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Int. J. Mol. Sci., Volume 11, Issue 10 (October 2010), Pages 3623-4174

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Open AccessArticle SwarmDock and the Use of Normal Modes in Protein-Protein Docking
Int. J. Mol. Sci. 2010, 11(10), 3623-3648; doi:10.3390/ijms11103623
Received: 2 July 2010 / Revised: 29 July 2010 / Accepted: 16 September 2010 / Published: 28 September 2010
Cited by 35 | PDF Full-text (1919 KB) | HTML Full-text | XML Full-text
Abstract
Here is presented an investigation of the use of normal modes in protein-protein docking, both in theory and in practice. Upper limits of the ability of normal modes to capture the unbound to bound conformational change are calculated on a large test [...] Read more.
Here is presented an investigation of the use of normal modes in protein-protein docking, both in theory and in practice. Upper limits of the ability of normal modes to capture the unbound to bound conformational change are calculated on a large test set, with particular focus on the binding interface, the subset of residues from which the binding energy is calculated. Further, the SwarmDock algorithm is presented, to demonstrate that the modelling of conformational change as a linear combination of normal modes is an effective method of modelling flexibility in protein-protein docking. Full article
(This article belongs to the Special Issue Advances in Molecular Recognition)
Open AccessArticle Mutual Solubility Study in Supercritical Fluid Extraction of Tocopherols from Crude Palm Oil Using CO2 Solvent
Int. J. Mol. Sci. 2010, 11(10), 3649-3659; doi:10.3390/ijms11103649
Received: 13 July 2010 / Revised: 24 August 2010 / Accepted: 7 September 2010 / Published: 28 September 2010
Cited by 2 | PDF Full-text (239 KB) | HTML Full-text | XML Full-text
Abstract
In this article, the mutual solubility of tocopherols from crude palm oil was studied using carbon dioxide as a solvent at the temperatures of 80, 100 and 120 ºC. Each sample from the phase equilibrium unit contained two parts. The liquid part [...] Read more.
In this article, the mutual solubility of tocopherols from crude palm oil was studied using carbon dioxide as a solvent at the temperatures of 80, 100 and 120 ºC. Each sample from the phase equilibrium unit contained two parts. The liquid part was analyzed by gas chromatography (GC) in order to measure the tocopherol composition and, on the other hand, the vapor phase was conducted in an expansion vessel in order to measure the pressure increment during the expansion process. Two phase equilibrium data was calculated using the liquid phase composition and pressure increments during the expansion process. Results showed that the maximum solubility of tocopherols was around 2.27% at a temperature of 120 ºC and at pressure of 5.44 MPa. Full article
(This article belongs to the Special Issue Supercritical Carbon Dioxide)
Open AccessArticle Uncertainty Determination Methodology, Sampling Maps Generation and Trend Studies with Biomass Thermogravimetric Analysis
Int. J. Mol. Sci. 2010, 11(10), 3660-3674; doi:10.3390/ijms11103660
Received: 11 August 2010 / Revised: 15 September 2010 / Accepted: 15 September 2010 / Published: 28 September 2010
Cited by 2 | PDF Full-text (463 KB) | HTML Full-text | XML Full-text
Abstract
This paper investigates a method for the determination of the maximum sampling error and confidence intervals of thermal properties obtained from thermogravimetric analysis (TG analysis) for several lignocellulosic materials (ground olive stone, almond shell, pine pellets and oak pellets), completing previous work [...] Read more.
This paper investigates a method for the determination of the maximum sampling error and confidence intervals of thermal properties obtained from thermogravimetric analysis (TG analysis) for several lignocellulosic materials (ground olive stone, almond shell, pine pellets and oak pellets), completing previous work of the same authors. A comparison has been made between results of TG analysis and prompt analysis. Levels of uncertainty and errors were obtained, demonstrating that properties evaluated by TG analysis were representative of the overall fuel composition, and no correlation between prompt and TG analysis exists. Additionally, a study of trends and time correlations is indicated. These results are particularly interesting for biomass energy applications. Full article
(This article belongs to the Section Green Chemistry)
Open AccessArticle Synthesis and Characterization of the Inclusion Complex of Dicationic Ionic Liquid and β-Cyclodextrin
Int. J. Mol. Sci. 2010, 11(10), 3675-3685; doi:10.3390/ijms11103675
Received: 18 August 2010 / Revised: 27 August 2010 / Accepted: 27 September 2010 / Published: 28 September 2010
Cited by 13 | PDF Full-text (303 KB) | HTML Full-text | XML Full-text
Abstract
The supramolecular structure of the inclusion complex of β-cyclodextrin (β-CD) with 1,1’,2,2’-tetramethyl-3,3’-(p-phenylenedimethylene) diimidazolium dibromide (TetraPhimBr), a dicationic ionic liquid, has been investigated. The inclusion complex with 1:1 molar ratio was prepared by a kneading method. Fourier transform infrared spectroscopy (FTIR), [...] Read more.
The supramolecular structure of the inclusion complex of β-cyclodextrin (β-CD) with 1,1’,2,2’-tetramethyl-3,3’-(p-phenylenedimethylene) diimidazolium dibromide (TetraPhimBr), a dicationic ionic liquid, has been investigated. The inclusion complex with 1:1 molar ratio was prepared by a kneading method. Fourier transform infrared spectroscopy (FTIR), powder X-ray diffraction (XRD) analysis, 1H NMR and thermogravimetric analysis (TGA) confirmed the formation of the inclusion complex. The results showed that the host-guest system is a fine crystalline powder. The decomposition temperature of the inclusion complex is lower than that of its parent molecules, TetraPhimBr and β-CD individually. Full article
(This article belongs to the Section Biochemistry, Molecular Biology and Biophysics)
Open AccessCommunication A Novel Pectin Material: Extraction, Characterization and Gelling Properties
Int. J. Mol. Sci. 2010, 11(10), 3686-3695; doi:10.3390/ijms11103686
Received: 20 August 2010 / Revised: 9 September 2010 / Accepted: 27 September 2010 / Published: 28 September 2010
Cited by 16 | PDF Full-text (315 KB) | HTML Full-text | XML Full-text
Abstract
A novel pectin was acid extracted from chickpea husk (CHP). CHP presented a 67% (w/w) of galacturonic acid, an intrinsic viscosity of 374 mL/g and a viscosimetric molecular weight of 110 kDa. Fourier transform infrared spectroscopy spectrum of CHP indicated a degree [...] Read more.
A novel pectin was acid extracted from chickpea husk (CHP). CHP presented a 67% (w/w) of galacturonic acid, an intrinsic viscosity of 374 mL/g and a viscosimetric molecular weight of 110 kDa. Fourier transform infrared spectroscopy spectrum of CHP indicated a degree of esterification of about 10%. The CHP-calcium system formed ionic gels with a storage (G’) modulus of 40 Pa and gel set time (G’ > G’’) of 3 min at 1% (w/v), and a G’ of 131 Pa and gel set time of 1 min at 2% (w/v). The G’ of CHP gels was not greatly affected by temperature. The results attained suggest that chickpea husk can be a potential source of a gelling pectin material. Full article
(This article belongs to the Section Biochemistry, Molecular Biology and Biophysics)
Open AccessArticle Effect of Salvianolic Acid b and Paeonol on Blood Lipid Metabolism and Hemorrheology in Myocardial Ischemia Rabbits Induced by Pituitruin
Int. J. Mol. Sci. 2010, 11(10), 3696-3704; doi:10.3390/ijms11103696
Received: 24 August 2010 / Revised: 15 September 2010 / Accepted: 16 September 2010 / Published: 28 September 2010
Cited by 13 | PDF Full-text (203 KB) | HTML Full-text | XML Full-text
Abstract
The purpose of this study was to determine the therapeutic effect of salvianolic acid b and paeonol on coronary disease. The ischemia myocardial animal model is induced by administering pituitrin (20 μg·kg−1) intravenously via the abdominal vein. A combination of [...] Read more.
The purpose of this study was to determine the therapeutic effect of salvianolic acid b and paeonol on coronary disease. The ischemia myocardial animal model is induced by administering pituitrin (20 μg·kg−1) intravenously via the abdominal vein. A combination of salvianolic acid b and paeonol (CSAP) (5, 10 and 15 mg/kg BW) was administrated to experimental rabbits. Biochemical indices were evaluated during six weeks of intervention. We found that the compound of salvianolic acid b and paeonol (5, 10 and 15 mg/kg BW) can markedly and dose-dependently reduce fibrinogen and malonaldehyde levels, increase the HDL level, improve blood viscosity and plasma viscosity in rabbits. In addition, the medicine can still reduce the ratio of NO/ET and the contents of lactate dehydrogenase (LDH) and creatine phosphokinase (CPK) in a dose-dependent manner. This study demonstrates that compound of salvianolic acid b and paeonol (5, 10 and 15 mg/kg BW) can improve the blood hemorrheology, decrease oxidative injury and repair the function of blood vessel endothelium, and subsequently prevent the development of Coronary disease. Full article
(This article belongs to the Section Biochemistry, Molecular Biology and Biophysics)
Open AccessArticle Molecular Modeling Studies of 4,5-Dihydro-1H-pyrazolo[4,3-h] quinazoline Derivatives as Potent CDK2/Cyclin A Inhibitors Using 3D-QSAR and Docking
Int. J. Mol. Sci. 2010, 11(10), 3705-3724; doi:10.3390/ijms11103705
Received: 19 July 2010 / Revised: 3 September 2010 / Accepted: 20 September 2010 / Published: 28 September 2010
Cited by 10 | PDF Full-text (612 KB) | HTML Full-text | XML Full-text
Abstract
CDK2/cyclin A has appeared as an attractive drug targets over the years with diverse therapeutic potentials. A computational strategy based on comparative molecular fields analysis (CoMFA) and comparative molecular similarity indices analysis (CoMSIA) followed by molecular docking studies were performed on a [...] Read more.
CDK2/cyclin A has appeared as an attractive drug targets over the years with diverse therapeutic potentials. A computational strategy based on comparative molecular fields analysis (CoMFA) and comparative molecular similarity indices analysis (CoMSIA) followed by molecular docking studies were performed on a series of 4,5-dihydro-1H-pyrazolo[4,3-h]quinazoline derivatives as potent CDK2/cyclin A inhibitors. The CoMFA and CoMSIA models, using 38 molecules in the training set, gave r2cv values of 0.747 and 0.518 and r2 values of 0.970 and 0.934, respectively. 3D contour maps generated by the CoMFA and CoMSIA models were used to identify the key structural requirements responsible for the biological activity. Molecular docking was applied to explore the binding mode between the ligands and the receptor. The information obtained from molecular modeling studies may be helpful to design novel inhibitors of CDK2/cyclin A with desired activity. Full article
(This article belongs to the Special Issue Recent Advances in QSAR/QSPR Theory)
Open AccessArticle Retro-MoRFs: Identifying Protein Binding Sites by Normal and Reverse Alignment and Intrinsic Disorder Prediction
Int. J. Mol. Sci. 2010, 11(10), 3725-3747; doi:10.3390/ijms11103725
Received: 3 September 2010 / Revised: 10 September 2010 / Accepted: 15 September 2010 / Published: 29 September 2010
Cited by 15 | PDF Full-text (267 KB) | HTML Full-text | XML Full-text
Abstract
Many cell functions in all living organisms rely on protein-based molecular recognition involving disorder-to-order transitions upon binding by molecular recognition features (MoRFs). A well accepted computational tool for identifying likely protein-protein interactions is sequence alignment. In this paper, we propose the combination [...] Read more.
Many cell functions in all living organisms rely on protein-based molecular recognition involving disorder-to-order transitions upon binding by molecular recognition features (MoRFs). A well accepted computational tool for identifying likely protein-protein interactions is sequence alignment. In this paper, we propose the combination of sequence alignment and disorder prediction as a tool to improve the confidence of identifying MoRF-based protein-protein interactions. The method of reverse sequence alignment is also rationalized here as a novel approach for finding additional interaction regions, leading to the concept of a retro-MoRF, which has the reversed sequence of an identified MoRF. The set of retro-MoRF binding partners likely overlap the partner-sets of the originally identified MoRFs. The high abundance of MoRF-containing intrinsically disordered proteins in nature suggests the possibility that the number of retro-MoRFs could likewise be very high. This hypothesis provides new grounds for exploring the mysteries of protein-protein interaction networks at the genome level. Full article
(This article belongs to the Special Issue Advances in Molecular Recognition)
Open AccessArticle Lewis Y Promotes Growth and Adhesion of Ovarian Carcinoma-Derived RMG-I Cells by Upregulating Growth Factors
Int. J. Mol. Sci. 2010, 11(10), 3748-3759; doi:10.3390/ijms11103748
Received: 9 August 2010 / Revised: 13 September 2010 / Accepted: 16 September 2010 / Published: 29 September 2010
Cited by 6 | PDF Full-text (2471 KB) | HTML Full-text | XML Full-text
Abstract
Lewis y (LeY) antigen is a difucosylated oligosaccharide carried by glycoconjugates on the cell surface. Overexpression of LeY is frequently observed in epithelial-derived cancers and has been correlated to the pathological staging and prognosis. However, the effects of LeY on ovarian cancer [...] Read more.
Lewis y (LeY) antigen is a difucosylated oligosaccharide carried by glycoconjugates on the cell surface. Overexpression of LeY is frequently observed in epithelial-derived cancers and has been correlated to the pathological staging and prognosis. However, the effects of LeY on ovarian cancer are not yet clear. Previously, we transfected the ovarian cancer cell line RMG-I with the α1,2-fucosyltransferase gene to obtain stable transfectants, RMG-I-H, that highly express LeY. In the present study, we examined the proliferation, tumorigenesis, adhesion and invasion of the cell lines with treatment of LeY monoclonal antibody (mAb). Additionally, we examined the expression of TGF-β1, VEGF and b-FGF in xenograft tumors. The results showed that the proliferation and adhesion in vitro were significantly inhibited by treatment of RMG-I-H cells with LeY mAb. When subcutaneously inoculated in nude mice, RMG-I-H cells produced large tumors, while mock-transfected cells RMG-I-C and the parental cells RMG-I produced small tumors. Moreover, the tumor formation by RMG-I-H cells was inhibited by preincubating the cells with LeY mAb. Notably, the expression of TGF-β1, VEGF and b-FGF all increased in RMG-I-H cells. In conclusion, LeY plays an important role in promoting cell proliferation, tumorigenecity and adhesion, and these effects may be related to increased levels of growth factors. The LeY antibody shows potential application in the treatment of LeY-positive tumors. Full article
(This article belongs to the Special Issue Cancer Molecules in Ovarian Cancer)
Open AccessArticle The Individual and Combined Effects of Deoxynivalenol and Aflatoxin B1 on Primary Hepatocytes of Cyprinus Carpio
Int. J. Mol. Sci. 2010, 11(10), 3760-3768; doi:10.3390/ijms11103760
Received: 26 August 2010 / Revised: 9 September 2010 / Accepted: 16 September 2010 / Published: 29 September 2010
Cited by 9 | PDF Full-text (370 KB) | HTML Full-text | XML Full-text
Abstract
Aflatoxin B1 (AFB1) and deoxynivalenol (DON) are important food-borne mycotoxins that have been implicated in animal and human health. In this study, individual and combinative effects of AFB1 and DON were tested in primary hepatocytes of Cyprinus carpio [...] Read more.
Aflatoxin B1 (AFB1) and deoxynivalenol (DON) are important food-borne mycotoxins that have been implicated in animal and human health. In this study, individual and combinative effects of AFB1 and DON were tested in primary hepatocytes of Cyprinus carpio. The results indicated that the combinative effects of AFB1 and DON (0.01 μg/mL AFB1 and 0.25 μg/mL DON; 0.02 μg/mL AFB1 and 0.25 μg/mL DON; 0.02 μg/mL AFB1 and 0.5 μg/mL DON) were higher than that of individual mycotoxin (P Full article
(This article belongs to the Special Issue Advances in Molecular Toxicology)
Open AccessArticle Reactive Oxygen Species Enhance TLR10 Expression in the Human Monocytic Cell Line THP-1
Int. J. Mol. Sci. 2010, 11(10), 3769-3782; doi:10.3390/ijms11103769
Received: 13 July 2010 / Revised: 10 September 2010 / Accepted: 17 September 2010 / Published: 29 September 2010
Cited by 14 | PDF Full-text (466 KB) | HTML Full-text | XML Full-text
Abstract
We investigated TLR10 expression in human monocytes, THP-1 cells, cultured in hypoxia (3% O2). Levels of both TLR10 mRNA and protein in THP-1 cells cultured in hypoxia were significantly higher than those cultured in normoxia (20% O2). We [...] Read more.
We investigated TLR10 expression in human monocytes, THP-1 cells, cultured in hypoxia (3% O2). Levels of both TLR10 mRNA and protein in THP-1 cells cultured in hypoxia were significantly higher than those cultured in normoxia (20% O2). We examined intracellular reactive oxygen species (ROS) content in hypoxic cells, and TLR10 expression in cells treated with hydrogen peroxide (H2O2), to determine whether the increase in TLR10 expression observed with hypoxia was due to an increase in intracellular ROS levels. We found that the level of intracellular ROS in cells subject to hypoxia was significantly higher than in normoxia. Experiments with ROS synthesis inhibitors revealed that hypoxia induced ROS production is mainly due to NADPH oxidase activity. TLR10 mRNA expression was increased by treatment with H2O2 at concentrations ranging from 50 to 250 μM. We screened the TLR10 promoter and found putative binding sites for transcription factors (TFs), such as NF-κB, NF-AT and AP-1. Next, we examined TF activities using a luciferase reporter assay. Activities of NF-κB, NF-AT and AP-1 in the cells treated with H2O2 were significantly higher than in untreated cells. The experiment with TF inhibitors revealed that ROS-induced upregulation of TLR10 expression is mainly due to NF-κB activation. Overall, our results suggest that hypoxia or ROS increase TLR10 expression in human monocytes and the transcriptional activities of NF-κB are involved in this process. Therefore, it is suggested that ROS produced by various exogenous stimuli may play a crucial role in the regulation of expression and function of TLR10 as second messengers. Full article
Open AccessArticle Purification and Characterization of Organic Solvent and Detergent Tolerant Lipase from Thermotolerant Bacillus sp. RN2
Int. J. Mol. Sci. 2010, 11(10), 3783-3792; doi:10.3390/ijms11103783
Received: 21 August 2010 / Revised: 17 September 2010 / Accepted: 18 September 2010 / Published: 29 September 2010
Cited by 14 | PDF Full-text (179 KB) | HTML Full-text | XML Full-text
Abstract
The aim of this study was to characterize the organic solvent and detergent tolerant properties of recombinant lipase isolated from thermotolerant Bacillus sp. RN2 (Lip-SBRN2). The isolation of the lipase-coding gene was achieved by the use of inverse and direct PCR. The [...] Read more.
The aim of this study was to characterize the organic solvent and detergent tolerant properties of recombinant lipase isolated from thermotolerant Bacillus sp. RN2 (Lip-SBRN2). The isolation of the lipase-coding gene was achieved by the use of inverse and direct PCR. The complete DNA sequencing of the gene revealed that the lip-SBRN2 gene contains 576 nucleotides which corresponded to 192 deduced amino acids. The purified enzyme was homogeneous with the estimated molecular mass of 19 kDa as determined by SDS-PAGE and gel filtration. The Lip-SBRN2 was stable in a pH range of 9–11 and temperature range of 45–60 °C. The enzyme was a non metallo-monomeric protein and was active against pNP-caprylate (C8) and pNP-laurate (C12) and coconut oil. The Lip-SBRN2 exhibited a high level of activity in the presence of 108% benzene, 102.4% diethylether and 112% SDS. It is anticipated that the organic solvent and detergent tolerant enzyme secreted by Bacillus sp. RN2 will be applicable as catalysts for reaction in the presence of organic solvents and detergents. Full article
(This article belongs to the Section Biochemistry, Molecular Biology and Biophysics)
Open AccessArticle Antigenotoxic Effect of Chamomilla recutita (L.) Rauschert Essential Oil in Mouse Spermatogonial Cells, and Determination of Its Antioxidant Capacity in Vitro
Int. J. Mol. Sci. 2010, 11(10), 3793-3802; doi:10.3390/ijms11103793
Received: 21 July 2010 / Revised: 12 September 2010 / Accepted: 17 September 2010 / Published: 30 September 2010
Cited by 10 | PDF Full-text (132 KB) | HTML Full-text | XML Full-text
Abstract
Chamomilla recutita (L.) Rauschert (Asteraceae), popularly known as chamomile, is a plant used in traditional medicine for various therapeutic purposes. Chamomile essential oil (CEO) is particularly known to inhibit the genotoxic damage produced by mutagens in mice somatic cells. The aim of [...] Read more.
Chamomilla recutita (L.) Rauschert (Asteraceae), popularly known as chamomile, is a plant used in traditional medicine for various therapeutic purposes. Chamomile essential oil (CEO) is particularly known to inhibit the genotoxic damage produced by mutagens in mice somatic cells. The aim of this research was to determine the inhibitory potential of CEO on the genotoxic damage produced by daunorubicin (DAU) in mice germ cells. We evaluated the effect of 5, 50, and 500 mg/kg of essential oil on the rate of sister chromatid exchange (SCE) induced in spermatogonia by 10 mg/kg of the mutagen. We found no genotoxicity of CEO, but detected an inhibition of SCE after the damage induced by DAU; from the lowest to the highest dose of CEO we found an inhibition of 47.5%, 61.9%, and 93.5%, respectively. As a possible mechanism of action, the antioxidant capacity of CEO was determined using the 1,1-diphenyl-2-picrylhydrazyl (DPPH) free radical scavenging method and ferric thiocyanate assays. In the first test we observed a moderate scavenging potential of the oil; nevertheless, the second assay showed an antioxidant capacity similar to that observed with vitamin E. In conclusion, we found that CEO is an efficient chemoprotective agent against the damage induced by DAU in the precursor cells of the germinal line of mice, and that its antioxidant capacity may induce this effect. Full article
(This article belongs to the Section Biochemistry, Molecular Biology and Biophysics)
Open AccessArticle Three-Dimensional Models of the Oligomeric Human Asialoglycoprotein Receptor (ASGP-R)
Int. J. Mol. Sci. 2010, 11(10), 3867-3884; doi:10.3390/ijms11103867
Received: 12 August 2010 / Revised: 27 September 2010 / Accepted: 27 September 2010 / Published: 11 October 2010
Cited by 2 | PDF Full-text (752 KB) | HTML Full-text | XML Full-text
Abstract
The work presented here is aimed at suggesting plausible hypotheses for functional oligomeric forms of the human asialoglycoprotein receptor (ASGP-R), by applying a combination of different computational techniques. The functional ASGP-R is a hetero-oligomer, that comprises of several subunits of two different [...] Read more.
The work presented here is aimed at suggesting plausible hypotheses for functional oligomeric forms of the human asialoglycoprotein receptor (ASGP-R), by applying a combination of different computational techniques. The functional ASGP-R is a hetero-oligomer, that comprises of several subunits of two different kinds (H1 and H2), which are highly homologous. Its stoichiometry is still unknown. An articulated step-wise modeling protocol was used in order to build the receptor model in a minimal oligomeric form, necessary for it to bind multi-antennary carbohydrate ligands. The ultimate target of the study is to contribute to increasing the knowledge of interactions between the human ASGP-R and carbohydrate ligands, at the molecular level, pertinent to applications in the field of hepatic tissue engineering. Full article
(This article belongs to the Section Biochemistry, Molecular Biology and Biophysics)
Open AccessArticle Effect of Different Light Intensities on Total Phenolics and Flavonoids Synthesis and Anti-oxidant Activities in Young Ginger Varieties (Zingiber officinale Roscoe)
Int. J. Mol. Sci. 2010, 11(10), 3885-3897; doi:10.3390/ijms11103885
Received: 13 August 2010 / Revised: 6 September 2010 / Accepted: 17 September 2010 / Published: 12 October 2010
Cited by 25 | PDF Full-text (216 KB) | HTML Full-text | XML Full-text
Abstract
Nowadays, phytochemicals and antioxidants in plants are raising interest in consumers for their roles in the maintenance of human health. Phenolics and flavonoids are known for their health-promoting properties due to protective effects against cardiovascular disease, cancers and other disease. Ginger ( [...] Read more.
Nowadays, phytochemicals and antioxidants in plants are raising interest in consumers for their roles in the maintenance of human health. Phenolics and flavonoids are known for their health-promoting properties due to protective effects against cardiovascular disease, cancers and other disease. Ginger (Zingiber officinale) is one of the traditional folk medicinal plants and it is widely used in cooking in Malaysia. In this study, four levels of glasshouse light intensities (310, 460, 630 and 790 μmol m−2s−1) were used in order to consider the effect of light intensity on the production, accumulation and partitioning of total phenolics (TP), total flavonoids (TF) and antioxidant activities in two varieties of Malaysian young ginger (Zingiber officinale). TF biosynthesis was highest in the Halia Bara variety under 310 μmol m−2s−1 and TP was high in this variety under a light intensity of 790 μmol m−2s−1. The highest amount of these components accumulated in the leaves and after that in the rhizomes. Also, antioxidant activities determined by the 1,1-Diphenyl-2-picryl-hydrazyl (DPPH) assay in both of varieties, increased significantly (p ≤ 0.01) with increasing TF concentration, and high antioxidant activity was observed in the leaves of Halia Bara grown under 310 μmol m−2s−1. The ferric reducing (FRAP) activity of the rhizomes was higher than that of the leaves in 310 μmol m−2s−1 of sun light. This study indicates the ability of different light intensities to enhance the medicinal components and antioxidant activities of the leaves and young rhizomes of Zingiber officinale varieties. Additionally, this study also validated their medicinal potential based on TF and TP contents. Full article
(This article belongs to the Section Biochemistry, Molecular Biology and Biophysics)
Open AccessArticle Effect of Accelerator in Green Synthesis of Silver Nanoparticles
Int. J. Mol. Sci. 2010, 11(10), 3898-3905; doi:10.3390/ijms11103898
Received: 19 August 2010 / Revised: 9 September 2010 / Accepted: 21 September 2010 / Published: 12 October 2010
Cited by 43 | PDF Full-text (469 KB) | HTML Full-text | XML Full-text
Abstract
Silver nanoparticles (Ag-NPs) were successfully synthesized in the natural polymeric matrix. Silver nitrate, gelatin, glucose, and sodium hydroxide have been used as silver precursor, stabilizer, reducing agent, and accelerator reagent, respectively. This study investigated the role of NaOH as the accelerator. The [...] Read more.
Silver nanoparticles (Ag-NPs) were successfully synthesized in the natural polymeric matrix. Silver nitrate, gelatin, glucose, and sodium hydroxide have been used as silver precursor, stabilizer, reducing agent, and accelerator reagent, respectively. This study investigated the role of NaOH as the accelerator. The resultant products have been confirmed to be Ag-NPs using powder X-ray diffraction (PXRD), UV-vis spectroscopy, and transmission electron microscopy (TEM). The colloidal sols of Ag-NPs obtained at different volumes of NaOH show strong and different surface plasmon resonance (SPR) peaks, which can be explained from the TEM images of Ag-NPs and their particle size distribution. Compared with other synthetic methods, this work is green, rapid, and simple to use. The newly prepared Ag-NPs may have many potential applications in chemical and biological industries. Full article
(This article belongs to the Section Biochemistry, Molecular Biology and Biophysics)
Open AccessArticle Preparation of an Adhesive in Emulsion for Maxillofacial Prosthetic
Int. J. Mol. Sci. 2010, 11(10), 3906-3921; doi:10.3390/ijms11103906
Received: 31 August 2010 / Accepted: 8 October 2010 / Published: 13 October 2010
PDF Full-text (664 KB) | HTML Full-text | XML Full-text
Abstract
Maxillofacial prostheses is a dental medicine specialty aimed at restoring anatomical facial defects caused by cancer, trauma or congenital malformations through an artificial device, which is commonly attached to the skin with the help of an adhesive. The purpose of our research [...] Read more.
Maxillofacial prostheses is a dental medicine specialty aimed at restoring anatomical facial defects caused by cancer, trauma or congenital malformations through an artificial device, which is commonly attached to the skin with the help of an adhesive. The purpose of our research was to develop a pressure-sensitive adhesive (PSA) based on acrylic monomers, characterizing and determining its drying kinetics, that is to say the time it takes to lose 50 to 90% of its moisture. The adhesive synthesis was realized by means of emulsion polymerization; the composition of formulations was: (AA‑MMA‑EA) and (AA‑MMA‑2EHA) with different molar ratios. The formulation based on (AA‑MMA‑2EHA) with 50 w% of solids, presented good adhesive properties such as tack, bond strength, and short drying time. We propose this formulation as a PSA, because it offers an alternative for systemically compromised patients, by less irritation compared to organic solvent-based adhesives. Full article
(This article belongs to the Section Biochemistry, Molecular Biology and Biophysics)
Open AccessArticle Optimization of Antibacterial Activity of Perilla frutescens var. acuta Leaf against Pseudomonas aeruginosa Using the Evolutionary Operation-Factorial Design Technique
Int. J. Mol. Sci. 2010, 11(10), 3922-3932; doi:10.3390/ijms11103922
Received: 7 September 2010 / Revised: 20 September 2010 / Accepted: 13 October 2010 / Published: 14 October 2010
Cited by 5 | PDF Full-text (311 KB) | HTML Full-text | XML Full-text
Abstract
This study was undertaken to optimize the conditions for the extraction of antibacterial activity of Perilla frutescens var. acuta leaf against Pseudomonas aeruginosa KCTC 2004 using the evolutionary operation-factorial (EVOP) design technique. Increased antibacterial activity was achieved at higher extraction temperatures and [...] Read more.
This study was undertaken to optimize the conditions for the extraction of antibacterial activity of Perilla frutescens var. acuta leaf against Pseudomonas aeruginosa KCTC 2004 using the evolutionary operation-factorial (EVOP) design technique. Increased antibacterial activity was achieved at higher extraction temperatures and with a longer extraction time. Antibacterial activity was not affected by differing ethanol concentration in the extraction solvent. The maximum antibacterial activity of ethanolic extract of P. frutescens var. acuta leaf against P. aeruginosa, determined by the EVOP factorial technique, was obtained at an extraction temperature of 80 °C (R = −0.800**), 26 h (R = −0.731**) extraction time, and 50% (R = −0.075) ethanol concentration. The population of P. aeruginosa also decreased from 6.660 log CFU/mL in the initial set to 4.060 log CFU/mL in the third set. Also, scanning electron microscopy study of the ethanolic extract of P. frutescens var. acuta revealed potential detrimental effects on the morphology of P. aeruginosa. Full article
(This article belongs to the Section Biochemistry, Molecular Biology and Biophysics)
Open AccessArticle Genetic Differentiation between Natural and Hatchery Stocks of Japanese Scallop (Mizuhopecten yessoensis) as Revealed by AFLP Analysis
Int. J. Mol. Sci. 2010, 11(10), 3933-3941; doi:10.3390/ijms11103933
Received: 19 September 2010 / Revised: 1 October 2010 / Accepted: 1 October 2010 / Published: 15 October 2010
Cited by 6 | PDF Full-text (161 KB) | HTML Full-text | XML Full-text
Abstract
Japanese scallop (Mizuhopecten yessoensis) is a cold-tolerant bivalve that was introduced to China for aquaculture in 1982. In this study, amplified fragment length polymorphism (AFLP) markers were used to investigate levels of genetic diversity within M. yessoensis cultured stocks and [...] Read more.
Japanese scallop (Mizuhopecten yessoensis) is a cold-tolerant bivalve that was introduced to China for aquaculture in 1982. In this study, amplified fragment length polymorphism (AFLP) markers were used to investigate levels of genetic diversity within M. yessoensis cultured stocks and compare them with wild populations. Six pairs of primer combinations generated 368 loci among 332 individuals, in four cultured and three wild populations. High polymorphism at AFLP markers was found within both cultured and wild M. yessoensis populations. The percentage of polymorphic loci ranged from 61.04% to 72.08%, while the mean heterozygosity ranged from 0.2116 to 0.2596. Compared with wild populations, the four hatchery populations showed significant genetic changes, such as lower expected heterozygosity and percentage of polymorphic loci, and smaller frequency of private alleles, all indicative of a reduction in genetic diversity. Some genetic structures were associated with the geographical distribution of samples; with all samples from Dalian and Japan being closely related, while the population from Russia fell into a distinct clade in the phylogenetic analysis. The genetic information derived from this study indicated that intentional or accidental release of selected Japanese scallops into natural sea areas might result in disturbance of local gene pools and loss of genetic variability. We recommend monitoring the genetic variability of selected hatchery populations to enhance conservation of natural Japanese scallop resources. Full article
(This article belongs to the Section Biochemistry, Molecular Biology and Biophysics)
Open AccessArticle Pharmacological Proprieties of the Ethanol Extract of Muehlenbeckia platyclada (F. Muell.) Meisn. Leaves
Int. J. Mol. Sci. 2010, 11(10), 3942-3953; doi:10.3390/ijms11103942
Received: 17 September 2010 / Revised: 29 September 2010 / Accepted: 12 October 2010 / Published: 15 October 2010
Cited by 5 | PDF Full-text (360 KB) | HTML Full-text | XML Full-text
Abstract
Antinociceptive and anti-inflammatory activities of the Muehlenbeckia platyclada leaves’ ethanol extract were investigated in animal models. The extract (p.o.) reduced the number of abdominal contortions induced by acetic acid by 21.57% (400 mg/kg). After intraplantar injection of formalin, a dose of 400 [...] Read more.
Antinociceptive and anti-inflammatory activities of the Muehlenbeckia platyclada leaves’ ethanol extract were investigated in animal models. The extract (p.o.) reduced the number of abdominal contortions induced by acetic acid by 21.57% (400 mg/kg). After intraplantar injection of formalin, a dose of 400 mg/kg (p.o.) inhibited the time spent paw licking in the first phase (26.43%), while the second phase was inhibited by 10.90 and 36.65% at the doses of 200 and 400 mg/kg, respectively. The extract (p.o.) increased the reaction time on a hot plate at a dose of 400 mg/kg (32.68 and 40.30%) after 60 and 90 minutes of treatment, respectively. The paw edema was reduced by extract (p.o.) at doses of 100 (15.46 and 16.67%), 200 (22.68 and 25.64%) and 400 mg/kg (29.50 and 37.33%) after 3 to 4 h of carrageenan application, respectively. Doses of 100, 200 and 400 mg/kg (p.o.), administered 4 h after the carrageenan injection, reduced the exudate volume (11.28, 21.54 and 45.13%), while leukocyte migration was reduced by 21.21 and 29.70% at the doses of 200 and 400 mg/kg, respectively. These results indicate that the ethanol extract from M. platyclada may constitute a potential target for the discovery of new molecules with antinociceptive and anti-inflammatory activities that can be explored for their therapeutic use. Full article
(This article belongs to the Section Biochemistry, Molecular Biology and Biophysics)
Open AccessArticle The Effect of Exercise on the Skeletal Muscle Phospholipidome of Rats Fed a High-Fat Diet
Int. J. Mol. Sci. 2010, 11(10), 3954-3964; doi:10.3390/ijms11103954
Received: 7 September 2010 / Revised: 8 October 2010 / Accepted: 12 October 2010 / Published: 15 October 2010
Cited by 5 | PDF Full-text (318 KB) | HTML Full-text | XML Full-text
Abstract
The aim of this study was to examine the effect of endurance training on skeletal muscle phospholipid molecular species from high-fat fed rats. Twelve female Sprague-Dawley rats were fed a high-fat diet (78.1% energy). The rats were randomly divided into two groups, [...] Read more.
The aim of this study was to examine the effect of endurance training on skeletal muscle phospholipid molecular species from high-fat fed rats. Twelve female Sprague-Dawley rats were fed a high-fat diet (78.1% energy). The rats were randomly divided into two groups, a sedentary control group and a trained group (125 min of treadmill running at 8 m/min, 4 days/wk for 4 weeks). Forty-eight hours after their last training bout phospholipids were extracted from the red and white vastus lateralis and analyzed by electrospray-ionization mass spectrometry. Exercise training was associated with significant alterations in the relative abundance of a number of phospholipid molecular species. These changes were more prominent in red vastus lateralis than white vastus lateralis. The largest observed change was an increase of ~30% in the abundance of 1-palmitoyl-2-linoleoyl phosphatidylcholine ions in oxidative fibers. Reductions in the relative abundance of a number of phospholipids containing long-chain n-3 polyunsaturated fatty acids were also observed. These data suggest a possible reduction in phospholipid remodeling in the trained animals. This results in a decrease in the phospholipid n-3 to n-6 ratio that may in turn influence endurance capacity. Full article
(This article belongs to the Special Issue Phospholipids: Molecular Sciences)
Open AccessArticle Distribution of Endogenous Farnesyl Pyrophosphate and Four Species of Lysophosphatidic Acid in Rodent Brain
Int. J. Mol. Sci. 2010, 11(10), 3965-3976; doi:10.3390/ijms11103965
Received: 24 August 2010 / Revised: 12 October 2010 / Accepted: 13 October 2010 / Published: 15 October 2010
Cited by 9 | PDF Full-text (247 KB) | HTML Full-text | XML Full-text
Abstract
Lysophosphatidic acid (LPA) is the umbrella term for lipid signaling molecules that share structural homology and activate the family of LPA receptors. Farnesyl Pyrophosphate (FPP) is commonly known as an intermediate in the synthesis of steroid hormones; however, its function as a [...] Read more.
Lysophosphatidic acid (LPA) is the umbrella term for lipid signaling molecules that share structural homology and activate the family of LPA receptors. Farnesyl Pyrophosphate (FPP) is commonly known as an intermediate in the synthesis of steroid hormones; however, its function as a signaling lipid is beginning to be explored. FPP was recently shown to an activator of the G-protein coupled receptor 92 (also known as LPA5) of the calcium channel TRPV3. The LPA receptors (including GPR92) are associated with the signal transduction of noxious stimuli, however, very little is known about the distribution of their signaling ligands (LPAs and FPP) in the brain. Here, using HPLC/MS/MS, we developed extraction and analytical methods for measuring levels of FPP and 4 species of LPA (palmitoyl, stearoyl, oleoyl and arachidonoyl-sn-glycerol-3 phosphate) in rodent brain. Relative distributions of each of the five compounds was significantly different across the brain suggesting divergent functionality for each as signaling molecules based on where and how much of each is being produced. Brainstem, midbrain, and thalamus contained the highest levels measured for each compound, though none in the same ratios while relatively small amounts were produced in cortex and cerebellum. These data provide a framework for investigations into functional relationships of these lipid ligands in specific brain areas, many of which are associated with the perception of pain. Full article
(This article belongs to the Special Issue Biomarkers)
Open AccessArticle Determination of the Thermodegradation of deoxyArbutin in Aqueous Solution by High Performance Liquid Chromatography
Int. J. Mol. Sci. 2010, 11(10), 3977-3987; doi:10.3390/ijms11103977
Received: 30 August 2010 / Revised: 30 September 2010 / Accepted: 13 October 2010 / Published: 15 October 2010
Cited by 5 | PDF Full-text (372 KB) | HTML Full-text | XML Full-text
Abstract
Tyrosinase is the key and rate-limiting enzyme responsible for the conversion of tyrosine into melanin. Competitive inhibition of tyrosinase enzymatic activity results in decreased or absent melanin synthesis by melanocytes in human skin. DeoxyArbutin (4-[(tetrahydro-2H-pyran-2-yl)oxy]phenol), a novel skin whitening agent, was synthesized [...] Read more.
Tyrosinase is the key and rate-limiting enzyme responsible for the conversion of tyrosine into melanin. Competitive inhibition of tyrosinase enzymatic activity results in decreased or absent melanin synthesis by melanocytes in human skin. DeoxyArbutin (4-[(tetrahydro-2H-pyran-2-yl)oxy]phenol), a novel skin whitening agent, was synthesized through the removal of hydroxyl groups from the glucose side-chain of arbutin. DeoxyArbutin not only shows greater inhibition of tyrosinase activity but is also safer than hydroquinone and arbutin. Hence, deoxyArbutin is a potential skin whitening agent for cosmetics and depigmenting drugs; however, stability of this compound under some conditions remains a problem. The lack of stability poses developmental and practical difficulties for the use of deoxyArbutin in cosmetics and medicines. Improving the thermostability of deoxyArbutin is an important issue for its development. In this research, we established an analytical procedure to verify the amount of deoxyArbutin in solutions using a high performance liquid chromatographic (HPLC) method. The results indicate that this novel skin whitening agent is a thermolabile compound in aqueous solutions. Additionally, the rate constant for thermodegradation (k) and the half-life (t1/2) of deoxyArbutin were determined and can be used to understand the thermodegradation kinetics of deoxyArbutin. This information can aid in the application of deoxyArbutin for many future uses. Full article
Open AccessArticle Lysophosphatidic Acid Level and the Incidence of Silent Brain Infarction in Patients with Nonvalvular Atrial Fibrillation
Int. J. Mol. Sci. 2010, 11(10), 3988-3998; doi:10.3390/ijms11103988
Received: 12 August 2010 / Revised: 25 September 2010 / Accepted: 12 October 2010 / Published: 19 October 2010
Cited by 6 | PDF Full-text (181 KB) | HTML Full-text | XML Full-text
Abstract
Lysophosphatidic acid (LPA), which is proposed to play an important role in normal physiological situations such as wound healing, vascular tone, vascular integrity and reproduction, may be involved in the etiology of some diseases such as atherosclerosis, cancer, obesity or myocardial infarction. Abnormal findings, including silent brain infarction (SBI), are frequently observed by magnetic resonance imaging (MRI) in patients with nonvalvular atrial fibrillation (NVAF). However, whether there is a relationship between LPA level and the prevalence of SBI has not been extensively studied. In the present study, the association between them was investigated. 235 patients with NVAF, 116 cases of SBI without NVAF and 120 cases of healthy volunteers (control group), who did not receive any antithrombotic therapy, were enrolled in this study. Plasma LPA levels in the NVAF with SBI group were significantly higher than that in the control group (p < 0.01), NVAF without SBI group (p < 0.01) and SBI without NVAF group (p < 0.01). The LPA levels are lower in the control group than in the NVAF without SBI and SBI without NVAF groups (p < 0.01), however, the latter two groups did not significantly differ from each other for LPA levels (p > 0.05) There were significant differences in the positive rate of platelet activation between each of the groups (p < 0.01). The positive rate of platelet activation was significantly higher in the NVAF with SBI group. We suggest that LPA might be a novel marker for estimation of the status of platelet activation and the risk factor for SBI onset in NVAF patients. We expected that plasma LPA levels could predict the occurrence of SBI in NVAF patients. Full article
(This article belongs to the Special Issue Phospholipids: Molecular Sciences)
Open AccessArticle Cyclin D1 Expression and the Inhibitory Effect of Celecoxib on Ovarian Tumor Growth in Vivo
Int. J. Mol. Sci. 2010, 11(10), 3999-4013; doi:10.3390/ijms11103999
Received: 7 September 2010 / Revised: 28 September 2010 / Accepted: 8 October 2010 / Published: 19 October 2010
Cited by 7 | PDF Full-text (380 KB) | HTML Full-text | XML Full-text
Abstract
The report aims to investigate the relationship between the expression of cyclin D1 and Cyclooxgenase-2 (COX-2), thus to explore the molecular mechanisms of the antitumor efficacy of Celecoxib, a COX-2 inhibitor. Human ovarian SKOV-3 carcinoma cell xenograft-bearing mice were treated with Celecoxib by infusing gaster (i.g.) twice/day for 21 days. The mRNA levels of COX-2 and cyclin D1 were determined by RT-PCR. The expression of cyclin D1 at the protein level was detected by immunohistochemistry, while COX-2 protein expression was determined by Western blot. A high-dose of Celecoxib (100 mg/kg) significantly inhibited tumor growth (P < 0.05), and the expression of cyclin D1 was reduced by 61%. Celecoxib decreased the proliferation cell index by 40% (P < 0.001) and increased apoptotic index by 52% (P < 0.05) in high-dose Celecoxib treated group. Our results suggest that the antitumor efficacy of Celecoxib against ovarian cancer in mice may in part be mediated through suppression of cyclin D1, which may contribute to its ability to suppress proliferation. Full article
(This article belongs to the Section Biochemistry, Molecular Biology and Biophysics)
Open AccessArticle Stability and Folding Behavior Analysis of Zinc-Finger Using Simple Models
Int. J. Mol. Sci. 2010, 11(10), 4014-4034; doi:10.3390/ijms11104014
Received: 7 September 2010 / Revised: 1 October 2010 / Accepted: 9 October 2010 / Published: 19 October 2010
Cited by 11 | PDF Full-text (805 KB) | HTML Full-text | XML Full-text
Abstract
Zinc-fingers play crucial roles in regulating gene expression and mediating protein-protein interactions. In this article, two different proteins (Sp1f2 and FSD-1) are investigated using the Gaussian network model and anisotropy elastic network model. By using these simple coarse-grained methods, we analyze the [...] Read more.
Zinc-fingers play crucial roles in regulating gene expression and mediating protein-protein interactions. In this article, two different proteins (Sp1f2 and FSD-1) are investigated using the Gaussian network model and anisotropy elastic network model. By using these simple coarse-grained methods, we analyze the structural stabilization and establish the unfolding pathway of the two different proteins, in good agreement with related experimental and molecular dynamics simulation data. From the analysis, it is also found that the folding process of the zinc-finger motif is predominated by several factors. Both the zinc ion and C-terminal loop affect the folding pathway of the zinc-finger motif. Knowledge about the stability and folding behavior of zinc-fingers may help in understanding the folding mechanisms of the zinc-finger motif and in designing new zinc-fingers. Meanwhile, these simple coarse-grained analyses can be used as a general and quick method for mechanistic studies of metalloproteins. Full article
(This article belongs to the Special Issue Protein Folding 2011)
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Open AccessArticle Characteristics of Lignin from Flax Shives as Affected by Extraction Conditions
Int. J. Mol. Sci. 2010, 11(10), 4035-4050; doi:10.3390/ijms11104035
Received: 10 September 2010 / Revised: 27 September 2010 / Accepted: 14 October 2010 / Published: 20 October 2010
Cited by 19 | PDF Full-text (272 KB) | HTML Full-text | XML Full-text
Abstract
Lignin, a polyphenolic molecule, is a major constituent of flax shives. This polyphenolic molecular structure renders lignin a potential source of a variety of commercially viable products such as fine chemicals. This work compares the performance of different lignin isolation methods. Lignin [...] Read more.
Lignin, a polyphenolic molecule, is a major constituent of flax shives. This polyphenolic molecular structure renders lignin a potential source of a variety of commercially viable products such as fine chemicals. This work compares the performance of different lignin isolation methods. Lignin from flax shive was isolated using both conventional alkaline extraction method and a novel experimental pressurized low polarity water (PLPW) extraction process. The lignin yields and chemical composition of the lignin fractions were determined. The conventional alkali treatment with 1.25 M NaOH, heated at 80 °C for 5 h, extracted 92 g lignin per kg flax shives, while lignin yields from the PLPW extracts ranged from 27 to 241 g lignin per kg flax shives. The purity and monomeric composition of the lignins obtained from the different extraction conditions was assessed via UV spectroscopy and alkaline nitrobenzene oxidation. Lignin obtained from conventional alkali treatment with 1.25 M NaOH, heated at 80 °C for 5 h was of low purity and exhibited the lowest yields of nitrobenzene oxidation products. With respect to alkali assisted PLPW extractions, temperature created an opposing effect on lignin yield and nitrobenzene oxidation products. More lignin was extracted as temperature increased, yet the yield of nitrobenzene oxidation products decreased. The low yield of nitrobenzene oxidation products may be attributed to either the formation of condensed structures or the selective dissolution of condensed structures of lignin during the pressurized alkaline high temperature treatment. Analytical pyrolysis, using pyroprobe GC-MS, was used to investigate the molecular composition of the lignin samples. The total yield of pyrolysis lignin products was 13.3, 64.7, and 30.5% for the 1.25 M NaOH extracted lignin, alkaline assisted PLPW extracted lignin, and the unprocessed flax shives, respectively. Key lignin derived compounds such as guaiacol, 4-vinyl guaiacol, 4-methyl guaiacol, syringol, eugenol, isoeugenol, catechol, homocatechol, and vanillin were detected in all of the samples. Full article
(This article belongs to the Section Biochemistry, Molecular Biology and Biophysics)
Open AccessArticle Carbonic Anhydrase I Is Recognized by an SOD1 Antibody upon Biotinylation of Human Spinal Cord Extracts
Int. J. Mol. Sci. 2010, 11(10), 4051-4062; doi:10.3390/ijms11104051
Received: 16 September 2010 / Revised: 14 October 2010 / Accepted: 18 October 2010 / Published: 20 October 2010
PDF Full-text (346 KB) | HTML Full-text | XML Full-text
Abstract
We recently reported the presence of a novel 32 kDa protein immunoreactive to a copper, zinc superoxide dismutase (SOD1) antibody within the spinal cord of patients with amyotrophic lateral sclerosis (ALS). This unique protein species was generated by biotinylation of spinal cord [...] Read more.
We recently reported the presence of a novel 32 kDa protein immunoreactive to a copper, zinc superoxide dismutase (SOD1) antibody within the spinal cord of patients with amyotrophic lateral sclerosis (ALS). This unique protein species was generated by biotinylation of spinal cord tissue extracts to detect conformational changes of SOD1 specific to ALS patients. To further characterize this protein, we enriched the protein by column chromatography and determined its protein identity by mass spectrometry. The protein that gave rise to the 32 kDa species upon biotinylation was identified as carbonic anhydrase I (CA I). Biotinylation of CA I from ALS spinal cord resulted in the generation of a novel epitope recognized by the SOD1 antibody. This epitope could also be generated by biotinylation of extracts from cultured cells expressing human CA I. Peptide competition assays identified the amino acid sequence in carbonic anhydrase I responsible for binding the SOD1 antibody. We conclude that chemical modifications used to identify pathogenic protein conformations can lead to the identification of unanticipated proteins that may participate in disease pathogenesis. Full article
(This article belongs to the Special Issue Biomarkers)
Open AccessArticle In Vitro Efficacy of Myxococcus fulvus ANSM068 to Biotransform Aflatoxin B1
Int. J. Mol. Sci. 2010, 11(10), 4063-4079; doi:10.3390/ijms11104063
Received: 29 September 2010 / Revised: 12 October 2010 / Accepted: 15 October 2010 / Published: 20 October 2010
Cited by 17 | PDF Full-text (317 KB) | HTML Full-text | XML Full-text
Abstract
Aflatoxin B1 (AFB1) is commonly found in cereals and animal feeds and causes a significant threat to the food industry and animal production. Several microbial isolates with high AFB1 transformation ability have been identified in our previous studies. [...] Read more.
Aflatoxin B1 (AFB1) is commonly found in cereals and animal feeds and causes a significant threat to the food industry and animal production. Several microbial isolates with high AFB1 transformation ability have been identified in our previous studies. The aim of this research was to characterize one of those isolates, Myxococcus fulvus ANSM068, and to explore its biotransformation mechanism. The bacterial isolate of M. fulvus ANSM068, isolated from deer feces, was able to transform AFB1 by 80.7% in liquid VY/2 medium after incubation at 30 °C for 72 h. The supernatant of the bacterial culture was more effective in transforming AFB1 as compared to the cells alone and the cell extract. The transformation activity was significantly reduced and eradicated after the culture supernatant was treated with proteinase K, proteinase K plus SDS and heating. Culture conditions, including nitrogen source, initial pH and incubation temperature were evaluated for an optimal AFB1 transformation. Liquid chromatography mass spectrometry (LCMS) analyses showed that AFB1 was transformed to a structurally different compound. Infrared analysis (IR) indicated that the lactone ring on the AFB1 molecule was modified by the culture supernatant. Chromatographies on DEAE-Ion exchange and Sephadex-Molecular sieve and SDS-PAGE electrophoresis were used to determine active components from the culture supernatant, indicating that enzyme(s) were responsible for the AFB1 biotransformation. This is the first report on AFB1 transformation by a strain of myxobacteria through enzymatic reaction(s). Full article
(This article belongs to the Section Biochemistry, Molecular Biology and Biophysics)
Open AccessArticle Antioxidant Activities of Extract and Fractions from the Hypocotyls of the Mangrove Plant Kandelia candel
Int. J. Mol. Sci. 2010, 11(10), 4080-4093; doi:10.3390/ijms11104080
Received: 30 September 2010 / Revised: 17 October 2010 / Accepted: 19 October 2010 / Published: 21 October 2010
Cited by 16 | PDF Full-text (227 KB) | HTML Full-text | XML Full-text
Abstract
The antioxidant activities of 70% acetone extract (70% AE) from the hypocotyls of the mangrove plant Kandelia candel and its fractions of petroleum ether (PF), ethyl acetate (EF), water (WF), and the LF (WF fraction further purified through a Sephadex LH‑20 column), [...] Read more.
The antioxidant activities of 70% acetone extract (70% AE) from the hypocotyls of the mangrove plant Kandelia candel and its fractions of petroleum ether (PF), ethyl acetate (EF), water (WF), and the LF (WF fraction further purified through a Sephadex LH‑20 column), were investigated by the 1,1-diphenyl-2-picrylhydrazyl (DPPH) free radical scavenging and ferric reducing/antioxidant power (FRAP) assays. The results showed that all the extract and fractions possessed potent antioxidant activity. There was a significant linear correlation between the total phenolics concentration and the ferric reducing power or free radical scavenging activity of the extract and fractions. Among the extract and fractions, the LF fraction exhibits the best antioxidant performance. The MALDT-TOF MS and HPLC analyses revealed that the phenolic compounds associated with the antioxidant activity of the LF fraction contains a large number of procyanidins and a small amount of prodelphinidins, and the epicatechin is the main extension unit. Full article
(This article belongs to the Section Biochemistry, Molecular Biology and Biophysics)
Open AccessArticle COMBO-FISH Enables High Precision Localization Microscopy as a Prerequisite for Nanostructure Analysis of Genome Loci
Int. J. Mol. Sci. 2010, 11(10), 4094-4105; doi:10.3390/ijms11104094
Received: 15 September 2010 / Revised: 16 October 2010 / Accepted: 18 October 2010 / Published: 21 October 2010
Cited by 15 | PDF Full-text (592 KB) | HTML Full-text | XML Full-text
Abstract
With the completeness of genome databases, it has become possible to develop a novel FISH (Fluorescence in Situ Hybridization) technique called COMBO-FISH (COMBinatorial Oligo FISH). In contrast to other FISH techniques, COMBO-FISH makes use of a bioinformatics approach for probe set design. [...] Read more.
With the completeness of genome databases, it has become possible to develop a novel FISH (Fluorescence in Situ Hybridization) technique called COMBO-FISH (COMBinatorial Oligo FISH). In contrast to other FISH techniques, COMBO-FISH makes use of a bioinformatics approach for probe set design. By means of computer genome database searching, several oligonucleotide stretches of typical lengths of 15–30 nucleotides are selected in such a way that all uniquely colocalize at the given genome target. The probes applied here were Peptide Nucleic Acids (PNAs)—synthetic DNA analogues with a neutral backbone—which were synthesized under high purity conditions. For a probe repetitively highlighted in centromere 9, PNAs labeled with different dyes were tested, among which Alexa 488Ò showed reversible photobleaching (blinking between dark and bright state) a prerequisite for the application of SPDM (Spectral Precision Distance/Position Determination Microscopy) a novel technique of high resolution fluorescence localization microscopy. Although COMBO-FISH labeled cell nuclei under SPDM conditions sometimes revealed fluorescent background, the specific locus was clearly discriminated by the signal intensity and the resulting localization accuracy in the range of 10–20 nm for a detected oligonucleotide stretch. The results indicate that COMBO-FISH probes with blinking dyes are well suited for SPDM, which will open new perspectives on molecular nanostructural analysis of the genome. Full article
(This article belongs to the Special Issue Biomarkers)
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Open AccessArticle Efficacy of Intra-Articular Injection of Celecoxib in a Rabbit Model of Osteoarthritis
Int. J. Mol. Sci. 2010, 11(10), 4106-4113; doi:10.3390/ijms11104106
Received: 13 September 2010 / Accepted: 15 October 2010 / Published: 21 October 2010
Cited by 10 | PDF Full-text (245 KB) | HTML Full-text | XML Full-text
Abstract
Introduction: Osteoarthritis is the most common form of arthritis. It is a slowly progressive joint disease typically seen in middle-age to elderly people. Intra-articular injection of hyaluronic acid is a well-documented treatment for knee osteoarthritis. Celebrex® (celecoxib) is a novel nonsteroidal [...] Read more.
Introduction: Osteoarthritis is the most common form of arthritis. It is a slowly progressive joint disease typically seen in middle-age to elderly people. Intra-articular injection of hyaluronic acid is a well-documented treatment for knee osteoarthritis. Celebrex® (celecoxib) is a novel nonsteroidal anti-inflammatory drug, which could help to reduce inflammation and to reduce pain. The aim of this study was to evaluate the effects of intra-articular injection of celecoxib in a rabbit osteoarthritis model. Methods: Thirty New Zealand white rabbits underwent unilateral knee joint surgery using the Hulth technique. Six weeks post-surgery, the animals were randomly divided into three groups, and each group was respectively given weekly intra-articular injections with Celebrex®, hyaluronic acid and saline. On the sixth week, the results were assessed in rabbit models by gross observation, histological evaluation, and expression of IL-1β, TNF-α, MMP-3. Results: In the group given Celebrex® and hyaluronic acid, the pathological changes in the rabbit articular cartilage improved significantly, much more than in the saline group. The statistically significant suppression of IL-1β, TNF-α, MMP-3 was shown in the Celebrex group. No significant differences were detected between two treatment groups. Conclusions: Intra-articular injection of celecoxib is beneficial for knee osteoarthritis. It might repair and protect early osteoarthritis cartilage by delaying cartilage degeneration and impairing the function of inflammatory mediators, therefore, intra-articular injection of celecoxib can be used as an alternative to the current treatment of osteoarthritis. Full article
Open AccessArticle Estrogen Stimulates Proliferation and Differentiation of Neural Stem/Progenitor Cells through Different Signal Transduction Pathways
Int. J. Mol. Sci. 2010, 11(10), 4114-4123; doi:10.3390/ijms11104114
Received: 13 October 2010 / Revised: 17 October 2010 / Accepted: 18 October 2010 / Published: 22 October 2010
Cited by 20 | PDF Full-text (343 KB) | HTML Full-text | XML Full-text
Abstract
Our previous study indicated that both 17β-estradiol (E2), known to be an endogenous estrogen, and bisphenol A (BPA), known to be a xenoestrogen, could positively influence the proliferation or differentiation of neural stem/progenitor cells (NS/PCs). The aim of the present study was [...] Read more.
Our previous study indicated that both 17β-estradiol (E2), known to be an endogenous estrogen, and bisphenol A (BPA), known to be a xenoestrogen, could positively influence the proliferation or differentiation of neural stem/progenitor cells (NS/PCs). The aim of the present study was to identify the signal transduction pathways for estrogenic activities promoting proliferation and differentiation of NS/PCs via well known nuclear estrogen receptors (ERs) or putative membrane-associated ERs. NS/PCs were cultured from the telencephalon of 15-day-old rat embryos. In order to confirm the involvement of nuclear ERs for estrogenic activities, their specific antagonist, ICI-182,780, was used. The presence of putative membrane-associated ER was functionally examined as to whether E2 can activate rapid intracellular signaling mechanism. In order to confirm the involvement of membrane-associated ERs for estrogenic activities, a cell-impermeable E2, bovine serum albumin-conjugated E2 (E2-BSA) was used. We showed that E2 could rapidly activate extracellular signal-regulated kinases 1/2 (ERK 1/2), which was not inhibited by ICI-182,780. ICI-182,780 abrogated the stimulatory effect of these estrogens (E2 and BPA) on the proliferation of NS/PCs, but not their effect on the differentiation of the NS/PCs into oligodendroglia. Furthermore, E2-BSA mimicked the activity of differentiation from NS/PCs into oligodendroglia, but not the activity of proliferation. Our study suggests that (1) the estrogen induced proliferation of NS/PCs is mediated via nuclear ERs; (2) the oligodendroglial generation from NS/PCs is likely to be stimulated via putative membrane‑associated ERs. Full article
(This article belongs to the Section Biochemistry, Molecular Biology and Biophysics)
Open AccessArticle On Heisenberg Uncertainty Relationship, Its Extension, and the Quantum Issue of Wave-Particle Duality
Int. J. Mol. Sci. 2010, 11(10), 4124-4139; doi:10.3390/ijms11104124
Received: 11 August 2010 / Revised: 27 September 2010 / Accepted: 17 October 2010 / Published: 22 October 2010
Cited by 4 | PDF Full-text (294 KB) | HTML Full-text | XML Full-text
Abstract
Within the path integral Feynman formulation of quantum mechanics, the fundamental Heisenberg Uncertainty Relationship (HUR) is analyzed in terms of the quantum fluctuation influence on coordinate and momentum estimations. While introducing specific particle and wave representations, as well as their ratio, in [...] Read more.
Within the path integral Feynman formulation of quantum mechanics, the fundamental Heisenberg Uncertainty Relationship (HUR) is analyzed in terms of the quantum fluctuation influence on coordinate and momentum estimations. While introducing specific particle and wave representations, as well as their ratio, in quantifying the wave-to-particle quantum information, the basic HUR is recovered in a close analytical manner for a large range of observable particle-wave Copenhagen duality, although with the dominant wave manifestation, while registering its progressive modification with the factor √1-n2, in terms of magnitude n ε [0,1] of the quantum fluctuation, for the free quantum evolution around the exact wave-particle equivalence. The practical implications of the present particle-to-wave ratio as well as of the free-evolution quantum picture are discussed for experimental implementation, broken symmetry and the electronic localization function. Full article
(This article belongs to the Special Issue Advances in Molecular Electronic Structure Calculations)
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Open AccessArticle In Vivo Biocompatibility Study of Electrospun Chitosan Microfiber for Tissue Engineering
Int. J. Mol. Sci. 2010, 11(10), 4140-4148; doi:10.3390/ijms11104140
Received: 28 September 2010 / Revised: 19 October 2010 / Accepted: 19 October 2010 / Published: 25 October 2010
Cited by 17 | PDF Full-text (498 KB) | HTML Full-text | XML Full-text
Abstract
In this work, we examined the biocompatibility of electrospun chitosan microfibers as a scaffold. The chitosan microfibers showed a three-dimensional pore structure by SEM. The chitosan microfibers supported attachment and viability of rat muscle-derived stem cells (rMDSCs). Subcutaneous implantation of the chitosan [...] Read more.
In this work, we examined the biocompatibility of electrospun chitosan microfibers as a scaffold. The chitosan microfibers showed a three-dimensional pore structure by SEM. The chitosan microfibers supported attachment and viability of rat muscle-derived stem cells (rMDSCs). Subcutaneous implantation of the chitosan microfibers demonstrated that implantation of rMDSCs containing chitosan microfibers induced lower host tissue responses with decreased macrophage accumulation than did the chitosan microfibers alone, probably due to the immunosuppression of the transplanted rMDSCs. Our results collectively show that chitosan microfibers could serve as a biocompatible in vivo scaffold for rMDSCs in rats. Full article
(This article belongs to the Special Issue Chitins)
Open AccessArticle Rapid Synthesis of Flavor Compound 4-Ethyloctanoic Acid under Microwave Irradiation
Int. J. Mol. Sci. 2010, 11(10), 4165-4174; doi:10.3390/ijms11104165
Received: 30 September 2010 / Revised: 20 October 2010 / Accepted: 21 October 2010 / Published: 25 October 2010
Cited by 5 | PDF Full-text (170 KB) | HTML Full-text | XML Full-text
Abstract
Rapid synthesis of 4-ethyloctanoic acid by means of microwave irradiation is described. Diethyl malonate reacted with 2-ethyl-1-bromohexane in the presence of sodium ethoxide to give diethyl (2-ethylhexyl)malonate (1b). 1b was saponified in the solution of ethanol and potassium hydroxide and [...] Read more.
Rapid synthesis of 4-ethyloctanoic acid by means of microwave irradiation is described. Diethyl malonate reacted with 2-ethyl-1-bromohexane in the presence of sodium ethoxide to give diethyl (2-ethylhexyl)malonate (1b). 1b was saponified in the solution of ethanol and potassium hydroxide and then acidified to form (2-ethylhexyl)propanedioic acid (1c), and 1c was heated and decarboxylized to give 4-ethyloctanoic acid (1d). The influence of reaction temperature and reaction time on the yield of 1b and the effect of reaction time on the yield of 1c and 1d were investigated in order to optimize the synthetic conditions. The relative optimal conditions for the synthesis of 1b were a mole ratio of sodium to diethyl malonate to 2-ethylhexyl bromide of 0.1:0.11:0.11, a reaction temperature of 80–85 °C, and a reaction time of 2–2.5 h. The yield of 1b was about 79%. 1b was saponified for 30 min and then acidified to form 1c, and the yield of 1c was 96%. 1c was heated for 16 min at 180°C to give 1d, and the yield of 1d was about 90%. The overall yield of 1d is 70% under microwave irradiation. The reaction time was reduced greatly. In order to compare the result of microwave irradiation with that of an oil bath, the reactions were also performed in an oil bath. The structures of intermediates, product and by-product were confirmed by HRMS, 1H NMR, 13C-NMR and IR. Full article
(This article belongs to the Section Green Chemistry)

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Open AccessReview Flexible Two-Dimensional Square-Grid Coordination Polymers: Structures and Functions
Int. J. Mol. Sci. 2010, 11(10), 3803-3845; doi:10.3390/ijms11103803
Received: 21 August 2010 / Revised: 19 September 2010 / Accepted: 20 September 2010 / Published: 30 September 2010
Cited by 42 | PDF Full-text (2172 KB) | HTML Full-text | XML Full-text
Abstract
Coordination polymers (CPs) or metal-organic frameworks (MOFs) have attracted considerable attention because of the tunable diversity of structures and functions. A 4,4'-bipyridine molecule, which is a simple, linear, exobidentate, and rigid ligand molecule, can construct two-dimensional (2D) square grid type CPs. Only [...] Read more.
Coordination polymers (CPs) or metal-organic frameworks (MOFs) have attracted considerable attention because of the tunable diversity of structures and functions. A 4,4'-bipyridine molecule, which is a simple, linear, exobidentate, and rigid ligand molecule, can construct two-dimensional (2D) square grid type CPs. Only the 2D-CPs with appropriate metal cations and counter anions exhibit flexibility and adsorb gas with a gate mechanism and these 2D-CPs are called elastic layer-structured metal-organic frameworks (ELMs). Such a unique property can make it possible to overcome the dilemma of strong adsorption and easy desorption, which is one of the ideal properties for practical adsorbents. Full article
(This article belongs to the Special Issue Metal Organic Frameworks)
Open AccessReview Recent Advances in Fragment-Based QSAR and Multi-Dimensional QSAR Methods
Int. J. Mol. Sci. 2010, 11(10), 3846-3866; doi:10.3390/ijms11103846
Received: 27 August 2010 / Revised: 17 September 2010 / Accepted: 23 September 2010 / Published: 8 October 2010
Cited by 36 | PDF Full-text (403 KB) | HTML Full-text | XML Full-text
Abstract
This paper provides an overview of recently developed two dimensional (2D) fragment-based QSAR methods as well as other multi-dimensional approaches. In particular, we present recent fragment-based QSAR methods such as fragment-similarity-based QSAR (FS-QSAR), fragment-based QSAR (FB-QSAR), Hologram QSAR (HQSAR), and top priority [...] Read more.
This paper provides an overview of recently developed two dimensional (2D) fragment-based QSAR methods as well as other multi-dimensional approaches. In particular, we present recent fragment-based QSAR methods such as fragment-similarity-based QSAR (FS-QSAR), fragment-based QSAR (FB-QSAR), Hologram QSAR (HQSAR), and top priority fragment QSAR in addition to 3D- and nD-QSAR methods such as comparative molecular field analysis (CoMFA), comparative molecular similarity analysis (CoMSIA), Topomer CoMFA, self-organizing molecular field analysis (SOMFA), comparative molecular moment analysis (COMMA), autocorrelation of molecular surfaces properties (AMSP), weighted holistic invariant molecular (WHIM) descriptor-based QSAR (WHIM), grid-independent descriptors (GRIND)-based QSAR, 4D-QSAR, 5D-QSAR and 6D-QSAR methods. Full article
(This article belongs to the Special Issue Recent Advances in QSAR/QSPR Theory)
Open AccessReview Lipid Based Therapy for Ulcerative Colitis—Modulation of Intestinal Mucus Membrane Phospholipids as a Tool to Influence Inflammation
Int. J. Mol. Sci. 2010, 11(10), 4149-4164; doi:10.3390/ijms11104149
Received: 6 September 2010 / Revised: 15 October 2010 / Accepted: 16 October 2010 / Published: 25 October 2010
Cited by 15 | PDF Full-text (485 KB) | HTML Full-text | XML Full-text
Abstract
Ulcerative colitis (UC) is the result of an inappropriate colonic inflammatory response triggered by environmental and genetic factors. We have recently shown that mucus from UC patients has a decreased phosphatidylcholine (PC) content, while clinical trials revealed that therapeutic addition of PC [...] Read more.
Ulcerative colitis (UC) is the result of an inappropriate colonic inflammatory response triggered by environmental and genetic factors. We have recently shown that mucus from UC patients has a decreased phosphatidylcholine (PC) content, while clinical trials revealed that therapeutic addition of PC to the colonic mucus alleviated the inflammatory activity. The mechanisms behind this are still unclear. We hypothesized that PC has at least two possible functions in the intestine: First, it establishes the surface hydrophobicity of the mucus and therefore protects the underlying tissue against intraluminal aggressors; recent experiments on surgical specimens revealed reduced surface tension and hydrophobicity in UC patients. Second, mucus phospholipids might also be integrated into the plasma membranes of enterocytes and thereby influence the signaling state of the mucosa. PC has been shown to inhibit TNF-α induced pro-inflammatory responses including: (1) assembly of plasma membrane actin; (2) activation of MAP kinases ERK and p38; and (3) activation of NF-κB and synthesis of pro-inflammatory gene products. Other phospholipids like phosphatidylethanolamine or sphingomyelin  had no effect. PC also inhibited latex bead phagosome actin assembly, killing of M. tuberculosis in macrophages, and sphingosine-1-phosphate induced actin assembly in macrophages. Collectively, these results provide a molecular foundation that shows PC, firstly, as an anti-inflammatory, and secondly, as a surface hydrophobicity increasing compound with promising therapeutic potential in the treatment of inflammatory bowel disease. Full article
(This article belongs to the Special Issue Phospholipids: Molecular Sciences)

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