology and Biophysics)
Open AccessArticle Quantitative and Chemical Fingerprint Analysis for the Quality Evaluation of Isatis indigotica based on Ultra-Performance Liquid Chromatography with Photodiode Array Detector Combined with Chemometric Methods
Int. J. Mol. Sci. 2012, 13(7), 9035-9050; doi:10.3390/ijms13079035
Received: 18 June 2012 / Revised: 5 July 2012 / Accepted: 12 July 2012 / Published: 20 July 2012
Cited by 16 | PDF Full-text (310 KB) | HTML Full-text | XML Full-text
Abstract
A simple and reliable method of ultra-performance liquid chromatography with photodiode array detector (UPLC-PDA) was developed to control the quality of Radix Isatidis (dried root of Isatis indigotica) for chemical fingerprint analysis and quantitative analysis of eight bioactive constituents, including R,
[...] Read more.
A simple and reliable method of ultra-performance liquid chromatography with photodiode array detector (UPLC-PDA) was developed to control the quality of Radix Isatidis (dried root of Isatis indigotica) for chemical fingerprint analysis and quantitative analysis of eight bioactive constituents, including R,S-goitrin, progoitrin, epiprogoitrin, gluconapin, adenosine, uridine, guanosine, and hypoxanthine. In quantitative analysis, the eight components showed good regression (R > 0.9997) within test ranges, and the recovery method ranged from 99.5% to 103.0%. The UPLC fingerprints of the Radix Isatidis samples were compared by performing chemometric procedures, including similarity analysis, hierarchical clustering analysis, and principal component analysis. The chemometric procedures classified Radix Isatidis and its finished products such that all samples could be successfully grouped according to crude herbs, prepared slices, and adulterant Baphicacanthis cusiae Rhizoma et Radix. The combination of quantitative and chromatographic fingerprint analysis can be used for the quality assessment of Radix Isatidis and its finished products. Full article
(This article belongs to the Section Biochemistry, Molecular Biology and Biophysics)
Figures

Open AccessArticle Ultrasonic-Assisted Enzymolysis to Improve the Antioxidant Activities of Peanut (Arachin conarachin L.) Antioxidant Hydrolysate
Int. J. Mol. Sci. 2012, 13(7), 9051-9068; doi:10.3390/ijms13079051
Received: 17 May 2012 / Revised: 12 July 2012 / Accepted: 13 July 2012 / Published: 20 July 2012
Cited by 10 | PDF Full-text (826 KB) | HTML Full-text | XML Full-text
Abstract
The objective of this work is to provide a theoretical basis for preparing peanut antioxidant hydrolysate in order to improve its antioxidant activities. Therefore, response surface methodology (RSM) based on the Box-Behnken design was used to optimize ultrasonic-assisted enzymolysis for the purpose of
[...] Read more.
The objective of this work is to provide a theoretical basis for preparing peanut antioxidant hydrolysate in order to improve its antioxidant activities. Therefore, response surface methodology (RSM) based on the Box-Behnken design was used to optimize ultrasonic-assisted enzymolysis for the purpose of preparing peanut antioxidant hydrolysate. Results indicated that the DPPH free radical scavenging activity of peanut hydrolysate could reach 90.06% under the following optimum conditions: ultrasonic power of 150.0 w, reaction temperature of 62.0 °C, incubation time of 25.0 min, and initial pH value of 8.5. The DPPH free radical scavenging rate of peanut hydrolysate from ultrasonic-assisted enzymolysis improved comparing with that of peanut hydrolysate from protease hydrolysis alone. The peanut antioxidant hydrolysate was found to display eight improved kinds of antioxidant activities. In conclusion, the optimal ultrasonic-assisted enzymolysis technology conditions described in this paper, appear to be beneficial for preparing peanut antioxidant hydrolysate. Full article
(This article belongs to the Section Biochemistry, Molecular Biology and Biophysics)
Open AccessArticle Decidual Macrophages Are Significantly Increased in Spontaneous Miscarriages and Over-Express FasL: A Potential Role for Macrophages in Trophoblast Apoptosis
Int. J. Mol. Sci. 2012, 13(7), 9069-9080; doi:10.3390/ijms13079069
Received: 24 May 2012 / Revised: 3 July 2012 / Accepted: 4 July 2012 / Published: 20 July 2012
Cited by 14 | PDF Full-text (9303 KB) | HTML Full-text | XML Full-text
Abstract
Decidual macrophages (DM) are the second most abundant population in the fetal-maternal interface. Their role has been so far identified as being local immuno-modulators favoring the maternal tolerance to the fetus. Herein we investigated tissue samples from 11 cases of spontaneous miscarriages and
[...] Read more.
Decidual macrophages (DM) are the second most abundant population in the fetal-maternal interface. Their role has been so far identified as being local immuno-modulators favoring the maternal tolerance to the fetus. Herein we investigated tissue samples from 11 cases of spontaneous miscarriages and from 9 cases of elective terminations of pregnancy. Using immunohistochemistry and dual immunofluorescence we have demonstrated that in spontaneous miscarriages the DM are significantly increased. Additionally, we noted a significant up-regulation of macrophage FasL expression. Our results further support a dual role for DM during pregnancy and miscarriages. We hypothesize that the baseline DM population in normal pregnancy is in line with an M2 phenotype supporting the ongoing gestation. In contrast, during spontaneous miscarriages, the increased FasL-expressing population could be a part of an M1 phenotype participating in Fas/FasL-related apoptosis. Our results highlight a new aspect of macrophage biology in pregnancy physiology and pathophysiology. Further studies with larger samples are needed to verify the current results and evaluate their clinical impact. Full article
(This article belongs to the collection Programmed Cell Death and Apoptosis)
Open AccessArticle The Structure Lacuna
Int. J. Mol. Sci. 2012, 13(7), 9081-9096; doi:10.3390/ijms13079081
Received: 6 June 2012 / Revised: 10 July 2012 / Accepted: 12 July 2012 / Published: 20 July 2012
Cited by 2 | PDF Full-text (223 KB) | HTML Full-text | XML Full-text
Abstract
Molecular symmetry is intimately connected with the classical concept ofthree-dimensional molecular structure. In a non-classical theory of wave-like interactionin four-dimensional space-time, both of these concepts and traditional quantum mechanicslose their operational meaning, unless suitably modified. A required reformulation shouldemphasize the importance of four-dimensional
[...] Read more.
Molecular symmetry is intimately connected with the classical concept ofthree-dimensional molecular structure. In a non-classical theory of wave-like interactionin four-dimensional space-time, both of these concepts and traditional quantum mechanicslose their operational meaning, unless suitably modified. A required reformulation shouldemphasize the importance of four-dimensional effects like spin and the symmetry effects ofspace-time curvature that could lead to a fundamentally different understanding of molecularsymmetry and structure in terms of elementary number theory. Isolated single moleculeshave no characteristic shape and macro-biomolecules only develop robust three-dimensionalstructure in hydrophobic response to aqueous cellular media. Full article
(This article belongs to the Special Issue Molecular Symmetry)
Figures

Open AccessArticle Curcumin Inhibits Glutamate Release from Rat Prefrontal Nerve Endings by Affecting Vesicle Mobilization
Int. J. Mol. Sci. 2012, 13(7), 9097-9109; doi:10.3390/ijms13079097
Received: 20 June 2012 / Revised: 11 July 2012 / Accepted: 16 July 2012 / Published: 20 July 2012
Cited by 7 | PDF Full-text (369 KB) | HTML Full-text | XML Full-text
Abstract
Curcumin, one of the major constituents of Curcuma longa, has been shown to inhibit depolarization-evoked glutamate release from rat prefrontocortical nerve terminals by reducing voltage-dependent Ca2+ entry. This study showed that curcumin inhibited ionomycin-induced glutamate release and KCl-evoked FM1-43 release, suggesting
[...] Read more.
Curcumin, one of the major constituents of Curcuma longa, has been shown to inhibit depolarization-evoked glutamate release from rat prefrontocortical nerve terminals by reducing voltage-dependent Ca2+ entry. This study showed that curcumin inhibited ionomycin-induced glutamate release and KCl-evoked FM1-43 release, suggesting that some steps after Ca2+ entry are regulated by curcumin. Furthermore, disrupting the cytoskeleton organization using cytochalasin D abolished the inhibitory action of curcumin on ionomycin-induced glutamate release. Mitogen-activated protein kinase kinase (MEK) inhibition also prevented the inhibitory effect of curcumin on ionomycin-induced glutamate release. Western blot analyses showed that curcumin decreased the ionomycin-induced phosphorylation of extracellular signal-regulated kinase 1 and 2 (ERK1/2) and synaptic vesicle-associated protein synapsin I, the main presynaptic target of ERK. These results show that curcumin-mediated inhibition of glutamate release involves modulating downstream events by controlling synaptic vesicle recruitment and exocytosis, possibly through a decrease of MAPK/ERK activation and synapsin I phosphorylation, thereby decreasing synaptic vesicle availability for exocytosis. Full article
(This article belongs to the Special Issue Plant-Derived Pharmaceuticals by Molecular Farming 2012)
Open AccessArticle HR4 Gene Is Induced in the Arabidopsis-Trichoderma atroviride Beneficial Interaction
Int. J. Mol. Sci. 2012, 13(7), 9110-9128; doi:10.3390/ijms13079110
Received: 8 May 2012 / Revised: 28 June 2012 / Accepted: 12 July 2012 / Published: 20 July 2012
Cited by 4 | PDF Full-text (2584 KB) | HTML Full-text | XML Full-text
Abstract
Plants are constantly exposed to microbes, for this reason they have evolved sophisticated strategies to perceive and identify biotic interactions. Thus, plants have large collections of so-called resistance (R) proteins that recognize specific microbe factors as signals of invasion. One of these proteins
[...] Read more.
Plants are constantly exposed to microbes, for this reason they have evolved sophisticated strategies to perceive and identify biotic interactions. Thus, plants have large collections of so-called resistance (R) proteins that recognize specific microbe factors as signals of invasion. One of these proteins is codified by the Arabidopsis thaliana HR4 gene in the Col-0 ecotype that is homologous to RPW8 genes present in the Ms-0 ecotype. In this study, we investigated the expression patterns of the HR4 gene in Arabidopsis seedlings interacting with the beneficial fungus Trichoderma atroviride. We observed the induction of the HR4 gene mainly at 96 hpi when the fungus interaction was established. Furthermore, we found that the HR4 gene was differentially regulated in interactions with the beneficial bacterium Pseudomonas fluorescens and the pathogenic bacterium P. syringae. When hormone treatments were applied to A. thaliana (Col-0), each hormone treatment induced changes in HR4 gene expression. On the other hand, the expression of the RPW8.1 and RPW8.2 genes of Arabidopsis ecotype Ms-0 in interaction with T. atroviride was assessed. Interestingly, these genes are interaction-responsive; in particular, the RPW8.1 gene shows a very high level of expression in the later stages of interaction. These results indicate that HR4 and RPW8 genes could play a role in the establishment of Arabidopsis interactions with beneficial microbes. Full article
(This article belongs to the Special Issue Advances in Molecular Plant Biology)
Figures

Open AccessArticle Pharmacokinetics and Tissue Distribution Study of Praeruptorin D from Radix Peucedani in Rats by High-Performance Liquid Chromatography (HPLC)
Int. J. Mol. Sci. 2012, 13(7), 9129-9141; doi:10.3390/ijms13079129
Received: 18 June 2012 / Revised: 16 July 2012 / Accepted: 17 July 2012 / Published: 20 July 2012
Cited by 7 | PDF Full-text (218 KB) | HTML Full-text | XML Full-text
Abstract
Praeruptorin D (PD), a major pyranocoumarin isolated from Radix Peucedani, exhibited antitumor and anti-inflammatory activities. The aim of this study was to investigate the pharmacokinetics and tissue distribution of PD in rats following intravenous (i.v.) administration. The levels of PD in plasma and
[...] Read more.
Praeruptorin D (PD), a major pyranocoumarin isolated from Radix Peucedani, exhibited antitumor and anti-inflammatory activities. The aim of this study was to investigate the pharmacokinetics and tissue distribution of PD in rats following intravenous (i.v.) administration. The levels of PD in plasma and tissues were measured by a simple and sensitive reversed-phase high-performance liquid chromatography (HPLC) method. The biosamples were treated by liquid-liquid extraction (LLE) with methyl tert-butyl ether (MTBE) and osthole was used as the internal standard (IS). The chromatographic separation was accomplished on a reversed-phase C18 column using methanol-water (75:25, v/v) as mobile phase at a flow rate of 0.8 mL/min and ultraviolet detection wave length was set at 323 nm. The results demonstrate that this method has excellent specificity, linearity, precision, accuracy and recovery. The pharmacokinetic study found that PD fitted well into a two-compartment model with a fast distribution phase and a relative slow elimination phase. Tissue distribution showed that the highest concentration was observed in the lung, followed by heart, liver and kidney. Furthermore, PD can also be detected in the brain, which indicated that PD could cross the blood-brain barrier after i.v. administration. Full article
(This article belongs to the Section Biochemistry, Molecular Biology and Biophysics)
Open AccessArticle TRAIL and Paclitaxel Synergize to Kill U87 Cells and U87-Derived Stem-Like Cells in Vitro
Int. J. Mol. Sci. 2012, 13(7), 9142-9156; doi:10.3390/ijms13079142
Received: 5 March 2012 / Revised: 11 July 2012 / Accepted: 11 July 2012 / Published: 20 July 2012
Cited by 13 | PDF Full-text (1900 KB) | HTML Full-text | XML Full-text
Abstract
U87-derived stem-like cells (U87-SLCs) were cultured using serum-free stem cell media and identified by both biological behaviors and markers. Tumor necrosis factor (TNF)-related apoptosis-inducing ligand (TRAIL) and paclitaxel (PX), in combination or alone, was used to treat U87-MG human glioma cells (U87 cells)
[...] Read more.
U87-derived stem-like cells (U87-SLCs) were cultured using serum-free stem cell media and identified by both biological behaviors and markers. Tumor necrosis factor (TNF)-related apoptosis-inducing ligand (TRAIL) and paclitaxel (PX), in combination or alone, was used to treat U87-MG human glioma cells (U87 cells) or U87-SLCs. The results showed that TRAIL/PX cannot only synergistically inhibit U87 cells but also U87-SLCs. We observed a significantly higher apoptotic rate in U87 cells simultaneously treated with TRAIL/PX for 24 h compared to cells treated with either drug alone. Furthermore, there was a remarkably higher apoptosis rate in U87-SLCs induced by the TRAIL/PX combination compared with either drug alone. Unlike the simultaneous treatment in U87 cells, U87-SLCs were pretreated for 24 h with 1 μmol/L of PX followed by 1000 ng/mL of TRAIL. Protein assays revealed that TRAIL/PX synergy was related to DR4, cleaved caspase-8 and cleaved caspase-3 upregulation, whereas the mitochondrial pathway was not involved in TRAIL-induced apoptosis. The present study indicates that PX can sensitize U87 cells and U87-SLCs to TRAIL treatment through an extrinsic pathway of cell apoptosis. The combined treatment of TRAIL and PX may be a promising glioma chemotherapy because of its successful inhibition of U87-SLCs, which are hypothesized to influence chemotherapeutic outcomes of gliomas. Full article
(This article belongs to the Section Biochemistry, Molecular Biology and Biophysics)
Open AccessArticle Reduction–Oxidation Photocycle Dynamics of Flavins in Starch Films
Int. J. Mol. Sci. 2012, 13(7), 9157-9183; doi:10.3390/ijms13079157
Received: 10 May 2012 / Revised: 2 July 2012 / Accepted: 11 July 2012 / Published: 23 July 2012
Cited by 4 | PDF Full-text (718 KB) | HTML Full-text | XML Full-text
Abstract
The blue-light photo-reduction (conversion of oxidized flavin quinone via flavin semiquinone to fully reduced flavin hydroquinone) and dark re-oxidation of the flavins riboflavin and lumiflavin in starch (α-amylose) films was studied by absorption and luminescence spectroscopy. Blue-light photo-excitation caused an absorption, fluorescence, and
[...] Read more.
The blue-light photo-reduction (conversion of oxidized flavin quinone via flavin semiquinone to fully reduced flavin hydroquinone) and dark re-oxidation of the flavins riboflavin and lumiflavin in starch (α-amylose) films was studied by absorption and luminescence spectroscopy. Blue-light photo-excitation caused an absorption, fluorescence, and phosphorescence decrease which recovered in the dark. The photo-reduction dark-oxidation cycle could be repeated. The efficiency of photo-reduction decreased with exposed excitation energy, and the speed of re-oxidation in the dark slowed down with time after excitation. The absorption did not fully recover. The fluorescence efficiency after a long time of storage in the dark increased beyond the initial flavin quinone fluorescence efficiency. Flavin photo-excitation is thought to cause starch-flavin restructuring (static fluorescence quenching center formation), enabling enhanced photo-induced starch to flavin electron transfer with subsequent flavin reduction and starch oxidation. In the dark, after light switch-off, thermal reversion of flavin reduction and starch oxidation occurred. Full article
(This article belongs to the Special Issue Flavins)
Open AccessArticle Effect of β,β-Dimethylacrylshikonin on Inhibition of Human Colorectal Cancer Cell Growth in Vitro and in Vivo
Int. J. Mol. Sci. 2012, 13(7), 9184-9193; doi:10.3390/ijms13079184
Received: 28 May 2012 / Revised: 2 July 2012 / Accepted: 9 July 2012 / Published: 23 July 2012
Cited by 6 | PDF Full-text (981 KB) | HTML Full-text | XML Full-text
Abstract
In traditional Chinese medicine, shikonin and its derivatives, has been used in East Asia for several years for the prevention and treatment of several diseases, including cancer. We previously identified that β,β-dimethylacrylshikonin (DA) could inhibit hepatocellular carcinoma growth. In the present study, we
[...] Read more.
In traditional Chinese medicine, shikonin and its derivatives, has been used in East Asia for several years for the prevention and treatment of several diseases, including cancer. We previously identified that β,β-dimethylacrylshikonin (DA) could inhibit hepatocellular carcinoma growth. In the present study, we investigated the inhibitory effects of DA on human colorectal cancer (CRC) cell line HCT-116 in vitro and in vivo. A viability assay showed that DA could inhibit tumor cell growth in a time- and dose-dependent manner. Flow cytometry showed that DA blocks the cell cycle at G0/G1 phase. Western blotting results demonstrated that the induction of apoptosis by DA correlated with the induction of pro-apoptotic proteins Bax, and Bid, and a decrease in the expression of anti-apoptotic proteins Bcl-2 and Bcl-xl. Furthermore, treatment of HCT-116 bearing nude mice with DA significantly retarded the growth of xenografts. Consistent with the results in vitro, the DA-mediated suppression of HCT-116 xenografts correlated with Bax and Bcl-2. Taken together, these results suggest that DA could be a novel and promising approach to the treatment of CRC. Full article
Open AccessArticle Antioxidative Properties of Crude Polysaccharides from Inonotus obliquus
Int. J. Mol. Sci. 2012, 13(7), 9194-9206; doi:10.3390/ijms13079194
Received: 22 May 2012 / Revised: 4 July 2012 / Accepted: 16 July 2012 / Published: 23 July 2012
Cited by 21 | PDF Full-text (998 KB) | HTML Full-text | XML Full-text
Abstract
The mushroom Inonotus obliquus has been widely used as a folk medicine in Russia, Poland and most of the Baltic countries. In this study, water-soluble and alkali-soluble crude polysaccharides (IOW and IOA) were isolated from I. obliquus, and the carbohydrate-rich fractions IOW-1
[...] Read more.
The mushroom Inonotus obliquus has been widely used as a folk medicine in Russia, Poland and most of the Baltic countries. In this study, water-soluble and alkali-soluble crude polysaccharides (IOW and IOA) were isolated from I. obliquus, and the carbohydrate-rich fractions IOW-1 and IOA-1 were obtained respectively after deproteination and depigmentation. Their contents, such as neutral carbohydrate, uronic acid and protein, were measured. Their antioxidant properties against chemicals-induced reactive species (ROS) including 1,1'-Diphenyl-2-picrylhydrazyl (DPPH) radical, hydroxyl radical and superoxide anion radical, as well as their protective effects on H2O2-induced PC12 cell death were investigated. Results showed that I. obliquus polysaccharides can scavenge all ROS tested above in a dose-dependent manner. IOA and its product IOA-1 could rescue PC12 cell viability from 38.6% to 79.8% and 83.0% at a concentration of 20µg/mL. Similarly, IOW and its product IOW-1 at the same dose, can also increase cell viability to 84.9% and 88.6% respectively. The antioxidative activities of water-soluble and alkali-soluble polysaccharide constituents from I. obliquus might contribute to diverse medicinal and nutritional values of this mushroom. Full article
Open AccessArticle 3D Structure Elucidation of Thermostable L2 Lipase from Thermophilic Bacillus sp. L2
Int. J. Mol. Sci. 2012, 13(7), 9207-9217; doi:10.3390/ijms13079207
Received: 16 May 2012 / Revised: 29 June 2012 / Accepted: 12 July 2012 / Published: 23 July 2012
Cited by 2 | PDF Full-text (1776 KB) | HTML Full-text | XML Full-text | Supplementary Files
Abstract
The crystallization of proteins makes it possible to determine their structure by X-ray crystallography, and is therefore important for the analysis of protein structure-function relationships. L2 lipase was crystallized by using the J-tube counter diffusion method. A crystallization consisting of 20% PEG 6000,
[...] Read more.
The crystallization of proteins makes it possible to determine their structure by X-ray crystallography, and is therefore important for the analysis of protein structure-function relationships. L2 lipase was crystallized by using the J-tube counter diffusion method. A crystallization consisting of 20% PEG 6000, 50 mM MES pH 6.5 and 50 mM NaCl was found to be the best condition to produce crystals with good shape and size (0.5 × 0.1 × 0.2 mm). The protein concentration used for the crystallization was 3 mg/mL. L2 lipase crystal has two crystal forms, Shape 1 and Shape 2. Shape 2 L2 lipase crystal was diffracted at 1.5 Å and the crystal belongs to the orthorhombic space group P212121, with unit-cell parameters a = 72.0, b = 81.8, c = 83.4 Å, α = β = γ = 90°. There is one molecule per asymmetric unit and the solvent content of the crystals is 56.9%, with a Matthew’s coefficient of 2.85 Å Da−1. The 3D structure of L2 lipase revealed topological organization of α/β-hydrolase fold consisting of 11 β-strands and 13 α-helices. Ser-113, His-358 and Asp-317 were assigned as catalytic triad residues. One Ca2+ and one Zn2+ were found in the L2 lipase molecule. Full article
(This article belongs to the Special Issue Protein Crystallography in Molecular Biology)
Open AccessArticle Bacterial Motility Measured by a Miniature Chamber for High-Pressure Microscopy
Int. J. Mol. Sci. 2012, 13(7), 9225-9239; doi:10.3390/ijms13079225
Received: 1 June 2012 / Revised: 3 July 2012 / Accepted: 10 July 2012 / Published: 24 July 2012
Cited by 10 | PDF Full-text (324 KB) | HTML Full-text | XML Full-text
Abstract
Hydrostatic pressure is one of the physical stimuli that characterize the environment of living matter. Many microorganisms thrive under high pressure and may even physically or geochemically require this extreme environmental condition. In contrast, application of pressure is detrimental to most life on
[...] Read more.
Hydrostatic pressure is one of the physical stimuli that characterize the environment of living matter. Many microorganisms thrive under high pressure and may even physically or geochemically require this extreme environmental condition. In contrast, application of pressure is detrimental to most life on Earth; especially to living organisms under ambient pressure conditions. To study the mechanism of how living things adapt to high-pressure conditions, it is necessary to monitor directly the organism of interest under various pressure conditions. Here, we report a miniature chamber for high-pressure microscopy. The chamber was equipped with a built-in separator, in which water pressure was properly transduced to that of the sample solution. The apparatus developed could apply pressure up to 150 MPa, and enabled us to acquire bright-field and epifluorescence images at various pressures and temperatures. We demonstrated that the application of pressure acted directly and reversibly on the swimming motility of Escherichia coli cells. The present technique should be applicable to a wide range of dynamic biological processes that depend on applied pressures. Full article
(This article belongs to the Special Issue Molecular Machines and Nanomachines)
Open AccessArticle Enhancing Oxidative Stability of Sunflower Oil during Convective and Microwave Heating Using Grape Seed Extract
Int. J. Mol. Sci. 2012, 13(7), 9240-9259; doi:10.3390/ijms13079240
Received: 22 May 2012 / Revised: 11 July 2012 / Accepted: 12 July 2012 / Published: 24 July 2012
Cited by 20 | PDF Full-text (435 KB) | HTML Full-text | XML Full-text
Abstract
This study was performed to investigate the effectiveness of grape seed extract (GSE) compared to butylated hydroxytoluene (BHT) on retarding lipid oxidation of sunflower oil subjected to convection and microwave heating up to 240 min under simulated frying conditions. The progress of lipid
[...] Read more.
This study was performed to investigate the effectiveness of grape seed extract (GSE) compared to butylated hydroxytoluene (BHT) on retarding lipid oxidation of sunflower oil subjected to convection and microwave heating up to 240 min under simulated frying conditions. The progress of lipid oxidation was assessed in terms of peroxide value (PV), p-anisidine value (p-AV), conjugated dienes and trienes (CD, CT), inhibition of oil oxidation (IO) and TOTOX value. In addition, total phenolic content (TP) was evaluated in samples before and after heating in order to assess the changes in these compounds relative to the extent of lipid oxidation. The results of this study highlight that GSE showed a significantly inhibitory effect on lipid oxidation during both treatments, although to a different extent. This ability was dose-dependent; therefore, the extent of lipid oxidation was inversely related to GSE level. Convective heating, respective microwave exposure for 240 min of samples supplemented by GSE to a level of 1000 ppm, resulted in significant decreases of investigated indices relative to the control values as follows: PV (48%; 30%), p-AV (29%; 40%), CD (45%; 30%), CT (41%; 36%), TOTOX (35%; 37%). GSE to a level of 600–800 ppm inhibited the lipid oxidation in a similar manner to BHT. These results suggested that GSE can be used as a potential natural extract for improving oxidative stability of sunflower oil during thermal applications. Full article
Figures

Open AccessArticle Correlation among Antioxidant, Antimicrobial, Hemolytic, and Antiproliferative Properties of Leiothrix spiralis Leaves Extract
Int. J. Mol. Sci. 2012, 13(7), 9260-9277; doi:10.3390/ijms13079260
Received: 20 April 2012 / Revised: 15 July 2012 / Accepted: 20 July 2012 / Published: 24 July 2012
Cited by 12 | PDF Full-text (1382 KB) | HTML Full-text | XML Full-text
Abstract
The biological activities of a plant extract depend on a complex sum of individual properties including the antioxidant activity. Several biological activities protect against the harmful action of reactive oxygen species (ROS), and here we focused our attention on the relationship between the
[...] Read more.
The biological activities of a plant extract depend on a complex sum of individual properties including the antioxidant activity. Several biological activities protect against the harmful action of reactive oxygen species (ROS), and here we focused our attention on the relationship between the biological activities tested and the antioxidant properties. In this study, the total flavonoid content as well as the antioxidant, antimicrobial, hemolytic and cytotoxicity activities of the methanolic extract of Leitothrix spiralis leaves were evaluated. The extract showed a total flavonoid content of 19.26% and the chemical characterization by HPLC-PAD confirmed the presence of flavonoids as the major secondary metabolite compounds. Significant antioxidant activity (IC50 = 1.743 µg/mL ± 0.063) was demonstrated and was effective against Gram-negative organisms and all Candida strains tested, and showed an ability to inhibit hyphal formation. Non-hemolytic and antiproliferative activity could be demonstrated. Full article
Open AccessArticle Activation of Propane C-H and C-C Bonds by Gas-Phase Pt Atom: A Theoretical Study
Int. J. Mol. Sci. 2012, 13(7), 9278-9297; doi:10.3390/ijms13079278
Received: 7 May 2012 / Revised: 20 June 2012 / Accepted: 16 July 2012 / Published: 24 July 2012
Cited by 3 | PDF Full-text (959 KB) | HTML Full-text | XML Full-text
Abstract
The reaction mechanism of the gas-phase Pt atom with C3H8 has been systematically investigated on the singlet and triplet potential energy surfaces at CCSD(T)//BPW91/6-311++G(d, p), Lanl2dz level. Pt atom prefers the attack of primary over secondary C-H bonds in propane.
[...] Read more.
The reaction mechanism of the gas-phase Pt atom with C3H8 has been systematically investigated on the singlet and triplet potential energy surfaces at CCSD(T)//BPW91/6-311++G(d, p), Lanl2dz level. Pt atom prefers the attack of primary over secondary C-H bonds in propane. For the Pt + C3H8 reaction, the major and minor reaction channels lead to PtC3H6 + H2 and PtCH2 + C2H6, respectively, whereas the possibility to form products PtC2H4 + CH4 is so small that it can be neglected. The minimal energy reaction pathway for the formation of PtC3H6 + H2, involving one spin inversion, prefers to start at the triplet state and afterward proceed along the singlet state. The optimal C-C bond cleavages are assigned to C-H bond activation as the first step, followed by cleavage of a C-C bond. The C-H insertion intermediates are kinetically favored over the C-C insertion intermediates. From C-C to C-H oxidative insertion, the lowering of activation barrier is mainly caused by the more stabilizing transition state interaction ΔEint, which is the actual interaction energy between the deformed reactants in the transition state. Full article
(This article belongs to the Section Material Sciences and Nanotechnology)
Open AccessArticle A Theoretical Study on Reductive Debromination of Polybrominated Diphenyl Ethers
Int. J. Mol. Sci. 2012, 13(7), 9332-9342; doi:10.3390/ijms13079332
Received: 24 May 2012 / Revised: 8 July 2012 / Accepted: 18 July 2012 / Published: 24 July 2012
Cited by 15 | PDF Full-text (474 KB) | HTML Full-text | XML Full-text | Supplementary Files
Abstract
Recent progress has been made in the reductive debromination of polybrominated diphenyl ethers (PBDEs) by nanoscale zero-valent iron (nZVI). To better understand the mechanism of this reaction, seven selected BDE congeners and their anions were investigated at the density functional theory (DFT) level
[...] Read more.
Recent progress has been made in the reductive debromination of polybrominated diphenyl ethers (PBDEs) by nanoscale zero-valent iron (nZVI). To better understand the mechanism of this reaction, seven selected BDE congeners and their anions were investigated at the density functional theory (DFT) level using four different methods, including B3LYP/6-31G(d), B3LYP/6-31+G(d), B3LYP/6-31G(d,p) and B3LYP/6-311G(d,p). The cleaved C–Br bonds observed in the equilibrium structures of anionic PBDEs were adopted as the probe of the susceptible debromination position of PBDEs in the presence of nZVI, and the proposed major reaction pathways based on our calculations can satisfactorily conform to the reported experimental results. The debromination preference is theoretically evaluated as meta-Br > ortho-Br > para-Br. In addition, both the calculated frontier orbital energies and adiabatic electronic affinities were found to be highly related to their experimental reductive debromination rate constants. The highest linear regression coefficient was observed in the case using the energy of lowest unoccupied molecular orbital as the molecular descriptor obtained from B3LYP/6-31G(d) (R2 = 0.961, n = 7) or B3LYP/6-31G(d,p) (R2 = 0.961, n = 7). The results clearly showed the evidence of an electron transfer mechanism associated with this reductive debromination reaction. Full article
(This article belongs to the Section Physical Chemistry, Theoretical and Computational Chemistry)
Open AccessArticle Molecular Characterization and Comparative Sequence Analysis of Defense-Related Gene, Oryza rufipogon Receptor-Like Protein Kinase 1
Int. J. Mol. Sci. 2012, 13(7), 9343-9362; doi:10.3390/ijms13079343
Received: 30 May 2012 / Revised: 6 July 2012 / Accepted: 6 July 2012 / Published: 24 July 2012
Cited by 2 | PDF Full-text (1838 KB) | HTML Full-text | XML Full-text | Supplementary Files
Abstract
Many of the plant leucine rich repeat receptor-like kinases (LRR-RLKs) have been found to regulate signaling during plant defense processes. In this study, we selected and sequenced an LRR-RLK gene, designated as Oryza rufipogon receptor-like protein kinase 1 (OrufRPK1), located within
[...] Read more.
Many of the plant leucine rich repeat receptor-like kinases (LRR-RLKs) have been found to regulate signaling during plant defense processes. In this study, we selected and sequenced an LRR-RLK gene, designated as Oryza rufipogon receptor-like protein kinase 1 (OrufRPK1), located within yield QTL yld1.1 from the wild rice Oryza rufipogon (accession IRGC105491). A 2055 bp coding region and two exons were identified. Southern blotting determined OrufRPK1 to be a single copy gene. Sequence comparison with cultivated rice orthologs (OsI219RPK1, OsI9311RPK1 and OsJNipponRPK1, respectively derived from O. sativa ssp. indica cv. MR219, O. sativa ssp. indica cv. 9311 and O. sativa ssp. japonica cv. Nipponbare) revealed the presence of 12 single nucleotide polymorphisms (SNPs) with five non-synonymous substitutions, and 23 insertion/deletion sites. The biological role of the OrufRPK1 as a defense related LRR-RLK is proposed on the basis of cDNA sequence characterization, domain subfamily classification, structural prediction of extra cellular domains, cluster analysis and comparative gene expression. Full article
(This article belongs to the Special Issue Advances in Molecular Plant Biology)
Figures

Open AccessArticle The Apoptotic Volume Decrease Is an Upstream Event of MAP Kinase Activation during Staurosporine-Induced Apoptosis in HeLa Cells
Int. J. Mol. Sci. 2012, 13(7), 9363-9379; doi:10.3390/ijms13079363
Received: 30 May 2012 / Revised: 18 July 2012 / Accepted: 19 July 2012 / Published: 24 July 2012
Cited by 12 | PDF Full-text (352 KB) | HTML Full-text | XML Full-text
Abstract
Persistent cell shrinkage, called apoptotic volume decrease (AVD), is a pivotal event of apoptosis. Activation of the volume-sensitive outwardly rectifying Cl channel (VSOR) is involved in the AVD induction. On the other hand, activation of the MAP kinase (MAPK) cascade is also
[...] Read more.
Persistent cell shrinkage, called apoptotic volume decrease (AVD), is a pivotal event of apoptosis. Activation of the volume-sensitive outwardly rectifying Cl channel (VSOR) is involved in the AVD induction. On the other hand, activation of the MAP kinase (MAPK) cascade is also known to play a critical role in apoptosis. In the present study, we investigated the relationship between the AVD induction and the stress-responsive MAPK cascade activation during the apoptosis process induced by staurosporine (STS) in HeLa cells. STS was found to induce AVD within 2–5 min and phosphorylation of c-Jun N-terminal kinase (JNK) and p38 MAPK after over 20–30 min. VSOR blockers suppressed not only STS-induced AVD but also phosphorylation of JNK and p38 as well as activation of caspase-3/7. Moreover, a p38 inhibitor, SB203580, and a JNK inhibitor, SP600125, failed to affect STS-induced AVD, whereas these compounds reduced STS-induced activation of caspase-3/7. Also, treatment with ASK1-specific siRNA suppressed STS-induced caspase-3/7 activation without affecting the AVD induction. Furthermore, sustained osmotic cell shrinkage per se was found to trigger phosphorylation of JNK and p38, caspase activation, and cell death. Thus, it is suggested that activation of p38 and JNK is a downstream event of AVD for the STS-induced apoptosis of HeLa cells. Full article
(This article belongs to the collection Programmed Cell Death and Apoptosis)
Open AccessArticle Secretome Survey of Human Plexiform Neurofibroma Derived Schwann Cells Reveals a Secreted form of the RARRES1 Protein
Int. J. Mol. Sci. 2012, 13(7), 9380-9399; doi:10.3390/ijms13079380
Received: 11 June 2012 / Revised: 12 July 2012 / Accepted: 19 July 2012 / Published: 24 July 2012
Cited by 6 | PDF Full-text (1336 KB) | HTML Full-text | XML Full-text | Supplementary Files
Abstract
To bring insights into neurofibroma biochemistry, a comprehensive secretome analysis was performed on cultured human primary Schwann cells isolated from surgically resected plexiform neurofibroma and from normal nerve tissue. Using a combination of SDS-PAGE and high precision LC-MS/MS, 907 proteins were confidently identified
[...] Read more.
To bring insights into neurofibroma biochemistry, a comprehensive secretome analysis was performed on cultured human primary Schwann cells isolated from surgically resected plexiform neurofibroma and from normal nerve tissue. Using a combination of SDS-PAGE and high precision LC-MS/MS, 907 proteins were confidently identified in the conditioned media of Schwann cell cultures combined. Label free proteome profiling revealed consistent release of high levels of 22 proteins by the four biological replicates of NF1 Schwann cell cultures relative to the two normal Schwann cell cultures. Inversely, 9 proteins displayed decreased levels in the conditioned media of NF1 relative to normal Schwann cells. The proteins with increased levels included proteins involved in cell growth, angiogenesis and complement pathway while proteins with decreased levels included those involved in cell adhesion, plasminogen pathway and extracellular matrix remodeling. Retinoic acid receptor responder protein-1 (RARRES1), previously described as an integral membrane tumor suppressor, was found exclusively secreted by NF1 Schwann cells but not by normal Schwann cells. All-trans retinoic acid modulated secretion of RARRES1 in a dose dependent manner. This study shows altered secretion of key proteins in NF1 derived Schwann cells. The potential implication of these proteins in neurofibroma biology is discussed. Full article
(This article belongs to the collection Advances in Proteomic Research)
Figures

Review

Jump to: Research, Other

Open AccessReview Molecular Targets of TRAIL-Sensitizing Agents in Colorectal Cancer
Int. J. Mol. Sci. 2012, 13(7), 7886-7901; doi:10.3390/ijms13077886
Received: 1 June 2012 / Revised: 18 June 2012 / Accepted: 20 June 2012 / Published: 25 June 2012
Cited by 9 | PDF Full-text (322 KB) | HTML Full-text | XML Full-text
Abstract
Tumor necrosis factor (TNF)-related apoptosis inducing ligand (TRAIL), a member of the TNF superfamily, interacts with its functional death receptors (DRs) and induces apoptosis in a wide range of cancer cell types. Therefore, TRAIL has been considered as an attractive agent for cancer
[...] Read more.
Tumor necrosis factor (TNF)-related apoptosis inducing ligand (TRAIL), a member of the TNF superfamily, interacts with its functional death receptors (DRs) and induces apoptosis in a wide range of cancer cell types. Therefore, TRAIL has been considered as an attractive agent for cancer therapy. However, many cancers are resistant to TRAIL-based therapies mainly due to the reduced expression of DRs and/or up-regulation of TRAIL pathway-related anti-apoptotic proteins. Compounds that revert such defects restore the sensitivity of cancer cells to TRAIL, suggesting that combined therapies could help manage neoplastic patients. In this article, we will focus on the TRAIL-sensitizing effects of natural products and synthetic compounds in colorectal cancer (CRC) cells and discuss the molecular mechanisms by which such agents enhance the response of CRC cells to TRAIL. Full article
(This article belongs to the collection Programmed Cell Death and Apoptosis)
Open AccessReview Glutamine Synthetase in Legumes: Recent Advances in Enzyme Structure and Functional Genomics
Int. J. Mol. Sci. 2012, 13(7), 7994-8024; doi:10.3390/ijms13077994
Received: 16 May 2012 / Revised: 18 June 2012 / Accepted: 19 June 2012 / Published: 28 June 2012
Cited by 20 | PDF Full-text (901 KB) | HTML Full-text | XML Full-text
Abstract
Glutamine synthetase (GS) is the key enzyme involved in the assimilation of ammonia derived either from nitrate reduction, N2 fixation, photorespiration or asparagine breakdown. A small gene family is encoding for different cytosolic (GS1) or plastidic (GS2) isoforms in legumes. We summarize
[...] Read more.
Glutamine synthetase (GS) is the key enzyme involved in the assimilation of ammonia derived either from nitrate reduction, N2 fixation, photorespiration or asparagine breakdown. A small gene family is encoding for different cytosolic (GS1) or plastidic (GS2) isoforms in legumes. We summarize here the recent advances carried out concerning the quaternary structure of GS, as well as the functional relationship existing between GS2 and processes such as nodulation, photorespiration and water stress, in this latter case by means of proline production. Functional genomic analysis using GS2-minus mutant reveals the key role of GS2 in the metabolic control of the plants and, more particularly, in carbon metabolism. Full article
(This article belongs to the Special Issue Advances in Molecular Plant Biology)
Figures

Open AccessReview From Evolution to Pathogenesis: The Link Between β-Barrel Assembly Machineries in the Outer Membrane of Mitochondria and Gram-Negative Bacteria
Int. J. Mol. Sci. 2012, 13(7), 8038-8050; doi:10.3390/ijms13078038
Received: 1 May 2012 / Revised: 21 June 2012 / Accepted: 21 June 2012 / Published: 28 June 2012
Cited by 8 | PDF Full-text (235 KB) | HTML Full-text | XML Full-text
Abstract
β-barrel proteins are the highly abundant in the outer membranes of Gram-negative bacteria and the mitochondria in eukaryotes. The assembly of β-barrels is mediated by two evolutionary conserved machineries; the β-barrel Assembly Machinery (BAM) in Gram-negative bacteria; and the Sorting and Assembly Machinery
[...] Read more.
β-barrel proteins are the highly abundant in the outer membranes of Gram-negative bacteria and the mitochondria in eukaryotes. The assembly of β-barrels is mediated by two evolutionary conserved machineries; the β-barrel Assembly Machinery (BAM) in Gram-negative bacteria; and the Sorting and Assembly Machinery (SAM) in mitochondria. Although the BAM and SAM have functionally conserved roles in the membrane integration and folding of β-barrel proteins, apart from the central BamA and Sam50 proteins, the remaining components of each of the complexes have diverged remarkably. For example all of the accessory components of the BAM complex characterized to date are located in the bacterial periplasm, on the same side as the N-terminal domain of BamA. This is the same side of the membrane as the substrates that are delivered to the BAM. On the other hand, all of the accessory components of the SAM complex are located on the cytosolic side of the membrane, the opposite side of the membrane to the N-terminus of Sam50 and the substrate receiving side of the membrane. Despite the accessory subunits being located on opposite sides of the membrane in each system, it is clear that each system is functionally equivalent with bacterial proteins having the ability to use the eukaryotic SAM and vice versa. In this review, we summarize the similarities and differences between the BAM and SAM complexes, highlighting the possible selecting pressures on bacteria and eukaryotes during evolution. It is also now emerging that bacterial pathogens utilize the SAM to target toxins and effector proteins to host mitochondria and this will also be discussed from an evolutionary perspective. Full article
(This article belongs to the Special Issue Membrane Transport)
Figures

Open AccessReview The Neuroprotective Functions of Transforming Growth Factor Beta Proteins
Int. J. Mol. Sci. 2012, 13(7), 8219-8258; doi:10.3390/ijms13078219
Received: 9 May 2012 / Revised: 24 May 2012 / Accepted: 19 June 2012 / Published: 3 July 2012
Cited by 46 | PDF Full-text (390 KB) | HTML Full-text | XML Full-text
Abstract
Transforming growth factor beta (TGF-β) proteins are multifunctional cytokines whose neural functions are increasingly recognized. The machinery of TGF-β signaling, including the serine kinase type transmembrane receptors, is present in the central nervous system. However, the 3 mammalian TGF-β subtypes have distinct distributions
[...] Read more.
Transforming growth factor beta (TGF-β) proteins are multifunctional cytokines whose neural functions are increasingly recognized. The machinery of TGF-β signaling, including the serine kinase type transmembrane receptors, is present in the central nervous system. However, the 3 mammalian TGF-β subtypes have distinct distributions in the brain suggesting different neural functions. Evidence of their involvement in the development and plasticity of the nervous system as well as their functions in peripheral organs suggested that they also exhibit neuroprotective functions. Indeed, TGF-β expression is induced following a variety of types of brain tissue injury. The neuroprotective function of TGF-βs is most established following brain ischemia. Damage in experimental animal models of global and focal ischemia was shown to be attenuated by TGF-βs. In addition, support for their neuroprotective actions following trauma, sclerosis multiplex, neurodegenerative diseases, infections, and brain tumors is also accumulating. The review will also describe the potential mechanisms of neuroprotection exerted by TGF-βs including anti-inflammatory, -apoptotic, -excitotoxic actions as well as the promotion of scar formation, angiogenesis, and neuroregeneration. The participation of these mechanisms in the neuroprotective effects of TGF-βs during different brain lesions will also be discussed. Full article
Open AccessReview Phage Display-based Strategies for Cloning and Optimization of Monoclonal Antibodies Directed against Human Pathogens
Int. J. Mol. Sci. 2012, 13(7), 8273-8292; doi:10.3390/ijms13078273
Received: 16 March 2012 / Revised: 25 June 2012 / Accepted: 27 June 2012 / Published: 4 July 2012
Cited by 31 | PDF Full-text (512 KB) | HTML Full-text | XML Full-text
Abstract
In the last two decades, several phage display-selected monoclonal antibodies (mAbs) have been described in the literature and a few of them have managed to reach the clinics. Among these, the anti-respiratory syncytial virus (RSV) Palivizumab, a phage-display optimized mAb, is the only
[...] Read more.
In the last two decades, several phage display-selected monoclonal antibodies (mAbs) have been described in the literature and a few of them have managed to reach the clinics. Among these, the anti-respiratory syncytial virus (RSV) Palivizumab, a phage-display optimized mAb, is the only marketed mAb directed against microbial pathogens. Palivizumab is a clear example of the importance of choosing the most appropriate strategy when selecting or optimizing an anti-infectious mAb. From this perspective, the extreme versatility of phage-display technology makes it a useful tool when setting up different strategies for the selection of mAbs directed against human pathogens, especially when their possible clinical use is considered. In this paper, we review the principal phage display strategies used to select anti-infectious mAbs, with particular attention focused on those used against hypervariable pathogens, such as HCV and influenza viruses. Full article
Open AccessReview Role of Endoplasmic Reticulum Aminopeptidases in Health and Disease: from Infection to Cancer
Int. J. Mol. Sci. 2012, 13(7), 8338-8352; doi:10.3390/ijms13078338
Received: 1 June 2012 / Revised: 27 June 2012 / Accepted: 29 June 2012 / Published: 4 July 2012
Cited by 17 | PDF Full-text (248 KB) | HTML Full-text | XML Full-text
Abstract
Endoplasmic reticulum (ER) aminopeptidases ERAP1 and ERAP2 (ERAPs) are essential for the maturation of a wide spectrum of proteins involved in various biological processes. In the ER, these enzymes work in concert to trim peptides for presentation on MHC class I molecules. Loss
[...] Read more.
Endoplasmic reticulum (ER) aminopeptidases ERAP1 and ERAP2 (ERAPs) are essential for the maturation of a wide spectrum of proteins involved in various biological processes. In the ER, these enzymes work in concert to trim peptides for presentation on MHC class I molecules. Loss of ERAPs function substantially alters the repertoire of peptides presented by MHC class I molecules, critically affecting recognition of both NK and CD8+ T cells. In addition, these enzymes are involved in the modulation of inflammatory responses by promoting the shedding of several cytokine receptors, and in the regulation of both blood pressure and angiogenesis. Recent genome-wide association studies have identified common variants of ERAP1 and ERAP2 linked to several human diseases, ranging from viral infections to autoimmunity and cancer. More recently, inhibition of ER peptide trimming has been shown to play a key role in stimulating innate and adaptive anti-tumor immune responses, suggesting that inhibition of ERAPs might be exploited for the establishment of innovative therapeutic approaches against cancer. This review summarizes data currently available for ERAP enzymes in ER peptide trimming and in other immunological and non-immunological functions, paying attention to the emerging role played by these enzymes in human diseases. Full article
(This article belongs to the Special Issue Advances in Molecular Immunology)
Figures

Open AccessReview Function and 3D Structure of the N-Glycans on Glycoproteins
Int. J. Mol. Sci. 2012, 13(7), 8398-8429; doi:10.3390/ijms13078398
Received: 31 May 2012 / Revised: 18 June 2012 / Accepted: 28 June 2012 / Published: 6 July 2012
Cited by 27 | PDF Full-text (3679 KB) | HTML Full-text | XML Full-text
Abstract
Glycosylation is one of the most common post-translational modifications in eukaryotic cells and plays important roles in many biological processes, such as the immune response and protein quality control systems. It has been notoriously difficult to study glycoproteins by X-ray crystallography since the
[...] Read more.
Glycosylation is one of the most common post-translational modifications in eukaryotic cells and plays important roles in many biological processes, such as the immune response and protein quality control systems. It has been notoriously difficult to study glycoproteins by X-ray crystallography since the glycan moieties usually have a heterogeneous chemical structure and conformation, and are often mobile. Nonetheless, recent technical advances in glycoprotein crystallography have accelerated the accumulation of 3D structural information. Statistical analysis of “snapshots” of glycoproteins can provide clues to understanding their structural and dynamic aspects. In this review, we provide an overview of crystallographic analyses of glycoproteins, in which electron density of the glycan moiety is clearly observed. These well-defined N-glycan structures are in most cases attributed to carbohydrate-protein and/or carbohydrate-carbohydrate interactions and may function as “molecular glue” to help stabilize inter- and intra-molecular interactions. However, the more mobile N-glycans on cell surface receptors, the electron density of which is usually missing on X-ray crystallography, seem to guide the partner ligand to its binding site and prevent irregular protein aggregation by covering oligomerization sites away from the ligand-binding site. Full article
(This article belongs to the Special Issue Protein Crystallography in Molecular Biology)
Figures

Open AccessReview Effect of PACAP in Central and Peripheral Nerve Injuries
Int. J. Mol. Sci. 2012, 13(7), 8430-8448; doi:10.3390/ijms13078430
Received: 11 May 2012 / Revised: 25 June 2012 / Accepted: 26 June 2012 / Published: 6 July 2012
Cited by 27 | PDF Full-text (145 KB) | HTML Full-text | XML Full-text
Abstract
Pituitary adenylate cyclase activating polypeptide (PACAP) is a bioactive peptide with diverse effects in the nervous system. In addition to its more classic role as a neuromodulator, PACAP functions as a neurotrophic factor. Several neurotrophic factors have been shown to play an important
[...] Read more.
Pituitary adenylate cyclase activating polypeptide (PACAP) is a bioactive peptide with diverse effects in the nervous system. In addition to its more classic role as a neuromodulator, PACAP functions as a neurotrophic factor. Several neurotrophic factors have been shown to play an important role in the endogenous response following both cerebral ischemia and traumatic brain injury and to be effective when given exogenously. A number of studies have shown the neuroprotective effect of PACAP in different models of ischemia, neurodegenerative diseases and retinal degeneration. The aim of this review is to summarize the findings on the neuroprotective potential of PACAP in models of different traumatic nerve injuries. Expression of endogenous PACAP and its specific PAC1 receptor is elevated in different parts of the central and peripheral nervous system after traumatic injuries. Some experiments demonstrate the protective effect of exogenous PACAP treatment in different traumatic brain injury models, in facial nerve and optic nerve trauma. The upregulation of endogenous PACAP and its receptors and the protective effect of exogenous PACAP after different central and peripheral nerve injuries show the important function of PACAP in neuronal regeneration indicating that PACAP may also be a promising therapeutic agent in injuries of the nervous system. Full article
(This article belongs to the Special Issue Neuroprotective Strategies 2012)
Open AccessReview Flexible and Versatile as a Chameleon—Sophisticated Functions of microRNA-199a
Int. J. Mol. Sci. 2012, 13(7), 8449-8466; doi:10.3390/ijms13078449
Received: 8 June 2012 / Revised: 29 June 2012 / Accepted: 2 July 2012 / Published: 9 July 2012
Cited by 18 | PDF Full-text (427 KB) | HTML Full-text | XML Full-text
Abstract
Although widely studied in the past decade, our knowledge of the functional role of microRNAs (miRNAs) remains limited. Among the many miRNAs identified in humans, we focus on miR-199a due to its varied and important functions in diverse models and systems. Its expression
[...] Read more.
Although widely studied in the past decade, our knowledge of the functional role of microRNAs (miRNAs) remains limited. Among the many miRNAs identified in humans, we focus on miR-199a due to its varied and important functions in diverse models and systems. Its expression is finely regulated by promoter methylation and direct binding of transcription factors such as TWIST1. During tumorigenesis, depending on the nature of the cancer, miR-199a, especially its -3p mature form, may act as either a potential tumor suppressor or an oncogene. Its 5p mature form has been shown to protect cardiomyocytes from hypoxic damage via its action on HIF1α. It also has a functional role in stem cell differentiation, embryo development, hepatitis, liver fibrosis, etc. Though it has varied biological activities, its regulation has not been reviewed. The varied and protean functions of miR-199a suggest that efforts to generalize the action of a miRNA are problematic. This review provides a comprehensive survey of the literature on miR-199a as an example of the complexity of miRNA biology and suggests future directions for miRNA research. Full article
(This article belongs to the Special Issue Non-Coding RNAs 2012)
Open AccessReview Green Extraction of Natural Products: Concept and Principles
Int. J. Mol. Sci. 2012, 13(7), 8615-8627; doi:10.3390/ijms13078615
Received: 21 May 2012 / Revised: 20 June 2012 / Accepted: 25 June 2012 / Published: 11 July 2012
Cited by 161 | PDF Full-text (375 KB) | HTML Full-text | XML Full-text
Abstract
The design of green and sustainable extraction methods of natural products is currently a hot research topic in the multidisciplinary area of applied chemistry, biology and technology. Herein we aimed to introduce the six principles of green-extraction, describing a multifaceted strategy to apply
[...] Read more.
The design of green and sustainable extraction methods of natural products is currently a hot research topic in the multidisciplinary area of applied chemistry, biology and technology. Herein we aimed to introduce the six principles of green-extraction, describing a multifaceted strategy to apply this concept at research and industrial level. The mainstay of this working protocol are new and innovative technologies, process intensification, agro-solvents and energy saving. The concept, principles and examples of green extraction here discussed, offer an updated glimpse of the huge technological effort that is being made and the diverse applications that are being developed. Full article
(This article belongs to the Section Green Chemistry)
Open AccessReview Recent Molecular Advances on Downstream Plant Responses to Abiotic Stress
Int. J. Mol. Sci. 2012, 13(7), 8628-8647; doi:10.3390/ijms13078628
Received: 4 June 2012 / Revised: 30 June 2012 / Accepted: 3 July 2012 / Published: 11 July 2012
Cited by 21 | PDF Full-text (173 KB) | HTML Full-text | XML Full-text
Abstract
Abiotic stresses such as extremes of temperature and pH, high salinity and drought, comprise some of the major factors causing extensive losses to crop production worldwide. Understanding how plants respond and adapt at cellular and molecular levels to continuous environmental changes is a
[...] Read more.
Abiotic stresses such as extremes of temperature and pH, high salinity and drought, comprise some of the major factors causing extensive losses to crop production worldwide. Understanding how plants respond and adapt at cellular and molecular levels to continuous environmental changes is a pre-requisite for the generation of resistant or tolerant plants to abiotic stresses. In this review we aimed to present the recent advances on mechanisms of downstream plant responses to abiotic stresses and the use of stress-related genes in the development of genetically engineered crops. Full article
(This article belongs to the Special Issue Advances in Molecular Plant Biology)
Figures

Open AccessReview Role of Prion Protein Aggregation in Neurotoxicity
Int. J. Mol. Sci. 2012, 13(7), 8648-8669; doi:10.3390/ijms13078648
Received: 21 May 2012 / Revised: 29 June 2012 / Accepted: 2 July 2012 / Published: 11 July 2012
Cited by 11 | PDF Full-text (796 KB) | HTML Full-text | XML Full-text
Abstract
In several neurodegenerative diseases, such as Parkinson, Alzheimer’s, Huntington, and prion diseases, the deposition of aggregated misfolded proteins is believed to be responsible for the neurotoxicity that characterizes these diseases. Prion protein (PrP), the protein responsible of prion diseases, has been deeply studied
[...] Read more.
In several neurodegenerative diseases, such as Parkinson, Alzheimer’s, Huntington, and prion diseases, the deposition of aggregated misfolded proteins is believed to be responsible for the neurotoxicity that characterizes these diseases. Prion protein (PrP), the protein responsible of prion diseases, has been deeply studied for the peculiar feature of its misfolded oligomers that are able to propagate within affected brains, inducing the conversion of the natively folded PrP into the pathological conformation. In this review, we summarize the available experimental evidence concerning the relationship between aggregation status of misfolded PrP and neuronal death in the course of prion diseases. In particular, we describe the main findings resulting from the use of different synthetic (mainly PrP106-126) and recombinant PrP-derived peptides, as far as mechanisms of aggregation and amyloid formation, and how these different spatial conformations can affect neuronal death. In particular, most data support the involvement of non-fibrillar oligomers rather than actual amyloid fibers as the determinant of neuronal death. Full article
Open AccessReview Multiple Mechanisms and Challenges for the Application of Allopolyploidy in Plants
Int. J. Mol. Sci. 2012, 13(7), 8696-8721; doi:10.3390/ijms13078696
Received: 30 May 2012 / Revised: 4 July 2012 / Accepted: 4 July 2012 / Published: 13 July 2012
Cited by 2 | PDF Full-text (498 KB) | HTML Full-text | XML Full-text
Abstract
An allopolyploid is an individual having two or more complete sets of chromosomes derived from different species. Generation of allopolyploids might be rare because of the need to overcome limitations such as co-existing populations of parental lines, overcoming hybrid incompatibility, gametic non-reduction, and
[...] Read more.
An allopolyploid is an individual having two or more complete sets of chromosomes derived from different species. Generation of allopolyploids might be rare because of the need to overcome limitations such as co-existing populations of parental lines, overcoming hybrid incompatibility, gametic non-reduction, and the requirement for chromosome doubling. However, allopolyploids are widely observed among plant species, so allopolyploids have succeeded in overcoming these limitations and may have a selective advantage. As techniques for making allopolyploids are developed, we can compare transcription, genome organization, and epigenetic modifications between synthesized allopolyploids and their direct parental lines or between several generations of allopolyploids. It has been suggested that divergence of transcription caused either genetically or epigenetically, which can contribute to plant phenotype, is important for the adaptation of allopolyploids. Full article
(This article belongs to the Special Issue Advances in Molecular Plant Biology)
Open AccessReview Molecular Mechanisms of Ursodeoxycholic Acid Toxicity & Side Effects: Ursodeoxycholic Acid Freezes Regeneration & Induces Hibernation Mode
Int. J. Mol. Sci. 2012, 13(7), 8882-8914; doi:10.3390/ijms13078882
Received: 1 June 2012 / Revised: 3 July 2012 / Accepted: 6 July 2012 / Published: 17 July 2012
Cited by 15 | PDF Full-text (518 KB) | HTML Full-text | XML Full-text
Abstract
Ursodeoxycholic acid (UDCA) is a steroid bile acid approved for primary biliary cirrhosis (PBC). UDCA is reported to have “hepato-protective properties”. Yet, UDCA has “unanticipated” toxicity, pronounced by more than double number of deaths, and eligibility for liver transplantation compared to the control
[...] Read more.
Ursodeoxycholic acid (UDCA) is a steroid bile acid approved for primary biliary cirrhosis (PBC). UDCA is reported to have “hepato-protective properties”. Yet, UDCA has “unanticipated” toxicity, pronounced by more than double number of deaths, and eligibility for liver transplantation compared to the control group in 28 mg/kg/day in primary sclerosing cholangitis, necessitating trial halt in North America. UDCA is associated with increase in hepatocellular carcinoma in PBC especially when it fails to achieve biochemical response (10 and 15 years incidence of 9% and 20% respectively). “Unanticipated” UDCA toxicity includes hepatitis, pruritus, cholangitis, ascites, vanishing bile duct syndrome, liver cell failure, death, severe watery diarrhea, pneumonia, dysuria, immune-suppression, mutagenic effects and withdrawal syndrome upon sudden halt. UDCA inhibits DNA repair, co-enzyme A, cyclic AMP, p53, phagocytosis, and inhibits induction of nitric oxide synthatase. It is genotoxic, exerts aneugenic activity, and arrests apoptosis even after cellular phosphatidylserine externalization. UDCA toxicity is related to its interference with drug detoxification, being hydrophilic and anti-apoptotic, has a long half-life, has transcriptional mutational abilities, down-regulates cellular functions, has a very narrow difference between the recommended (13 mg/kg/day) and toxic dose (28 mg/kg/day), and it typically transforms into lithocholic acid that induces DNA strand breakage, it is uniquely co-mutagenic, and promotes cell transformation. UDCA beyond PBC is unjustified. Full article
(This article belongs to the Special Issue Molecular Mechanisms of Organ-Specific Toxicity)
Open AccessReview The Immunomodulatory and Neuroprotective Effects of Mesenchymal Stem Cells (MSCs) in Experimental Autoimmune Encephalomyelitis (EAE): A Model of Multiple Sclerosis (MS)
Int. J. Mol. Sci. 2012, 13(7), 9298-9331; doi:10.3390/ijms13079298
Received: 18 May 2012 / Revised: 11 July 2012 / Accepted: 11 July 2012 / Published: 24 July 2012
Cited by 23 | PDF Full-text (540 KB) | HTML Full-text | XML Full-text
Abstract
Mesenchymal stem cells (MSCs) are multipotent cells that differentiate into the mesenchymal lineages of adipocytes, osteocytes and chondrocytes. MSCs can also transdifferentiate and thereby cross lineage barriers, differentiating for example into neurons under certain experimental conditions. MSCs have anti-proliferative, anti-inflammatory and anti-apoptotic effects
[...] Read more.
Mesenchymal stem cells (MSCs) are multipotent cells that differentiate into the mesenchymal lineages of adipocytes, osteocytes and chondrocytes. MSCs can also transdifferentiate and thereby cross lineage barriers, differentiating for example into neurons under certain experimental conditions. MSCs have anti-proliferative, anti-inflammatory and anti-apoptotic effects on neurons. Therefore, MSCs were tested in experimental autoimmune encephalomyelitis (EAE), an animal model of multiple sclerosis (MS), for their effectiveness in modulating the pathogenic process in EAE to develop effective therapies for MS. The data in the literature have shown that MSCs can inhibit the functions of autoreactive T cells in EAE and that this immunomodulation can be neuroprotective. In addition, MSCs can rescue neural cells via a mechanism that is mediated by soluble factors, which provide a suitable environment for neuron regeneration, remyelination and cerebral blood flow improvement. In this review, we discuss the effectiveness of MSCs in modulating the immunopathogenic process and in providing neuroprotection in EAE. Full article
(This article belongs to the Special Issue Recent Advances in the Research of Multiple Sclerosis)

Other

Jump to: Research, Review

Open AccessShort Note Development of 20 Microsatellite Markers for Solenocera crassicornis and Their Cross-Species Application in Solenocera melantho
Int. J. Mol. Sci. 2012, 13(7), 9218-9224; doi:10.3390/ijms13079218
Received: 28 June 2012 / Revised: 11 July 2012 / Accepted: 17 July 2012 / Published: 23 July 2012
Cited by 4 | PDF Full-text (90 KB) | HTML Full-text | XML Full-text
Abstract
Twenty microsatellite markers were isolated and characterized for Solenocera crassicornis from a (GT)13-enriched genomic library. Their polymorphisms were investigated using 44 wild individuals from the South Yellow Sea. Our investigation revealed that all the markers were polymorphic. The number of alleles
[...] Read more.
Twenty microsatellite markers were isolated and characterized for Solenocera crassicornis from a (GT)13-enriched genomic library. Their polymorphisms were investigated using 44 wild individuals from the South Yellow Sea. Our investigation revealed that all the markers were polymorphic. The number of alleles per locus varied from 6 to 19 with an average of 12.35. The observed and expected heterozygosities ranged from 0.400 to 0.977 and from 0.609 to 0.940, with averages of 0.788 and 0.859, respectively. Four loci significantly deviated from Hardy-Weinberg equilibrium after Bonferroni’s correction. Cross-species amplification was also conducted in Solenocera melantho collected from the East China Sea. The result showed that 14 loci could be amplified from Solenocera melantho DNAs. These polymorphic markers would be useful for assessment of genetic variation and population structure of S. crassicornis and S. melantho. Full article
(This article belongs to the Section Molecular Diagnostics)

Journal Contact

MDPI AG
IJMS Editorial Office
St. Alban-Anlage 66, 4052 Basel, Switzerland
ijms@mdpi.com
Tel. +41 61 683 77 34
Fax: +41 61 302 89 18
Editorial Board
Contact Details Submit to IJMS
Back to Top