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Int. J. Mol. Sci., Volume 12, Issue 12 (December 2011), Pages 8316-9604

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Editorial

Jump to: Research, Review, Other

Open AccessEditorial Molecular System Bioenergics of the Heart: Experimental Studies of Metabolic Compartmentation and Energy Fluxes versus Computer Modeling
Int. J. Mol. Sci. 2011, 12(12), 9296-9331; doi:10.3390/ijms12129296
Received: 10 November 2011 / Revised: 30 November 2011 / Accepted: 30 November 2011 / Published: 13 December 2011
Cited by 12 | PDF Full-text (801 KB) | HTML Full-text | XML Full-text
Abstract
In this review we analyze the recent important and remarkable advancements in studies of compartmentation of adenine nucleotides in muscle cells due to their binding to macromolecular complexes and cellular structures, which results in non-equilibrium steady state of the creatine kinase reaction. We
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In this review we analyze the recent important and remarkable advancements in studies of compartmentation of adenine nucleotides in muscle cells due to their binding to macromolecular complexes and cellular structures, which results in non-equilibrium steady state of the creatine kinase reaction. We discuss the problems of measuring the energy fluxes between different cellular compartments and their simulation by using different computer models. Energy flux determinations by 18O transfer method have shown that in heart about 80% of energy is carried out of mitochondrial intermembrane space into cytoplasm by phosphocreatine fluxes generated by mitochondrial creatine kinase from adenosine triphosphate (ATP), produced by ATP Synthasome. We have applied the mathematical model of compartmentalized energy transfer for analysis of experimental data on the dependence of oxygen consumption rate on heart workload in isolated working heart reported by Williamson et al. The analysis of these data show that even at the maximal workloads and respiration rates, equal to 174 µmol O2 per min per g dry weight, phosphocreatine flux, and not ATP, carries about 80–85% percent of energy needed out of mitochondria into the cytosol. We analyze also the reasons of failures of several computer models published in the literature to correctly describe the experimental data. Full article
(This article belongs to the Special Issue Molecular System Bioenergetics 2011)

Research

Jump to: Editorial, Review, Other

Open AccessArticle Inhibition of Extracellular Signal-Regulated Kinases Ameliorates Hypertension-Induced Renal Vascular Remodeling in Rat Models
Int. J. Mol. Sci. 2011, 12(12), 8333-8346; doi:10.3390/ijms12128333
Received: 26 August 2011 / Revised: 19 September 2011 / Accepted: 21 October 2011 / Published: 28 November 2011
Cited by 3 | PDF Full-text (1709 KB) | HTML Full-text | XML Full-text
Abstract
The aim of this study is to investigate the effect of the extracellular signal-regulated kinases 1/2 (ERK1/2) inhibitor, PD98059, on high blood pressure and related vascular changes. Blood pressure was recorded, thicknesses of renal small artery walls were measured and ERK1/2 immunoreactivity and
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The aim of this study is to investigate the effect of the extracellular signal-regulated kinases 1/2 (ERK1/2) inhibitor, PD98059, on high blood pressure and related vascular changes. Blood pressure was recorded, thicknesses of renal small artery walls were measured and ERK1/2 immunoreactivity and erk2 mRNA in renal vascular smooth muscle cells (VSMCs) and endothelial cells were detected by immunohistochemistry and in situ hybridization in normotensive wistar kyoto (WKY) rats, spontaneously hypertensive rats (SHR) and PD98059-treated SHR. Compared with normo-tensive WKY rats, SHR developed hypertension at 8 weeks of age, thickened renal small artery wall and asymmetric arrangement of VSMCs at 16 and 24 weeks of age. Phospho-ERK1/2 immunoreactivity and erk2 mRNA expression levels were increased in VSMCs and endothelial cells of the renal small arteries in the SHR. Treating SHR with PD98059 reduced the spontaneous hypertension-induced vascular wall thickening. This effect was associated with suppressions of erk2 mRNA expression and ERK1/2 phosphorylation in VSMCs and endothelial cells of the renal small arteries. It is concluded that inhibition of ERK1/2 ameliorates hypertension induced vascular remodeling in renal small arteries. Full article
(This article belongs to the Special Issue Advances in Molecular Neuropathology)
Open AccessArticle Prediction of Lysine Ubiquitylation with Ensemble Classifier and Feature Selection
Int. J. Mol. Sci. 2011, 12(12), 8347-8361; doi:10.3390/ijms12128347
Received: 27 July 2011 / Revised: 14 November 2011 / Accepted: 15 November 2011 / Published: 28 November 2011
Cited by 26 | PDF Full-text (247 KB) | HTML Full-text | XML Full-text
Abstract
Ubiquitylation is an important process of post-translational modification. Correct identification of protein lysine ubiquitylation sites is of fundamental importance to understand the molecular mechanism of lysine ubiquitylation in biological systems. This paper develops a novel computational method to effectively identify the lysine ubiquitylation
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Ubiquitylation is an important process of post-translational modification. Correct identification of protein lysine ubiquitylation sites is of fundamental importance to understand the molecular mechanism of lysine ubiquitylation in biological systems. This paper develops a novel computational method to effectively identify the lysine ubiquitylation sites based on the ensemble approach. In the proposed method, 468 ubiquitylation sites from 323 proteins retrieved from the Swiss-Prot database were encoded into feature vectors by using four kinds of protein sequences information. An effective feature selection method was then applied to extract informative feature subsets. After different feature subsets were obtained by setting different starting points in the search procedure, they were used to train multiple random forests classifiers and then aggregated into a consensus classifier by majority voting. Evaluated by jackknife tests and independent tests respectively, the accuracy of the proposed predictor reached 76.82% for the training dataset and 79.16% for the test dataset, indicating that this predictor is a useful tool to predict lysine ubiquitylation sites. Furthermore, site-specific feature analysis was performed and it was shown that ubiquitylation is intimately correlated with the features of its surrounding sites in addition to features derived from the lysine site itself. The feature selection method is available upon request. Full article
(This article belongs to the Section Biochemistry, Molecular Biology and Biophysics)
Open AccessArticle Knockdown of Ephrin-A5 Expression by 40% Does not Affect Motor Axon Growth or Migration into the Chick Hindlimb
Int. J. Mol. Sci. 2011, 12(12), 8362-8371; doi:10.3390/ijms12128362
Received: 20 October 2011 / Revised: 9 November 2011 / Accepted: 11 November 2011 / Published: 29 November 2011
Cited by 3 | PDF Full-text (1453 KB) | HTML Full-text | XML Full-text
Abstract
Bidirectional signaling between Eph receptor tyrosine kinases and their cell-surface protein signals, the ephrins, comprises one mechanism for guiding motor axons to their proper targets. During projection of motor axons from the lateral motor column (LMC) motor neurons of the spinal cord to
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Bidirectional signaling between Eph receptor tyrosine kinases and their cell-surface protein signals, the ephrins, comprises one mechanism for guiding motor axons to their proper targets. During projection of motor axons from the lateral motor column (LMC) motor neurons of the spinal cord to the hindlimb muscles in chick embryos, ephrin-A5 has been shown to be expressed in the LMC motor axons until they reach the base of the limb bud and initiate sorting into their presumptive dorsal and ventral nerve trunks, at which point expression is extinguished. We tested the hypothesis that this dynamic pattern of ephrin-A5 expression in LMC motor axons is important for the growth and guidance of the axons to, and into, the hindlimb by knocking down endogenous ephrin-A5 expression in the motor neurons and their axons. No perturbation of LMC motor axon projections was observed in response to this treatment, suggesting that ephrin-A5 is not needed for LMC motor axon growth or guidance. Full article
(This article belongs to the Special Issue Studies of Motor Molecules)
Figures

Open AccessArticle Functional Properties of Pea (Pisum sativum, L.) Protein Isolates Modified with Chymosin
Int. J. Mol. Sci. 2011, 12(12), 8372-8387; doi:10.3390/ijms12128372
Received: 17 October 2011 / Revised: 11 November 2011 / Accepted: 14 November 2011 / Published: 29 November 2011
Cited by 10 | PDF Full-text (275 KB) | HTML Full-text | XML Full-text
Abstract
In this paper, the effects of limited hydrolysis on functional properties, as well as on protein composition of laboratory-prepared pea protein isolates, were investigated. Pea protein isolates were hydrolyzed for either 15, 30 and 60 min with recombined chymosin (Maxiren). The effect of
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In this paper, the effects of limited hydrolysis on functional properties, as well as on protein composition of laboratory-prepared pea protein isolates, were investigated. Pea protein isolates were hydrolyzed for either 15, 30 and 60 min with recombined chymosin (Maxiren). The effect of enzymatic action on solubility, emulsifying and foaming properties at different pH values (3.0; 5.0; 7.0 and 8.0) was monitored. Chymosin can be a very useful agent for improvement of functional properties of isolates. Action of this enzyme caused a low degree of hydrolysis (3.9–4.7%), but improved significantly functional properties of pea protein isolates (PPI), especially at lower pH values (3.0–5.0). At these pH values all hydrolysates had better solubility, emulsifying activity and foaming stability, while longer-treated samples (60 min) formed more stable emulsions at higher pH values (7.0, 8.0) than initial isolates. Also, regardless of pH value, all hydrolysates showed improved foaming ability. A moderate positive correlation between solubility and emulsifying activity index (EAI) (0.74) and negative correlation between solubility and foam stability (−0.60) as well as between foam stability (FS) and EAI (−0.77) were observed. Detected enhancement in functional properties was a result of partial hydrolysis of insoluble protein complexes. Full article
(This article belongs to the Section Biochemistry, Molecular Biology and Biophysics)
Open AccessArticle Enhanced Antiproliferative and Apoptotic Response of HT-29 Adenocarcinoma Cells to Combination of Photoactivated Hypericin and Farnesyltransferase Inhibitor Manumycin A
Int. J. Mol. Sci. 2011, 12(12), 8388-8405; doi:10.3390/ijms12128388
Received: 27 October 2011 / Revised: 15 November 2011 / Accepted: 21 November 2011 / Published: 29 November 2011
Cited by 7 | PDF Full-text (1325 KB) | HTML Full-text | XML Full-text
Abstract
Several photodynamically-active substances and farnesyltransferase inhibitors are currently being investigated as promising anticancer drugs. In this study, the combined effect of hypericin (the photodynamically-active pigment from Hypericum perforatum) and selective farnesyltransferase inhibitor manumycin (manumycin A; the selective farnesyltransferase inhibitor from Streptomyces parvulus
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Several photodynamically-active substances and farnesyltransferase inhibitors are currently being investigated as promising anticancer drugs. In this study, the combined effect of hypericin (the photodynamically-active pigment from Hypericum perforatum) and selective farnesyltransferase inhibitor manumycin (manumycin A; the selective farnesyltransferase inhibitor from Streptomyces parvulus) on HT-29 adenocarcinoma cells was examined. We found that the combination treatment of cells with photoactivated hypericin and manumycin resulted in enhanced antiproliferative and apoptotic response compared to the effect of single treatments. This was associated with increased suppression of clonogenic growth, S phase cell cycle arrest, elevated caspase-3/7 activity and time-dependent total cleavage of procaspase-3 and lamin B, cleavage of p21Bax into p18Bax and massive PARP cleavage. Moreover, we found that the apoptosis-inducing factor is implicated in signaling events triggered by photoactivated hypericin. Our results showed the relocalization of apoptosis-inducing factor (AIF) to the nuclei after hypericin treatment. In addition, we discovered that not only manumycin but also photoactivated hypericin induced the reduction of total Ras protein level. Manumycin decreased the amount of farnesylated Ras, and the combination treatment decreased the amount of both farnesylated and non-farnesylated Ras protein more dramatically. The present findings indicate that the inhibition of Ras processing may be the determining factor for enhancing the antiproliferative and apoptotic effects of combination treatment on HT-29 cells. Full article
(This article belongs to the Section Biochemistry, Molecular Biology and Biophysics)
Open AccessArticle Predicting Antitumor Activity of Peptides by Consensus of Regression Models Trained on a Small Data Sample
Int. J. Mol. Sci. 2011, 12(12), 8415-8430; doi:10.3390/ijms12128415
Received: 11 November 2011 / Revised: 15 November 2011 / Accepted: 17 November 2011 / Published: 29 November 2011
Cited by 4 | PDF Full-text (296 KB) | HTML Full-text | XML Full-text | Supplementary Files
Abstract
Predicting antitumor activity of compounds using regression models trained on a small number of compounds with measured biological activity is an ill-posed inverse problem. Yet, it occurs very often within the academic community. To counteract, up to some extent, overfitting problems caused by
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Predicting antitumor activity of compounds using regression models trained on a small number of compounds with measured biological activity is an ill-posed inverse problem. Yet, it occurs very often within the academic community. To counteract, up to some extent, overfitting problems caused by a small training data, we propose to use consensus of six regression models for prediction of biological activity of virtual library of compounds. The QSAR descriptors of 22 compounds related to the opioid growth factor (OGF, Tyr-Gly-Gly-Phe-Met) with known antitumor activity were used to train regression models: the feed-forward artificial neural network, the k-nearest neighbor, sparseness constrained linear regression, the linear and nonlinear (with polynomial and Gaussian kernel) support vector machine. Regression models were applied on a virtual library of 429 compounds that resulted in six lists with candidate compounds ranked by predicted antitumor activity. The highly ranked candidate compounds were synthesized, characterized and tested for an antiproliferative activity. Some of prepared peptides showed more pronounced activity compared with the native OGF; however, they were less active than highly ranked compounds selected previously by the radial basis function support vector machine (RBF SVM) regression model. The ill-posedness of the related inverse problem causes unstable behavior of trained regression models on test data. These results point to high complexity of prediction based on the regression models trained on a small data sample. Full article
(This article belongs to the Section Physical Chemistry, Theoretical and Computational Chemistry)
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Open AccessArticle Transcriptomic Analysis in Diabetic Nephropathy of Streptozotocin-Induced Diabetic Rats
Int. J. Mol. Sci. 2011, 12(12), 8431-8448; doi:10.3390/ijms12128431
Received: 15 September 2011 / Revised: 12 November 2011 / Accepted: 14 November 2011 / Published: 29 November 2011
Cited by 6 | PDF Full-text (874 KB) | HTML Full-text | XML Full-text
Abstract
Diabetic nephropathy (DN) is a major complication of diabetes and is caused by an imbalance in the expression of certain genes that activate or inhibit vital cellular functions of kidney. Despite several recent advances, the pathogenesis of DN remains far from clear, suggesting
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Diabetic nephropathy (DN) is a major complication of diabetes and is caused by an imbalance in the expression of certain genes that activate or inhibit vital cellular functions of kidney. Despite several recent advances, the pathogenesis of DN remains far from clear, suggesting the need to carry out studies identifying molecular aspects, such as gene expression, that could play a key role in the development of DN. There are several techniques to analyze transcriptome in living organisms. In this study, the suppression subtractive hybridization (SSH) method was used to generate up- and down-regulated subtracted cDNA libraries in the kidney of streptozotocin (STZ)-induced diabetic rats. Northern-blot analysis was used to confirm differential expression ratios from the obtained SSH clones to identify genes related to DN. 400 unique SSH clones were randomly chosen from the two subtraction libraries (200 of each) and verified as differentially expressed. According to blast screening and functional annotation, 20.2% and 20.9% of genes were related to metabolism proteins, 9% and 3.6% to transporters and channels, 16% and 6.3% to transcription factors, 19% and 17.2% to hypothetical proteins, and finally 24.1 and 17.2% to unknown genes, from the down- and up-regulated libraries, respectively. The down- and up-regulated cDNA libraries differentially expressed in the kidney of STZ diabetic rats have been successfully constructed and some identified genes could be highly important in DN. Full article
(This article belongs to the Section Molecular Diagnostics)
Open AccessArticle A Comparative Study of the Second-Order Hydrophobic Moments for Globular Proteins: The Consensus Scale of Hydrophobicity and the CHARMM Partial Atomic Charges
Int. J. Mol. Sci. 2011, 12(12), 8449-8465; doi:10.3390/ijms12128449
Received: 15 September 2011 / Accepted: 15 November 2011 / Published: 29 November 2011
Cited by 3 | PDF Full-text (539 KB) | HTML Full-text | XML Full-text
Abstract
In this paper, the second-order hydrophobic moment for fifteen globular proteins in 150 nonhomologous protein chains was performed in a comparative study involving two sets of hydrophobicity: one selected from the consensus scale and the other derived from the CHARMM partial atomic charges.
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In this paper, the second-order hydrophobic moment for fifteen globular proteins in 150 nonhomologous protein chains was performed in a comparative study involving two sets of hydrophobicity: one selected from the consensus scale and the other derived from the CHARMM partial atomic charges. These proteins were divided into three groups, based on their number of residues (N) and the asphericity (δ). Proteins in Group I were spherical and those in Groups II and III were prolate. The size of the proteins is represented by the mean radius of gyration (Rg), which follows the Flory scaling law, Rg Nv. The mean value of v was 0.35, which is similar to a polymer chain in a poor solvent. The spatial distributions of the second-order moment for each of the proteins, obtained from the two sets of hydrophobicity, were compared using the Pearson correlation coefficient; the results reveal that there is a strong correlation between the two data sets for each protein structure when the CHARMM partial atomic charges, |qi|  ≥ 0.3, assigned for polar atoms, are used. The locations at which these distributions vanish and approach a negative value are at approximately 50% of the percentage of solvent accessibility, indicating that there is a transition point from hydrophobic interior to hydrophilic exterior in the proteins. This may suggest that there is a position for the proteins to determine the residues at exposed sites beyond this range. Full article
(This article belongs to the Section Biochemistry, Molecular Biology and Biophysics)
Open AccessArticle Dietary Lipoic Acid Influences Antioxidant Capability and Oxidative Status of Broilers
Int. J. Mol. Sci. 2011, 12(12), 8476-8488; doi:10.3390/ijms12128476
Received: 6 September 2011 / Revised: 5 November 2011 / Accepted: 14 November 2011 / Published: 29 November 2011
Cited by 17 | PDF Full-text (159 KB) | HTML Full-text | XML Full-text
Abstract
The effects of lipoic acid (LA) on the antioxidant status of broilers were investigated. Birds (1 day old) were randomly assigned to four groups and fed corn-soybean diets supplemented with 0, 100, 200, 300 mg/kg LA, respectively. The feeding program included a starter
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The effects of lipoic acid (LA) on the antioxidant status of broilers were investigated. Birds (1 day old) were randomly assigned to four groups and fed corn-soybean diets supplemented with 0, 100, 200, 300 mg/kg LA, respectively. The feeding program included a starter diet from 1 to 21 days of age and a grower diet from 22 to 42 days of age. Serum, liver and muscle samples were collected at 42 days of age. For antioxidant enzymes, superoxide dismutase (SOD) and glutathione peroxidase (GSH-Px) activity in serum, liver and breast muscle significantly increased in chickens fed with LA. The concentration of malondiadehyde (MDA), an indicator of lipid peroxidation, was significantly lower in serum, liver and leg muscle in birds that received LA than in the control group. Treatments with LA significantly increased glutathione (GSH) content in liver and increased α-tocopherol content in leg muscle as compared to the control. These results indicate that dietary supplementation with 300 mg/kg LA may enhance antioxidant capability and depress oxidative stress in broilers. Full article
(This article belongs to the Section Biochemistry, Molecular Biology and Biophysics)
Open AccessArticle Pilot Study: Alteration of Deleted in Liver Cancer1 and Phosphorylated Focal Adhesion Kinase Y397 Cytoplasmic Expression and the Prognostic Value in Advanced Epithelial Ovarian Carcinoma
Int. J. Mol. Sci. 2011, 12(12), 8489-8501; doi:10.3390/ijms12128489
Received: 9 October 2011 / Revised: 3 November 2011 / Accepted: 7 November 2011 / Published: 29 November 2011
Cited by 6 | PDF Full-text (867 KB) | HTML Full-text | XML Full-text
Abstract
Background: Deletion in liver cancer gene (DLC1) and phosphorylated focal adhesion kinase (p-FAK) have recently been reported as metastasis-related genes. However, the roles and prognostic values of their expression in epithelial ovarian carcinomas (EOCs) remain unclear. Methods: The expression and prognostic value of
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Background: Deletion in liver cancer gene (DLC1) and phosphorylated focal adhesion kinase (p-FAK) have recently been reported as metastasis-related genes. However, the roles and prognostic values of their expression in epithelial ovarian carcinomas (EOCs) remain unclear. Methods: The expression and prognostic value of DLC1 and p-FAK Y397 in EOC were evaluated by immunohistochemistry and multivariate analysis. Results: Low expression of DLC1 and high expression of p-FAK Y397 were found in the 76 cases of EOC. The expression of DLC1 and p-FAK Y397 were negatively correlated. Multivariate analysis showed that the combination of them was an independent prognostic marker of EOC (P = 0.0319). Conclusions: DLC1 and pFAK Y397 had an association with the clinicopathologic characteristics of EOC. Expression of neither of these genes was a prognostic factor alone, but the combination revealed a significant prognostic value in the 60 cases of advanced stage EOC. Full article
Open AccessArticle Effects of Soybean Agglutinin on Intestinal Barrier Permeability and Tight Junction Protein Expression in Weaned Piglets
Int. J. Mol. Sci. 2011, 12(12), 8502-8512; doi:10.3390/ijms12128502
Received: 8 October 2011 / Revised: 1 November 2011 / Accepted: 11 November 2011 / Published: 29 November 2011
Cited by 11 | PDF Full-text (844 KB) | HTML Full-text | XML Full-text
Abstract
This study was developed to provide further information on the intestinal barrier permeability and the tight junction protein expression in weaned piglets fed with different levels of soybean agglutinin (SBA). Twenty-five weaned crossbred barrows (Duroc × Landrace × Yorkshire) were selected and randomly
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This study was developed to provide further information on the intestinal barrier permeability and the tight junction protein expression in weaned piglets fed with different levels of soybean agglutinin (SBA). Twenty-five weaned crossbred barrows (Duroc × Landrace × Yorkshire) were selected and randomly allotted to five groups, each group with five replicates. The piglets in the control group were not fed with leguminous products. 0.05, 0.1, 0.15 and 0.2% SBA was added to the control diet to form four experimental diets, respectively. After the experimental period of 7 days (for each group), all the piglets were anesthetized with excess procaine and slaughtered. The D-lactic acid in plasma and the Ileal mucosa diamine oxidase (DAO) was analyzed to observe the change in the intestinal permeability. The tight junction proteins occludin and ZO-1 in the jejunum tissue distribution and relative expression were detected by immunohistochemistry and Western Blot. The results illustrated that a high dose of SBA (0.1–0.2%) could increase the intestinal permeability and reduce piglet intestinal epithelial tight junction protein occludin or ZO-1 expression, while low dose of SBA (0.05% of total diet) had no significant affects. The contents of DAO, D-lactic acid, occludin or ZO-1, had a linear relationship with the SBA levels (0–0.2%) in diets. The high dose SBA (0.1–0.2%) could increase the intestinal permeability and reduce piglet intestinal epithelial tight junction protein occludin or ZO-1 expression, while low dose of SBA (0.05% of total diet) had no affects. Full article
(This article belongs to the Section Biochemistry, Molecular Biology and Biophysics)
Open AccessArticle Caffeine Abolishes the Ultraviolet-Induced REV3 Translesion Replication Pathway in Mouse Cells
Int. J. Mol. Sci. 2011, 12(12), 8513-8529; doi:10.3390/ijms12128513
Received: 16 September 2011 / Revised: 8 November 2011 / Accepted: 17 November 2011 / Published: 29 November 2011
PDF Full-text (2108 KB) | HTML Full-text | XML Full-text
Abstract
When a replicative DNA polymerase stalls upon encountering a photoproduct on the template strand, it is relieved by other low-processivity polymerase(s), which insert nucleotide(s) opposite the lesion. Using an alkaline sucrose density gradient sedimentation technique, we previously classified this process termed UV-induced translesion
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When a replicative DNA polymerase stalls upon encountering a photoproduct on the template strand, it is relieved by other low-processivity polymerase(s), which insert nucleotide(s) opposite the lesion. Using an alkaline sucrose density gradient sedimentation technique, we previously classified this process termed UV-induced translesion replication (UV-TLS) into two types. In human cancer cells or xeroderma pigmentosum variant (XP-V) cells, UV-TLS was inhibited by caffeine or proteasome inhibitors. However, in normal human cells, the process was insensitive to these reagents. Reportedly, in yeast or mammalian cells, REV3 protein (a catalytic subunit of DNA polymerase ζ) is predominantly involved in the former type of TLS. Here, we studied UV-TLS in fibroblasts derived from the Rev3-knockout mouse embryo (Rev3KO-MEF). In the wild-type MEF, UV-TLS was slow (similar to that of human cancer cells or XP-V cells), and was abolished by caffeine or MG-262. In 2 cell lines of Rev3KO-MEF (Rev3−/− p53−/−), UV-TLS was not observed. In p53KO-MEF, which is a strict control for Rev3KO-MEF, the UV-TLS response was similar to that of the wild-type. Introduction of the Rev3 expression plasmid into Rev3KO-MEF restored the UV-TLS response in selected stable transformants. In some transformants, viability to UV was the same as that in the wild-type, and the death rate was increased by caffeine. Our findings indicate that REV3 is predominantly involved in UV-TLS in mouse cells, and that the REV3 translesion pathway is suppressed by caffeine or proteasome inhibitors. Full article
(This article belongs to the Special Issue UV-Induced Cell Death)
Open AccessArticle Biochip-Based Detection of KRAS Mutation in Non-Small Cell Lung Cancer
Int. J. Mol. Sci. 2011, 12(12), 8530-8538; doi:10.3390/ijms12128530
Received: 18 September 2011 / Revised: 17 November 2011 / Accepted: 17 November 2011 / Published: 29 November 2011
Cited by 3 | PDF Full-text (239 KB) | HTML Full-text | XML Full-text
Abstract
This study is aimed at evaluating the potential of a biochip assay to sensitively detect KRAS mutation in DNA from non-small cell lung cancer (NSCLC) tissue samples. The assay covers 10 mutations in codons 12 and 13 of the KRAS gene, and is
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This study is aimed at evaluating the potential of a biochip assay to sensitively detect KRAS mutation in DNA from non-small cell lung cancer (NSCLC) tissue samples. The assay covers 10 mutations in codons 12 and 13 of the KRAS gene, and is based on mutant-enriched PCR followed by reverse-hybridization of biotinylated amplification products to an array of sequence-specific probes immobilized on the tip of a rectangular plastic stick (biochip). Biochip hybridization identified 17 (21%) samples to carry a KRAS mutation of which 16 (33%) were adenocarcinomas and 1 (3%) was a squamous cell carcinoma. All mutations were confirmed by DNA sequencing. Using 10 ng of starting DNA, the biochip assay demonstrated a detection limit of 1% mutant sequence in a background of wild-type DNA. Our results suggest that the biochip assay is a sensitive alternative to protocols currently in use for KRAS mutation testing on limited quantity samples. Full article
(This article belongs to the Special Issue Advances in Molecular Diagnostics)
Open AccessArticle Insulin Like Growth Factor-1 (IGF-1) Causes Overproduction of IL-8, an Angiogenic Cytokine and Stimulates Neovascularization in Isoproterenol-Induced Myocardial Infarction in Rats
Int. J. Mol. Sci. 2011, 12(12), 8562-8574; doi:10.3390/ijms12128562
Received: 20 August 2011 / Revised: 18 October 2011 / Accepted: 20 October 2011 / Published: 29 November 2011
Cited by 5 | PDF Full-text (718 KB) | HTML Full-text | XML Full-text
Abstract
Angiogenesis factors are produced in response to hypoxic or ischemic insult at the site of pathology, which will cause neovascularization. Insulin like growth factor-1 (IGF-1) exerts potent proliferative, angiogenic and anti-apoptotic effects in target tissues. The present study was aimed to evaluate the
[...] Read more.
Angiogenesis factors are produced in response to hypoxic or ischemic insult at the site of pathology, which will cause neovascularization. Insulin like growth factor-1 (IGF-1) exerts potent proliferative, angiogenic and anti-apoptotic effects in target tissues. The present study was aimed to evaluate the effects of IGF-1 on circulating level of angiogenic cytokine interleukin-8 (IL-8), in experimentally-induced myocardial ischemia in rats. Male Sprague-Dawley rats were divided into control, IGF-1 treated (2 µg/kg/day subcutaneously, for 5 and 10 days), isoproterenol (ISO) treated (85 mg/kg, subcutaneously for two days) and ISO with IGF-1 treated (for 5 and 10 days). Heart weight, serum IGF-1, IL-8 and cardiac marker enzymes (CK-MB and LDH) were recorded after 5 and 10 days of treatment. Histopathological analyses of the myocardium were also done. There was a significant increase in serum cardiac markers with ISO treatment indicating myocardial infarction in rats. IGF-1 level increased significantly in ISO treated groups and the level of IGF-1 was significantly higher after 10 days of treatment. IL-8 level increased significantly after ISO treatment after 5 and 10 days and IGF-1 concurrent treatment to ISO rats had significantly increased IL-8 levels. Histopathologically, myocyte necrosis and nuclear pyknosis were reduced significantly in IGF-1 treated group and there were numerous areas of capillary sprouting suggestive of neovascularization in the myocardium. Thus, IGF-1 protects the ischemic myocardium with increased production of circulating angiogenic cytokine, IL-8 and increased angiogenesis. Full article
(This article belongs to the Section Biochemistry, Molecular Biology and Biophysics)
Open AccessArticle Comparative Study Using Different Infrared Zones of the Solventless Activation of Organic Reactions
Int. J. Mol. Sci. 2011, 12(12), 8575-8580; doi:10.3390/ijms12128575
Received: 18 October 2011 / Revised: 21 November 2011 / Accepted: 22 November 2011 / Published: 29 November 2011
Cited by 3 | PDF Full-text (194 KB) | HTML Full-text | XML Full-text
Abstract
In this work, the results of a study comparing the use of irradiation from different regions of the infrared spectrum for the promotion of several organic reactions, are presented and discussed. This use of eco-conditions provides a green approach to chemical synthesis. A
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In this work, the results of a study comparing the use of irradiation from different regions of the infrared spectrum for the promotion of several organic reactions, are presented and discussed. This use of eco-conditions provides a green approach to chemical synthesis. A set of ten different organic reactions were evaluated, including the Knoevenagel, Hantzsch, Biginelli and Meldrum reactions. It is important to highlight the use of a commercial device that produces infrared irradiation in the near infrared region and its distribution by convection providing heating uniformity, significantly reducing reaction times, achieving good yields and proceeding in the absence of solvent. It is also worth noting that a variety of different reactions may be performed at the same time. Finally, the products obtained were identified using TLC, together with corresponding MS-data, complementarily in comparison of NMR 1H and 13C data with literature information. Full article
(This article belongs to the Special Issue Advances in Green Chemistry and Sustainable Chemistry 2011)
Open AccessArticle Effects of Conjugated Linoleic Acid, Fish Oil and Soybean Oil on PPARs (α & γ) mRNA Expression in Broiler Chickens and Their Relation to Body Fat Deposits
Int. J. Mol. Sci. 2011, 12(12), 8581-8595; doi:10.3390/ijms12128581
Received: 1 September 2011 / Revised: 23 September 2011 / Accepted: 1 November 2011 / Published: 29 November 2011
Cited by 8 | PDF Full-text (295 KB) | HTML Full-text | XML Full-text
Abstract
An experiment was conducted on broiler chickens to study the effects of different dietary fats (Conjugated linoleic acid (CLA), fish oil, soybean oil, or their mixtures, as well as palm oil, as a more saturated fat), with a as fed dose of 7%
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An experiment was conducted on broiler chickens to study the effects of different dietary fats (Conjugated linoleic acid (CLA), fish oil, soybean oil, or their mixtures, as well as palm oil, as a more saturated fat), with a as fed dose of 7% for single fat and 3.5 + 3.5% for the mixtures, on Peroxisome Proliferator-Activated Receptors (PPARs) gene expression and its relation with body fat deposits. The CLA used in this experiment was CLA LUTA60 which contained 60% CLA, so 7% and 3.5% dietary inclusions of CLA LUTA60 were equal to 4.2% and 2.1% CLA, respectively. Higher abdominal fat pad was found in broiler chickens fed with a diet containing palm oil compared to chickens in the other experimental groups (P ≤ 0.05). The diets containing CLA resulted in an increased fat deposition in the liver of broiler chickens (P ≤ 0.05). The only exception was related to the birds fed with diets containing palm oil or fish oil + soybean oil, where contents of liver fat were compared to the CLA + fish oil treatment. PPARγ gene in adipose tissue of chickens fed with palm oil diet was up-regulated compared to other treatments (P ≤ 0.001), whereas no significant differences were found in adipose PPARγ gene expression between chickens fed with diets containing CLA, fish oil, soybean oil or the mixture of these fats. On the other hand, the PPARα gene expression in liver tissue was up-regulated in response to the dietary fish oil inclusion and the differences were also significant for both fish oil and CLA + fish oil diets compared to the diets with palm oil, soybean oil or CLA as the only oil source (P ≤ 0.001). In conclusion, the results of present study showed that there was a relationship between the adipose PPARγ gene up-regulation and abdominal fat pad deposition for birds fed with palm oil diet, while no deference was detected in n-3 and n-6 fatty acids, as well as CLA on PPARγ down regulation in comparison to a more saturated fat. When used on its own, fish oil was found to be a more effective fat in up-regulating hepatic PPARα gene expression and this effect was related to a less fat deposition in liver tissue. A negative correlation coefficient (−0.3) between PPARα relative gene expression and liver tissue fat content confirm the anti-lipogenic effect of PPARα, however, the change in these parameters was not completely parallel. Full article
(This article belongs to the Section Biochemistry, Molecular Biology and Biophysics)
Open AccessArticle Bioactive Compounds, Antioxidant, Xanthine Oxidase Inhibitory, Tyrosinase Inhibitory and Anti-Inflammatory Activities of Selected Agro-Industrial By-products
Int. J. Mol. Sci. 2011, 12(12), 8610-8625; doi:10.3390/ijms12128610
Received: 10 October 2011 / Revised: 6 November 2011 / Accepted: 8 November 2011 / Published: 29 November 2011
Cited by 17 | PDF Full-text (215 KB) | HTML Full-text | XML Full-text
Abstract
Evaluation of abundantly available agro-industrial by-products for their bioactive compounds and biological activities is beneficial in particular for the food and pharmaceutical industries. In this study, rapeseed meal, cottonseed meal and soybean meal were investigated for the presence of bioactive compounds and antioxidant,
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Evaluation of abundantly available agro-industrial by-products for their bioactive compounds and biological activities is beneficial in particular for the food and pharmaceutical industries. In this study, rapeseed meal, cottonseed meal and soybean meal were investigated for the presence of bioactive compounds and antioxidant, anti-inflammatory, xanthine oxidase and tyrosinase inhibitory activities. Methanolic extracts of rapeseed meal showed significantly (P < 0.01) higher phenolics and flavonoids contents; and significantly (P < 0.01) higher DPPH and nitric oxide free radical scavenging activities when compared to that of cottonseed meal and soybean meal extracts. Ferric thiocyanate and thiobarbituric acid tests results showed rapeseed meal with the highest antioxidant activity (P < 0.01) followed by BHT, cotton seed meal and soybean meal. Rapeseed meal extract in xanthine oxidase and tyrosinase inhibitory assays showed the lowest  IC50 values  followed by cottonseed and soybean meals. Anti-inflammatory assay using IFN-γ/LPS stimulated RAW 264.7 cells indicated rapeseed meal is a potent source of anti-inflammatory agent. Correlation analysis showed that phenolics and flavonoids were highly correlated to both antioxidant and anti-inflammatory activities. Rapeseed meal was found to be promising as a natural source of bioactive compounds with high antioxidant, anti-inflammatory, xanthine oxidase and tyrosinase inhibitory activities in contrast to cotton and soybean meals. Full article
(This article belongs to the Section Biochemistry, Molecular Biology and Biophysics)
Open AccessArticle Validation of Quantitative Structure-Activity Relationship (QSAR) Model for Photosensitizer Activity Prediction
Int. J. Mol. Sci. 2011, 12(12), 8626-8644; doi:10.3390/ijms12128626
Received: 19 August 2011 / Revised: 2 November 2011 / Accepted: 15 November 2011 / Published: 29 November 2011
Cited by 10 | PDF Full-text (215 KB) | HTML Full-text | XML Full-text
Abstract
Photodynamic therapy is a relatively new treatment method for cancer which utilizes a combination of oxygen, a photosensitizer and light to generate reactive singlet oxygen that eradicates tumors via direct cell-killing, vasculature damage and engagement of the immune system. Most of photosensitizers that
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Photodynamic therapy is a relatively new treatment method for cancer which utilizes a combination of oxygen, a photosensitizer and light to generate reactive singlet oxygen that eradicates tumors via direct cell-killing, vasculature damage and engagement of the immune system. Most of photosensitizers that are in clinical and pre-clinical assessments, or those that are already approved for clinical use, are mainly based on cyclic tetrapyrroles. In an attempt to discover new effective photosensitizers, we report the use of the quantitative structure-activity relationship (QSAR) method to develop a model that could correlate the structural features of cyclic tetrapyrrole-based compounds with their photodynamic therapy (PDT) activity. In this study, a set of 36 porphyrin derivatives was used in the model development where 24 of these compounds were in the training set and the remaining 12 compounds were in the test set. The development of the QSAR model involved the use of the multiple linear regression analysis (MLRA) method. Based on the method, r2 value, r2 (CV) value and r2 prediction value of 0.87, 0.71 and 0.70 were obtained. The QSAR model was also employed to predict the experimental compounds in an external test set. This external test set comprises 20 porphyrin-based compounds with experimental IC50 values ranging from 0.39 µM to 7.04 µM. Thus the model showed good correlative and predictive ability, with a predictive correlation coefficient (r2 prediction for external test set) of 0.52. The developed QSAR model was used to discover some compounds as new lead photosensitizers from this external test set. Full article
(This article belongs to the Section Physical Chemistry, Theoretical and Computational Chemistry)
Open AccessArticle Effects of Newcastle Disease Virus Strains AF2240 and V4-UPM on Cytolysis and Apoptosis of Leukemia Cell Lines
Int. J. Mol. Sci. 2011, 12(12), 8645-8660; doi:10.3390/ijms12128645
Received: 14 September 2011 / Revised: 14 November 2011 / Accepted: 15 November 2011 / Published: 30 November 2011
Cited by 10 | PDF Full-text (410 KB) | HTML Full-text | XML Full-text
Abstract
Newcastle disease virus (NDV) is used as an antineoplastic agent in clinical tumor therapy. It has prompted much interest as an anticancer agent because it can replicate up to 10,000 times better in human cancer cells than in most normal cells. This study
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Newcastle disease virus (NDV) is used as an antineoplastic agent in clinical tumor therapy. It has prompted much interest as an anticancer agent because it can replicate up to 10,000 times better in human cancer cells than in most normal cells. This study was carried out to determine the oncolytic potential of NDV strain AF2240 and V4-UPM on WEHI-3B leukemia cell line. Results from MTT cytotoxicity assay showed that the CD50 values for both strains were 2 and 8 HAU for AF2240 and V4-UPM, respectively. In addition, bromodeoxyuridine (BrdU) and trypan blue dye exclusion assays showed inhibition in cell proliferation after different periods. Increase in the cellular level of caspase-3 and detection of DNA laddering using agarose gel electrophoresis on treated cells with NDV confirmed that the mode of cell death was apoptosis. In addition, flow-cytometry analysis of cellular DNA content showed that the virus caused an increase in the sub-G1 region (apoptosis peaks). In conclusion, NDV strains AF2240 and V4-UPM caused cytolytic effects against WEHI-3B leukemic cell line. Full article
(This article belongs to the Section Biochemistry, Molecular Biology and Biophysics)
Open AccessArticle Genetic Association and Altered Gene Expression of Mir-155 in Multiple Sclerosis Patients
Int. J. Mol. Sci. 2011, 12(12), 8695-8712; doi:10.3390/ijms12128695
Received: 19 September 2011 / Revised: 31 October 2011 / Accepted: 22 November 2011 / Published: 1 December 2011
Cited by 39 | PDF Full-text (423 KB) | HTML Full-text | XML Full-text
Abstract
Multiple sclerosis (MS) is a complex autoimmune disease of the central nervous system characterized by chronic inflammation, demyelination, and axonal damage. As microRNA (miRNA)-dependent alterations in gene expression in hematopoietic cells are critical for mounting an appropriate immune response, miRNA deregulation may result
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Multiple sclerosis (MS) is a complex autoimmune disease of the central nervous system characterized by chronic inflammation, demyelination, and axonal damage. As microRNA (miRNA)-dependent alterations in gene expression in hematopoietic cells are critical for mounting an appropriate immune response, miRNA deregulation may result in defects in immune tolerance. In this frame, we sought to explore the possible involvement of miRNAs in MS pathogenesis by monitoring the differential expression of 22 immunity-related miRNAs in peripheral blood mononuclear cells of MS patients and healthy controls, by using a microbead-based technology. Three miRNAs resulted >2 folds up-regulated in MS vs controls, whereas none resulted down-regulated. Interestingly, the most up-regulated miRNA (mir-155; fold change = 3.30; P = 0.013) was previously reported to be up-regulated also in MS brain lesions. Mir-155 up-regulation was confirmed by qPCR experiments. The role of mir-155 in MS susceptibility was also investigated by genotyping four single nucleotide polymorphisms (SNPs) mapping in the mir-155 genomic region. A haplotype of three SNPs, corresponding to a 12-kb region encompassing the last exon of BIC (the B-cell Integration Cluster non-coding RNA, from which mir-155 is processed), resulted associated with the disease status (P = 0.035; OR = 1.36, 95% CI = 1.05–1.77), suggesting that this locus strongly deserves further investigations. Full article
(This article belongs to the Special Issue Non-Coding RNAs)
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Open AccessArticle Combined Pharmacophore Modeling, Docking, and 3D-QSAR Studies of PLK1 Inhibitors
Int. J. Mol. Sci. 2011, 12(12), 8713-8739; doi:10.3390/ijms12128713
Received: 4 September 2011 / Revised: 1 November 2011 / Accepted: 21 November 2011 / Published: 1 December 2011
Cited by 7 | PDF Full-text (1112 KB) | HTML Full-text | XML Full-text
Abstract
Polo-like kinase 1, an important enzyme with diverse biological actions in cell mitosis, is a promising target for developing novel anticancer drugs. A combined molecular docking, structure-based pharmacophore modeling and three-dimensional quantitative structure-activity relationship (3D-QSAR) study was performed on a set of 4,5-dihydro-1
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Polo-like kinase 1, an important enzyme with diverse biological actions in cell mitosis, is a promising target for developing novel anticancer drugs. A combined molecular docking, structure-based pharmacophore modeling and three-dimensional quantitative structure-activity relationship (3D-QSAR) study was performed on a set of 4,5-dihydro-1H-pyrazolo[4,3-h]quinazoline derivatives as PLK1 inhibitors. The common substructure, molecular docking and pharmacophore-based alignment were used to develop different 3D-QSAR models. The comparative molecular field analysis (CoMFA) and comparative molecule similarity indices analysis (CoMSIA) models gave statistically significant results. These models showed good q2 and r2pred values and revealed a good response to test set validation. All of the structural insights obtained from the 3D-QSAR contour maps are consistent with the available crystal structure of PLK1. The contour maps obtained from the 3D-QSAR models in combination with the structure based pharmacophore model help to better interpret the structure-activity relationship. These satisfactory results may aid the design of novel PLK1 inhibitors. This is the first report on 3D-QSAR study of PLK1 inhibitors. Full article
(This article belongs to the Section Physical Chemistry, Theoretical and Computational Chemistry)
Open AccessArticle Chromatographic Fingerprint and the Simultaneous Determination of Five Bioactive Components of Geranium carolinianum L. Water Extract by High Performance Liquid Chromatography
Int. J. Mol. Sci. 2011, 12(12), 8740-8749; doi:10.3390/ijms12128740
Received: 10 October 2011 / Revised: 5 November 2011 / Accepted: 18 November 2011 / Published: 2 December 2011
Cited by 14 | PDF Full-text (399 KB) | HTML Full-text | XML Full-text
Abstract
A simple and sensitive HPLC method has been developed in combination with fingerprint analysis and simultaneous determination of five markers, namely gallic acid, corilagin, methyl brevifolincarboxylate, ellagic acid and rutin for evaluation and quality control of Geranium carolinianum L. water extract. Extraction methods
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A simple and sensitive HPLC method has been developed in combination with fingerprint analysis and simultaneous determination of five markers, namely gallic acid, corilagin, methyl brevifolincarboxylate, ellagic acid and rutin for evaluation and quality control of Geranium carolinianum L. water extract. Extraction methods were optimized by comparing the hydrolysis efficiency of geraniin, a major tannin of the herb, resulting in the method of extraction with water under reflux. Water extracts were analyzed by HPLC, with a mobile phase of 0.1% aqueous phosphoric acid (v/v) and acetonitrile in a gradient program within 65 min. Compounds were detected at 274 nm UV wavelength. For fingerprint analysis, 17 peaks were selected as the characteristic peaks to evaluate the similarities of different samples collected from the suburb of Nanjing. The correlation coefficients of similarity were greater than 0.993. In quantitative analysis, the five selected markers showed good regression (R > 0.9991) within test ranges, and the average recoveries were between 97.2–101.7% and their RSD values were less than 4.50%. The total contents of the five markers varied from 44.28 to 71.84 mg/g. The method can be very useful for further development of G. carolinianum L. extracts and preparations. Full article
Open AccessArticle Physicochemical Properties of Glycine-Based Ionic Liquid [QuatGly-OEt][EtOSO3] (2-Ethoxy-1-ethyl-1,1-dimethyl-2-oxoethanaminium ethyl sulfate) and Its Binary Mixtures with Poly(ethylene glycol) (Mw = 200) at Various Temperatures
Int. J. Mol. Sci. 2011, 12(12), 8750-8772; doi:10.3390/ijms12128750
Received: 1 September 2011 / Revised: 24 October 2011 / Accepted: 16 November 2011 / Published: 2 December 2011
Cited by 13 | PDF Full-text (516 KB) | HTML Full-text | XML Full-text
Abstract
This work includes specific basic characterization of synthesized glycine-based Ionic Liquid (IL) [QuatGly-OEt][EtOSO3] by NMR, elementary analysis and water content. Thermophysical properties such as density, ρ, viscosity, η, refractive index, n, and conductivity, κ, for the binary mixture of [QuatGly-OEt][EtOSO
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This work includes specific basic characterization of synthesized glycine-based Ionic Liquid (IL) [QuatGly-OEt][EtOSO3] by NMR, elementary analysis and water content. Thermophysical properties such as density, ρ, viscosity, η, refractive index, n, and conductivity, κ, for the binary mixture of [QuatGly-OEt][EtOSO3] with poly(ethylene glycol) (PEG) [Mw = 200] are measured over the whole composition range. The temperature dependence of density and dynamic viscosity for neat [QuatGly-OEt][EtOSO3] and its binary mixture can be described by an empirical polynomial equation and by the Vogel-Tammann-Fucher (VTF) equation, respectively. The thermal expansion coefficient of the ILs is ascertained using the experimental density results, and the excess volume expansivity is evaluated. The negative values of excess molar volume for the mixture indicate the ion-dipole interactions and packing between IL and PEG oligomer. The results of binary excess property (VmE) and deviations (Δη, ∆xn, ∆Фn, ∆xR, and ∆ФR) are discussed in terms of molecular interactions and molecular structures in the binary mixture. Full article
(This article belongs to the Section Physical Chemistry, Theoretical and Computational Chemistry)
Open AccessArticle Scoring Function Based on Weighted Residue Network
Int. J. Mol. Sci. 2011, 12(12), 8773-8786; doi:10.3390/ijms12128773
Received: 27 September 2011 / Revised: 4 November 2011 / Accepted: 28 November 2011 / Published: 2 December 2011
Cited by 6 | PDF Full-text (378 KB) | HTML Full-text | XML Full-text
Abstract
Molecular docking is an important method for the research of protein-protein interaction and recognition. A protein can be considered as a network when the residues are treated as its nodes. With the contact energy between residues as link weight, a weighted residue network
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Molecular docking is an important method for the research of protein-protein interaction and recognition. A protein can be considered as a network when the residues are treated as its nodes. With the contact energy between residues as link weight, a weighted residue network is constructed in this paper. Two weighted parameters (strength and weighted average nearest neighbors’ degree) are introduced into this model at the same time. The stability of a protein is characterized by its strength. The global topological properties of the protein-protein complex are reflected by the weighted average nearest neighbors’ degree. Based on this weighted network model and these two parameters, a new docking scoring function is proposed in this paper. The scoring and ranking for 42 systems’ bound and unbounded docking results are performed with this new scoring function. Comparing the results obtained from this new scoring function with that from the pair potentials scoring function, we found that this new scoring function has a similar performance to the pair potentials on some items, and this new scoring function can get a better success rate. The calculation of this new scoring function is easy, and the result of its scoring and ranking is acceptable. This work can help us better understand the mechanisms of protein-protein interactions and recognition. Full article
(This article belongs to the Section Physical Chemistry, Theoretical and Computational Chemistry)
Open AccessCommunication Melanogenesis Inhibitory Activity of Two Generic Drugs: Cinnarizine and Trazodone in Mouse B16 Melanoma Cells
Int. J. Mol. Sci. 2011, 12(12), 8787-8796; doi:10.3390/ijms12128787
Received: 21 October 2011 / Revised: 26 November 2011 / Accepted: 28 November 2011 / Published: 2 December 2011
Cited by 2 | PDF Full-text (270 KB) | HTML Full-text | XML Full-text
Abstract
More than 200 generic drugs were screened to identify the inhibitory activity on melanogenesis in mouse B16 melanoma cells. Cinnarizine and trazodone were identified as melanogenesis inhibitors. The inhibitory effects of the two drugs on cell survival, melanogenesis, and tyrosinase activity were investigated.
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More than 200 generic drugs were screened to identify the inhibitory activity on melanogenesis in mouse B16 melanoma cells. Cinnarizine and trazodone were identified as melanogenesis inhibitors. The inhibitory effects of the two drugs on cell survival, melanogenesis, and tyrosinase activity were investigated. The results showed that both cinnarizine and trazodone inhibited melanogenesis in B16 cells by a dose-dependent manner at the non-cytotoxic concentrations. Based on the results of the present study, seeking new melanogenesis inhibitors from generic drugs is an alternative approach to developing new depigmenting agents in cosmeceuticals. Moreover, cinnarizine and trazodone were proven to be good candidates as skin-whitening agents for treatment of skin hyperpigmentation. Full article
(This article belongs to the Section Biochemistry, Molecular Biology and Biophysics)
Open AccessArticle The Effect of Raw Soybean on Oxidative Status of Digestive Organs in Mice
Int. J. Mol. Sci. 2011, 12(12), 8836-8845; doi:10.3390/ijms12128836
Received: 23 October 2011 / Revised: 10 November 2011 / Accepted: 21 November 2011 / Published: 2 December 2011
Cited by 5 | PDF Full-text (106 KB) | HTML Full-text | XML Full-text
Abstract
The present study was undertaken to specify the effect of raw soybean on oxidative status of digestive organs in mice. For this purpose, thirty male (C57BL/6J) mice were randomly divided into three groups and fed on different diets as follows: Group 1 was
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The present study was undertaken to specify the effect of raw soybean on oxidative status of digestive organs in mice. For this purpose, thirty male (C57BL/6J) mice were randomly divided into three groups and fed on different diets as follows: Group 1 was fed on control diet, Group 2 was fed on raw soybean diet and Group 3 was fed on raw soybean diet supplemented with 30 mg/kg cysteamine. After two weeks of feeding, duodenum, liver and pancreas samples were collected to measure oxidative and antioxidative parameters. The results show that ingestion of raw soybean markedly increased contents of superoxide anion and malondialdehyde (MDA) and activity of inducible nitric oxide synthase (iNOS), decreased activity of superoxide dismutase (SOD), T-AOC and content of reduced glutathione (GSH) in digestive organs of mice (P < 0.05). In the group fed with raw soybean diet supplemented with cysteamine, oxidative stress was mitigated. However, oxidative parameter levels were still higher than those of control diet-fed group. The present study indicates that ingestion of raw soybean could result in an imbalance between oxidant and antioxidant, and thus induce oxidative stress in digestive organs of mice. Full article
(This article belongs to the Section Biochemistry, Molecular Biology and Biophysics)
Open AccessArticle Compositional Studies: Antioxidant and Antidiabetic Activities of Capparis decidua (Forsk.) Edgew
Int. J. Mol. Sci. 2011, 12(12), 8846-8861; doi:10.3390/ijms12128846
Received: 25 October 2011 / Revised: 7 November 2011 / Accepted: 14 November 2011 / Published: 5 December 2011
Cited by 35 | PDF Full-text (212 KB) | HTML Full-text | XML Full-text
Abstract
Capparis decidua is one of the traditional remedies used for various medicinal treatments in Pakistan. This study presents the determination of proximate composition, amino acids, fatty acids, tocopherols, sterols, glucosinolate and phenolic content in extracts obtained from different aerial parts of C. decidua
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Capparis decidua is one of the traditional remedies used for various medicinal treatments in Pakistan. This study presents the determination of proximate composition, amino acids, fatty acids, tocopherols, sterols, glucosinolate and phenolic content in extracts obtained from different aerial parts of C. decidua, as well as their antidiabetic and antioxidant activity. All examined extracts were prominently rich in phenolics and glucosinates, and they showed potent antidiabetic and antihemolytic activity. The present study could be helpful in developing medicinal preparations for the treatment of diabetes and related symptoms. Full article
(This article belongs to the Section Biochemistry, Molecular Biology and Biophysics)
Open AccessArticle 3D-QSPR Method of Computational Technique Applied on Red Reactive Dyes by Using CoMFA Strategy
Int. J. Mol. Sci. 2011, 12(12), 8862-8877; doi:10.3390/ijms12128862
Received: 14 September 2011 / Revised: 31 October 2011 / Accepted: 15 November 2011 / Published: 5 December 2011
Cited by 3 | PDF Full-text (426 KB) | HTML Full-text | XML Full-text
Abstract
Cellulose fiber is a tremendous natural resource that has broad application in various productions including the textile industry. The dyes, which are commonly used for cellulose printing, are “reactive dyes” because of their high wet fastness and brilliant colors. The interaction of various
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Cellulose fiber is a tremendous natural resource that has broad application in various productions including the textile industry. The dyes, which are commonly used for cellulose printing, are “reactive dyes” because of their high wet fastness and brilliant colors. The interaction of various dyes with the cellulose fiber depends upon the physiochemical properties that are governed by specific features of the dye molecule. The binding pattern of the reactive dye with cellulose fiber is called the ligand-receptor concept. In the current study, the three dimensional quantitative structure property relationship (3D-QSPR) technique was applied to understand the red reactive dyes interactions with the cellulose by the Comparative Molecular Field Analysis (CoMFA) method. This method was successfully utilized to predict a reliable model. The predicted model gives satisfactory statistical results and in the light of these, it was further analyzed. Additionally, the graphical outcomes (contour maps) help us to understand the modification pattern and to correlate the structural changes with respect to the absorptivity. Furthermore, the final selected model has potential to assist in understanding the charachteristics of the external test set. The study could be helpful to design new reactive dyes with better affinity and selectivity for the cellulose fiber. Full article
(This article belongs to the Section Physical Chemistry, Theoretical and Computational Chemistry)
Open AccessArticle Increased Glutathione Synthesis Following Nrf2 Activation by Vanadyl Sulfate in Human Chang Liver Cells
Int. J. Mol. Sci. 2011, 12(12), 8878-8894; doi:10.3390/ijms12128878
Received: 1 September 2011 / Revised: 3 November 2011 / Accepted: 21 November 2011 / Published: 5 December 2011
Cited by 5 | PDF Full-text (1504 KB) | HTML Full-text | XML Full-text
Abstract
Jeju ground water, containing vanadium compounds, was shown to increase glutathione (GSH) levels as determined by a colorimetric assay and confocal microscopy. To investigate whether the effects of Jeju ground water on GSH were specifically mediated by vanadium compounds, human Chang liver cells
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Jeju ground water, containing vanadium compounds, was shown to increase glutathione (GSH) levels as determined by a colorimetric assay and confocal microscopy. To investigate whether the effects of Jeju ground water on GSH were specifically mediated by vanadium compounds, human Chang liver cells were incubated for 10 passages in media containing deionized distilled water (DDW), Jeju ground water (S1 and S3), and vanadyl sulfate (VOSO4). Vanadyl sulfate scavenged superoxide anion, hydroxyl radical and intracellular reactive oxygen species. Vanadyl sulfate effectively increased cellular GSH level and up-regulated mRNA and protein expression of a catalytic subunit of glutamate cysteine ligase (GCLC), which is involved in GSH synthesis. The induction of GCLC expression by vanadyl sulfate was found to be mediated by transcription factor erythroid transcription factor NF-E2 (Nrf2), which critically regulates GCLC by binding to the antioxidant response elements (AREs). Vanadyl sulfate treatment increased the nuclear translocation of Nrf2 and the accumulation of phosphorylated Nrf2. Extracellular regulated kinase (ERK) contributed to ARE-driven GCLC expression via Nrf2 activation. Vanadyl sulfate induced the expression of the active phospho form of ERK. Taken together, these results suggest that the increase in GSH level by Jeju ground water is, at least in part, due to the effects of vanadyl sulfate via the Nrf2-mediated induction of GCLC. Full article
(This article belongs to the Section Biochemistry, Molecular Biology and Biophysics)
Open AccessArticle Spectroscopic Study of Solvent Effects on the Electronic Absorption Spectra of Flavone and 7-Hydroxyflavone in Neat and Binary Solvent Mixtures
Int. J. Mol. Sci. 2011, 12(12), 8895-8912; doi:10.3390/ijms12128895
Received: 6 September 2011 / Revised: 5 November 2011 / Accepted: 14 November 2011 / Published: 5 December 2011
Cited by 15 | PDF Full-text (764 KB) | HTML Full-text | XML Full-text | Supplementary Files
Abstract
The solvatochromic characteristics of flavone and 7-hydroxyflavone were investigated in neat and binary solvent mixtures. The spectral shifts of these solutes were correlated with the Kamlet and Taft parameters (α, β and π*) using linear solvation energy relationships. The multiparametric analysis indicates that
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The solvatochromic characteristics of flavone and 7-hydroxyflavone were investigated in neat and binary solvent mixtures. The spectral shifts of these solutes were correlated with the Kamlet and Taft parameters (α, β and π*) using linear solvation energy relationships. The multiparametric analysis indicates that both specific hydrogen bond donor ability and non-specific dipolar interactions of the solvents play an important role in absorption maxima of flavone in pure solvents. The hydrogen bond acceptor ability of the solvent was the main parameter affecting the absorption maxima of 7-hydroxyflavone. The simulated absorption spectra using a TD-DFT method were in good agreement with the experimental ones for both flavones. Index of preferential solvation was calculated as a function of solvent composition. Preferential solvation by ethanol was detected in cyclohexane-ethanol and acetonitrile-ethanol mixtures for flavone and in acetonitrile-ethanol mixtures for 7-hydroxyflavone. These results indicate that intermolecular hydrogen bonds between solute and solvent are responsible for the non-linear variation of the solvatochromic shifts on the mole fraction of ethanol in the analyzed binary mixtures. Full article
(This article belongs to the Special Issue Advances in Molecular Electronic Structure Calculations)
Open AccessArticle Production and Radioprotective Effects of Pyrroloquinoline Quinone
Int. J. Mol. Sci. 2011, 12(12), 8913-8923; doi:10.3390/ijms12128913
Received: 28 October 2011 / Revised: 22 November 2011 / Accepted: 24 November 2011 / Published: 5 December 2011
Cited by 9 | PDF Full-text (144 KB) | HTML Full-text | XML Full-text
Abstract
Pyrroloquinoline quinone (PQQ) was produced by fermentation of the Methylovorus sp. MP688 strain and purified by ion-exchange chromatography, crystallization and recrystallization. The yield of PQQ reached approximately 125 mg/L and highly pure PQQ was obtained. To determine the optimum dose of PQQ
[...] Read more.
Pyrroloquinoline quinone (PQQ) was produced by fermentation of the Methylovorus sp. MP688 strain and purified by ion-exchange chromatography, crystallization and recrystallization. The yield of PQQ reached approximately 125 mg/L and highly pure PQQ was obtained. To determine the optimum dose of PQQ for radioprotection, three doses (2 mg/kg, 4 mg/kg, 8 mg/kg) of PQQ were orally administrated to the experimental animals subjected to a lethal dose of 8.0 Gy in survival test. Survival of mice in the irradiation + PQQ (4 mg/kg) group was found to be significantly higher in comparison with the irradiation and irradiation + nilestriol (10 mg/kg) groups. The numbers of hematocytes and bone marrow cells were measured for 21 days after sublethal 4 Gy gamma-ray irradiation with per os of 4 mg/kg of PQQ. The recovery of white blood cells, reticulocytes and bone marrow cells in the irradiation + PQQ group was faster than that in the irradiation group. Furthermore, the recovery of bone marrow cell in the irradiation + PQQ group was superior to that in irradiation + nilestriol group. Our results clearly indicate favourable effects on survival under higher lethal radiation doses and the ability of pyrroloquinoline quinine to enhance haemopoietic recovery after sublethal radiation exposure. Full article
(This article belongs to the Section Biochemistry, Molecular Biology and Biophysics)
Open AccessArticle Structural Requirements of N-Substituted Spiropiperidine Analogues as Agonists of Nociceptin/Orphanin FQ Receptor
Int. J. Mol. Sci. 2011, 12(12), 8961-8981; doi:10.3390/ijms12128961
Received: 14 September 2011 / Revised: 10 November 2011 / Accepted: 21 November 2011 / Published: 6 December 2011
Cited by 3 | PDF Full-text (1334 KB) | HTML Full-text | XML Full-text | Supplementary Files
Abstract
The nociceptin/orphanin FQ (NOP) receptor is involved in a wide range of biological functions, including pain, anxiety, depression and drug abuse. Especially, its agonists have great potential to be developed into anxiolytics. In this work, both the ligand- and receptor-based three-dimensional quantitative structure–activity
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The nociceptin/orphanin FQ (NOP) receptor is involved in a wide range of biological functions, including pain, anxiety, depression and drug abuse. Especially, its agonists have great potential to be developed into anxiolytics. In this work, both the ligand- and receptor-based three-dimensional quantitative structure–activity relationship (3D-QSAR) studies were carried out using comparative molecular field analysis (CoMFA) and comparative molecular similarity indices analysis (CoMSIA) techniques on 103 N-substituted spiropiperidine analogues as NOP agonists. The resultant optimal ligand-based CoMSIA model exhibited Q2 of 0.501, R2ncv of 0.912 and its predictive ability was validated by using an independent test set of 26 compounds which gave R2pred value of 0.818. In addition, docking analysis and molecular dynamics simulation (MD) were also applied to elucidate the probable binding modes of these agonists. Interpretation of the 3D contour maps, in the context of the topology of the active site of NOP, provided insight into the NOP-agonist interactions. The information obtained from this work can be used to accurately predict the binding affinity of related agonists and also facilitate the future rational design of novel agonists with improved activity. Full article
(This article belongs to the Section Physical Chemistry, Theoretical and Computational Chemistry)
Open AccessArticle Lycium barbarum Polysaccharides Attenuate Cisplatin-Induced Hair Cell Loss in Rat Cochlear Organotypic Cultures
Int. J. Mol. Sci. 2011, 12(12), 8982-8992; doi:10.3390/ijms12128982
Received: 29 September 2011 / Revised: 6 November 2011 / Accepted: 25 November 2011 / Published: 6 December 2011
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Abstract
The aim of the present study was to investigate the effects of Lycium barbarum polysaccharides (LBP) on cisplatin-induced hair cell damage in the organ of Corti explant. The neonatal (P2-3) rat organ of Corti explant was exposed to cisplatin (20 μM; 48 h)
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The aim of the present study was to investigate the effects of Lycium barbarum polysaccharides (LBP) on cisplatin-induced hair cell damage in the organ of Corti explant. The neonatal (P2-3) rat organ of Corti explant was exposed to cisplatin (20 μM; 48 h) with or without LBP pretreatment (150 and 600 μg/mL; 24 h). Hair cell loss was indicated by FITC-labeled phalloidin staining. The level of reactive oxygen species (ROS) and alteration of mitochondrial membrane potential (ΔΨm) in hair cells were analyzed using fluorescent probes 2′,7′-dichlorofluorescein diacetate and JC-1, respectively. The results showed that LBP significantly attenuated hair cell loss (p < 0.01). Hair cells pretreated with LBP showed significant reduction in ROS production and the decline of ΔΨm compared with cisplatin alone group (p < 0.01), indicating the protective effect of LBP on cisplatin-induced hair cell loss. Taken together, these results indicate that LBP was effective in attenuating cisplatin-induced hair cell loss by reducing the production of ROS and maintaining mitochondrial ΔΨm. Full article
(This article belongs to the Section Biochemistry, Molecular Biology and Biophysics)
Open AccessArticle New Approaches to Clarify Antinociceptive and Anti-Inflammatory Effects of the Ethanol Extract from Vernonia condensata Leaves
Int. J. Mol. Sci. 2011, 12(12), 8993-9008; doi:10.3390/ijms12128993
Received: 14 October 2011 / Revised: 8 November 2011 / Accepted: 23 November 2011 / Published: 7 December 2011
Cited by 9 | PDF Full-text (248 KB) | HTML Full-text | XML Full-text
Abstract
The present study was aimed at evaluating the antinociceptive and anti-inflammatory effects of the ethanol extract from Vernonia condensata leaves in animal models, in order to afford a better understanding of these properties. The extract reduced the number of abdominal contortions at doses
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The present study was aimed at evaluating the antinociceptive and anti-inflammatory effects of the ethanol extract from Vernonia condensata leaves in animal models, in order to afford a better understanding of these properties. The extract reduced the number of abdominal contortions at doses of 100 (51.00 ± 3.00), 200 (42.00 ± 2.98) and 400 mg/kg (39.00 ± 4.00). In formalin tests, a significant reduction in the licking time (p < 0.01) was observed in the first phase by 25.14 (200 mg/kg = 51.50 ± 4.44) and 31.15% (400 mg/kg = 48.00 ± 4.37). The doses of 100 (43.37 ± 5.15), 200 (34.62 ± 4.16) and 400 mg/kg (28.37 ± 3.98) inhibited (p < 0.001) the second phase. After 60 and 90 min of treatment, a dose of 400 mg/kg (10.13 ± 0.39 and 11.14 ± 1.33, respectively) increased the latency time. Doses of 200 and 400 mg/kg potentiated the sleeping time induced by diazepam, pentobarbital and meprobamate. The extracts (100, 200 and 400 mg/kg) showed anti-inflammatory effects by a decrease in paw edema. The extracts also reduced the exudate volume at the doses of 200 and 400 mg/kg. The leukocyte migration had significant effect (p < 0.001) at doses of 100, 200 and 400 mg/kg. The completion of additional experiments in the investigation of the antinociceptive and anti-inflammatory activities of V. condensata allowed a better understanding of the central and peripheral mechanisms involved. Full article
(This article belongs to the Section Biochemistry, Molecular Biology and Biophysics)
Open AccessArticle Enhanced Immunomodulatory Activity of Gelatin-Encapsulated Rubus coreanus Miquel Nanoparticles
Int. J. Mol. Sci. 2011, 12(12), 9031-9056; doi:10.3390/ijms12129031
Received: 24 November 2011 / Accepted: 29 November 2011 / Published: 7 December 2011
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Abstract
The aim of this work was to investigate the immunomodulatory activities of Rubus coreanus Miquel extract-loaded gelatin nanoparticles. The mean size of the produced nanoparticles was 143 ± 18 nm with a bandwidth of 76 nm in the size distribution and a maximum
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The aim of this work was to investigate the immunomodulatory activities of Rubus coreanus Miquel extract-loaded gelatin nanoparticles. The mean size of the produced nanoparticles was 143 ± 18 nm with a bandwidth of 76 nm in the size distribution and a maximum size of ~200 nm, which allows effective nanoparticle uptake by cells. Confocal imaging confirmed this, since the nanoparticles were internalized within 30 min and heterogeneously distributed throughout the cell. Zeta-potential measurements showed that from pH = 5 onwards, the nanoparticles were highly negatively charged, which prevents agglomeration to clusters by electrostatic repulsion. This was confirmed by TEM imaging, which showed a well dispersed colloidal solution. The encapsulation efficiency was nearly 60%, which is higher than for other components encapsulated in gelatin nanoparticles. Measurements of immune modulation in immune cells showed a significant effect by the crude extract, which was only topped by the nanoparticles containing the extract. Proliferation of B-, T- and NK cells was notably enhanced by Rubus coreanus-gelatin nanoparticles and in general ~2–3 times higher than control and on average ~2 times higher than ferulic acid. R. coreanus-gelatin nanoparticles induced cytokine secretion (IL-6 and TNF-α) from B- and T-cells on average at a ~2–3 times higher rate compared with the extract and ferulic acid. In vivo immunomodulatory activity in mice fed with R. coreanus-gelatin nanoparticles at 1 mL/g body weight showed a ~5 times higher antibody production compared to control, a ~1.3 times higher production compared to the extract only, and a ~1.6 times higher production compared to ferulic acid. Overall, our results suggest that gelatin nanoparticles represent an excellent transport vehicle for Rubus coreanus extract and extracts from other plants generally used in traditional Asian medicine. Such nanoparticles ensure a high local concentration that results in enhancement of immune cell activities, including proliferation, cytokine secretion, and antibody production. Full article
(This article belongs to the Section Material Sciences and Nanotechnology)
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Open AccessCommunication Investigating Ionic Effects Applied to Water Based Organocatalysed Aldol Reactions
Int. J. Mol. Sci. 2011, 12(12), 9083-9094; doi:10.3390/ijms12129083
Received: 28 October 2011 / Revised: 26 November 2011 / Accepted: 29 November 2011 / Published: 7 December 2011
Cited by 7 | PDF Full-text (142 KB) | HTML Full-text | XML Full-text | Supplementary Files
Abstract
Saturated aqueous solutions of various common salts were examined for their effect on aqueous aldol reactions catalysted by a highly active C2-symmetric diprolinamide organocatalyst developed in our laboratory. With respect to the aldol reaction between cyclohexanone and 4-nitrobenzaldehyde, deionised water was
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Saturated aqueous solutions of various common salts were examined for their effect on aqueous aldol reactions catalysted by a highly active C2-symmetric diprolinamide organocatalyst developed in our laboratory. With respect to the aldol reaction between cyclohexanone and 4-nitrobenzaldehyde, deionised water was always a superior medium to salt solutions though some correlation to increasing anion size and depression in enantiomeric excess could be observed. Additionally, the complete inhibition of catalyst activity observed when employing tap water could be alleviated by the inclusion of ethylenediaminetetraacetate (EDTA) into the aqueous media prior to reaction initiation. Extension of these reaction conditions demonstrated that these ionic effects vary on a case-to-case basis depending on the ketone/aldehyde combination. Full article
(This article belongs to the Special Issue Advances in Green Chemistry and Sustainable Chemistry 2011)
Open AccessArticle Intracluster Ion Molecule Reactions Following the Generation of Mg+ Within Polar Clusters
Int. J. Mol. Sci. 2011, 12(12), 9095-9107; doi:10.3390/ijms12129095
Received: 10 October 2011 / Revised: 11 November 2011 / Accepted: 22 November 2011 / Published: 7 December 2011
Cited by 3 | PDF Full-text (370 KB) | HTML Full-text | XML Full-text
Abstract
In this work we investigated the intracluster ion molecule reactions following the generation of Mg+ within the polar clusters (water, methanol, ether and acetonitrile), using time of flight mass spectrometry. In the case of Mg+/water and Mg+/methanol, dehydrogenation
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In this work we investigated the intracluster ion molecule reactions following the generation of Mg+ within the polar clusters (water, methanol, ether and acetonitrile), using time of flight mass spectrometry. In the case of Mg+/water and Mg+/methanol, dehydrogenation reactions are observed after the addition of five molecules. However, no dehydrogenation reactions are observed in the case of Mg+/ether or Mg+/acetonitrile clusters. This confirms the role of the H atom in (O–H) in the dehydrogenation reaction, and rules out any contribution from the H atom in the CH3 group. In addition, the magic numbers in the time of flight (TOF) mass spectra of the Mg+Xn clusters (X = H2O, CH3OH, CH3OCH3 and CH3CN) have been investigated. Finally, the role of ground electronic magnesium ion Mg+(2S1/2), and excited electronic magnesium ion Mg+(2P1/2) in the dehydrogenation reaction were investigated using Ion Mobility Mass spectrometry. The results offer direct evidence confirming the absence of the electronically excited, Mg+(2P1/2). Full article
(This article belongs to the Section Physical Chemistry, Theoretical and Computational Chemistry)
Open AccessArticle Loop-Mediated Amplification Accelerated by Stem Primers
Int. J. Mol. Sci. 2011, 12(12), 9108-9124; doi:10.3390/ijms12129108
Received: 31 August 2011 / Revised: 6 November 2011 / Accepted: 29 November 2011 / Published: 8 December 2011
Cited by 12 | PDF Full-text (931 KB) | HTML Full-text | XML Full-text
Abstract
Isothermal nucleic acid amplifications (iNAATs) have become an important alternative to PCR for in vitro molecular diagnostics in all fields. Amongst iNAATs Loop-mediated amplification (LAMP) has gained much attention over the last decade because of the simplicity of hardware requirements. LAMP demonstrates performance
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Isothermal nucleic acid amplifications (iNAATs) have become an important alternative to PCR for in vitro molecular diagnostics in all fields. Amongst iNAATs Loop-mediated amplification (LAMP) has gained much attention over the last decade because of the simplicity of hardware requirements. LAMP demonstrates performance equivalent to that of PCR, but its application has been limited by the challenging primer design. The design of six primers in LAMP requires a selection of eight priming sites with significant restrictions imposed on their respective positioning and orientation. In order to relieve primer design constraints we propose an alternative approach which uses Stem primers instead of Loop primers and demonstrate the application of STEM-LAMP in assaying for Clostridium difficile, Listeria monocytogenes and HIV. Stem primers used in LAMP in combination with loop-generating and displacement primers gave significant benefits in speed and sensitivity, similar to those offered by Loop primers, while offering additional options of forward and reverse orientations, multiplexing, use in conjunction with Loop primers or even omission of one or two displacement primers, where necessary. Stem primers represent a valuable alternative to Loop primers and an additional tool for IVD assay development by offering more choices for primer design at the same time increasing assay speed, sensitivity, and reproducibility. Full article
(This article belongs to the Special Issue Advances in Molecular Diagnostics)
Open AccessArticle Swelling-Activated Anion Channels Are Essential for Volume Regulation of Mouse Thymocytes
Int. J. Mol. Sci. 2011, 12(12), 9125-9137; doi:10.3390/ijms12129125
Received: 25 October 2011 / Revised: 10 November 2011 / Accepted: 24 November 2011 / Published: 8 December 2011
Cited by 10 | PDF Full-text (158 KB) | HTML Full-text | XML Full-text
Abstract
Channel-mediated trans-membrane chloride movement is a key process in the active cell volume regulation under osmotic stress in most cells. However, thymocytes were hypothesized to regulate their volume by activating a coupled K-Cl cotransport mechanism. Under the patch-clamp, we found that osmotic swelling
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Channel-mediated trans-membrane chloride movement is a key process in the active cell volume regulation under osmotic stress in most cells. However, thymocytes were hypothesized to regulate their volume by activating a coupled K-Cl cotransport mechanism. Under the patch-clamp, we found that osmotic swelling activates two types of macroscopic anion conductance with different voltage-dependence and pharmacology. At the single-channel level, we identified two types of events: one corresponded to the maxi-anion channel, and the other one had characteristics of the volume-sensitive outwardly rectifying (VSOR) chloride channel of intermediate conductance. A VSOR inhibitor, phloretin, significantly suppressed both macroscopic VSOR-type conductance and single-channel activity of intermediate amplitude. The maxi-anion channel activity was largely suppressed by Gd3+ ions but not by phloretin. Surprisingly, [(dihydroindenyl)oxy] alkanoic acid (DIOA), a known antagonist of K-Cl cotransporter, was found to significantly suppress the activity of the VSOR-type single-channel events with no effect on the maxi-anion channels at 10 μM. The regulatory volume decrease (RVD) phase of cellular response to hypotonicity was mildly suppressed by Gd3+ ions and was completely abolished by phloretin suggesting a major impact of the VSOR chloride channel and modulatory role of the maxi-anion channel. The inhibitory effect of DIOA was also strong, and, most likely, it occurred via blocking the VSOR Cl channels. Full article
(This article belongs to the Special Issue Membrane Transport)
Open AccessArticle Effect of Tween Series on Growth and cis-9, trans-11 Conjugated Linoleic Acid Production of Lactobacillus acidophilus F0221 in the Presence of Bile Salts
Int. J. Mol. Sci. 2011, 12(12), 9138-9154; doi:10.3390/ijms12129138
Received: 20 October 2011 / Revised: 8 November 2011 / Accepted: 16 November 2011 / Published: 8 December 2011
Cited by 7 | PDF Full-text (197 KB) | HTML Full-text | XML Full-text
Abstract
Cis-9, trans-11 conjugated linoleic acid (c9, t11 CLA) producing bacteria have attracted much attention as novel probiotics which have shown beneficial effects on host health. However, bile salts are able to inhibit bacterial growth and c9, t
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Cis-9, trans-11 conjugated linoleic acid (c9, t11 CLA) producing bacteria have attracted much attention as novel probiotics which have shown beneficial effects on host health. However, bile salts are able to inhibit bacterial growth and c9, t11 CLA production. For recovering growth and c9, t11 CLA production of Lactobacillus acidophilus F0221 in the presence of bile salts, Tween series (Tween 20, Tween 40, Tween 60 and Tween 80) were added in growth culture containing 0.3% oxgall. Results showed that the viable counts were significantly (P < 0.05) recovered to 8.58–8.75 log CFU/mL in the presence of all Tween treatments. However, recovery of c9, t11 CLA production was only demonstrated in the presence of Tween 80 (72.89 μg/mL). Stepwise increasing oxgall in a concentrations range from 0.1% to 0.9% according to human intestinal physiological environments, Tween 80 still showed significant (P < 0.05) recovery ability on growth (8.91–8.04 log CFU/mL) and c9, t11 CLA (69.22–34.27 μg/mL) production. The effect of Tween 80 on growth and production was also investigated in the presence of different types of bile salts (sodium salts of cholic acid (CA), deoxycholic acid (DCA), chendeoxycholic acid (CDCA), glycocholic acid (GCA) and taurocholic acid (TCA)). Results showed that Tween 80 could significantly (P < 0.05) recover c9, t11 CLA production in the presence of all types of bile salts, but the Tween 80 could only significantly (P < 0.05) recover viable counts of the strain in the presence of CA, DCA and CDCA. This recovery ability could be attributed to the protection of leakage of intracellular material. Additionally, although bile salts inhibited growth and c9, t11 CLA production by the growing cell, it promoted the c9, t11 CLA production by the resting cell. Full article
Open AccessArticle Dynamics of Protein Phosphatase Gene Expression in Corbicula fluminea Exposed to Microcystin-LR and to Toxic Microcystis aeruginosa Cells
Int. J. Mol. Sci. 2011, 12(12), 9172-9188; doi:10.3390/ijms12129172
Received: 1 August 2011 / Revised: 21 November 2011 / Accepted: 30 November 2011 / Published: 8 December 2011
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Abstract
This study investigated the in vivo effects of microcystins on gene expression of several phosphoprotein phosphatases (PPP) in the freshwater clam Corbicula fluminea with two different exposure scenarios. Clams were exposed for 96 h to 5 µg L−1 of dissolved microcystin-LR and
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This study investigated the in vivo effects of microcystins on gene expression of several phosphoprotein phosphatases (PPP) in the freshwater clam Corbicula fluminea with two different exposure scenarios. Clams were exposed for 96 h to 5 µg L−1 of dissolved microcystin-LR and the relative changes of gene expression of three different types of PPP (PPP1, 2 and 4) were analyzed by quantitative real-time PCR. The results showed a significant induction of PPP2 gene expression in the visceral mass. In contrast, the cyanotoxin did not cause any significant changes on PPP1 and PPP4 gene expression. Based on these results, we studied alterations in transcriptional patterns in parallel with enzymatic activity of C. fluminea for PPP2, induced by a Microcystis aeruginosa toxic strain (1 × 105 cells cm−3) during 96 h. The relative changes of gene expression and enzyme activity in visceral mass were analyzed by quantitative real-time PCR and colorimetric assays respectively. The clams exhibited a significant reduction of PPP2 activity with a concomitant enhancement of gene expression. Considering all the results we can conclude that the exposure to an ecologically relevant concentration of pure or intracellular microcystins (-LR) promoted an in vivo effect on PPP2 gene expression in C. fluminea. Full article
(This article belongs to the Section Molecular Toxicology)
Open AccessArticle Wild and Hatchery Populations of Korean Starry Flounder (Platichthys stellatus) Compared Using Microsatellite DNA Markers
Int. J. Mol. Sci. 2011, 12(12), 9189-9202; doi:10.3390/ijms12129189
Received: 22 November 2011 / Revised: 2 December 2011 / Accepted: 5 December 2011 / Published: 9 December 2011
Cited by 10 | PDF Full-text (612 KB) | HTML Full-text | XML Full-text
Abstract
Starry flounder (Platichthys stellatus) is an important sport and food fish found around the margins of the North Pacific. Aquaculture production of this species in Korea has increased because of its commercial value. Microsatellite DNA markers are a useful DNA-based tool
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Starry flounder (Platichthys stellatus) is an important sport and food fish found around the margins of the North Pacific. Aquaculture production of this species in Korea has increased because of its commercial value. Microsatellite DNA markers are a useful DNA-based tool for monitoring the genetic variation of starry flounder populations. In this study, 12 polymorphic microsatellite DNA markers were identified from a partial genomic starry flounder DNA library enriched in CA repeats, and used to compare allelic variation between wild and hatchery starry flounder populations in Korea. All loci were readily amplified and demonstrated high allelic diversity, with the number of alleles ranging from 6 to 18 in the wild population and from 2 to 12 in the farmed population. A total of 136 alleles were detected at the 12 microsatellite loci in the two populations. The mean observed and expected heterozygosities were 0.62 and 0.68, respectively, in the hatchery samples and 0.67 and 0.75, respectively, in the wild samples. These results indicate lower genetic variability in the hatchery population as compared to the wild population. Significant shifts in allelic frequencies were detected at eight loci, which resulted in a small but significant genetic differences between the wild and hatchery populations (FST = 0.043, P < 0.05). Further studies with additional starry flounder sample collections are needed for comprehensive determinations of the genetic varieties between the wild and hatchery populations. These microsatellite loci may be valuable for future population genetic studies, monitoring the genetic variation for successful aquaculture management and the preservation of aquatic biodiversity. Full article
(This article belongs to the Section Biochemistry, Molecular Biology and Biophysics)
Open AccessArticle Differential Motor Neuron Impairment and Axonal Regeneration in Sporadic and Familiar Amyotrophic Lateral Sclerosis with SOD-1 Mutations: Lessons from Neurophysiology
Int. J. Mol. Sci. 2011, 12(12), 9203-9215; doi:10.3390/ijms12129203
Received: 9 October 2011 / Revised: 11 November 2011 / Accepted: 29 November 2011 / Published: 9 December 2011
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Abstract
Amyotrophic Lateral Sclerosis (ALS) is a degenerative disorder of the motor system. About 10% of cases are familial and 20% of these families have point mutations in the Cu/Zn superoxide dismutase 1 (SOD-1) gene. SOD-1 catalyses the superoxide radical (O2)
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Amyotrophic Lateral Sclerosis (ALS) is a degenerative disorder of the motor system. About 10% of cases are familial and 20% of these families have point mutations in the Cu/Zn superoxide dismutase 1 (SOD-1) gene. SOD-1 catalyses the superoxide radical (O2) into hydrogen peroxide and molecular oxygen. The clinical neurophysiology in ALS plays a fundamental role in differential diagnosis between the familial and sporadic forms and in the assessment of its severity and progression. Sixty ALS patients (34 males; 26 females) were enrolled in the study and examined basally (T0) and every 4 months (T1, T2, and T3). Fifteen of these patients are SOD-1 symptomatic mutation carriers (nine males, six females). We used Macro-EMG and Motor Unit Number Estimation (MUNE) in order to evaluate the neuronal loss and the re-innervation process at the onset of disease and during follow-up period. Results and Discussion: SOD-1 mutation carriers have a higher number of motor units at the moment of diagnosis when compared with the sporadic form, despite a more dramatic drop in later stages. Moreover, in familiar SOD-1 ALS there is not a specific time interval in which the axonal regeneration can balance the neuronal damage. Taken together, these results strengthen the idea of a different pathogenetic mechanism at the base of sALS and fALS. Full article
(This article belongs to the Special Issue Studies of Motor Molecules)
Open AccessArticle The Effect of the Acetone Extract of Arctotis arctotoides (Asteraceae) on the Growth and Ultrastructure of Some Opportunistic Fungi Associated with HIV/AIDS
Int. J. Mol. Sci. 2011, 12(12), 9226-9235; doi:10.3390/ijms12129226
Received: 18 October 2011 / Revised: 23 November 2011 / Accepted: 24 November 2011 / Published: 9 December 2011
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Abstract
In this study, the effect of the acetone extract of Arctotis arctotoides (L.f.) O. Hoffm. (Asteraceae) on the growth and ultrastructure of some opportunistic fungi associated with HIV/AIDS was analyzed by means of scanning electron microscope (SEM). Remarkable morphological alterations in the fungal mycelia
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In this study, the effect of the acetone extract of Arctotis arctotoides (L.f.) O. Hoffm. (Asteraceae) on the growth and ultrastructure of some opportunistic fungi associated with HIV/AIDS was analyzed by means of scanning electron microscope (SEM). Remarkable morphological alterations in the fungal mycelia which were attributed to the loss of cell wall strength ranged from loss of turgidity and uniformity, collapse of entire hyphae to evident destruction of the hyphae. The elements responsible for giving the fungi their characteristic virulence were detected and quantified by energy dispersive X-ray microanalysis techniques. X-ray microanalysis showed the specific spectra of sodium, potassium and sulfur as the principal intersection of the four pathogenic fungi studied. Since these ions have the potential of fostering fungal invasion by altering the permeability of hosts’ membranes, their presence was considered inherent to the pathogenicity of the opportunistic fungi. Hence, these findings indicate the potential of the crude extract of A. arctotoides in preventing fungal invasion and subsequent infection of host’s membranes. Full article
Open AccessArticle 3D QSAR Pharmacophore Modeling, in Silico Screening, and Density Functional Theory (DFT) Approaches for Identification of Human Chymase Inhibitors
Int. J. Mol. Sci. 2011, 12(12), 9236-9264; doi:10.3390/ijms12129236
Received: 24 October 2011 / Revised: 18 November 2011 / Accepted: 23 November 2011 / Published: 12 December 2011
Cited by 24 | PDF Full-text (861 KB) | HTML Full-text | XML Full-text
Abstract
Human chymase is a very important target for the treatment of cardiovascular diseases. Using a series of theoretical methods like pharmacophore modeling, database screening, molecular docking and Density Functional Theory (DFT) calculations, an investigation for identification of novel chymase inhibitors, and to specify
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Human chymase is a very important target for the treatment of cardiovascular diseases. Using a series of theoretical methods like pharmacophore modeling, database screening, molecular docking and Density Functional Theory (DFT) calculations, an investigation for identification of novel chymase inhibitors, and to specify the key factors crucial for the binding and interaction between chymase and inhibitors is performed. A highly correlating (r = 0.942) pharmacophore model (Hypo1) with two hydrogen bond acceptors, and three hydrophobic aromatic features is generated. After successfully validating “Hypo1”, it is further applied in database screening. Hit compounds are subjected to various drug-like filtrations and molecular docking studies. Finally, three structurally diverse compounds with high GOLD fitness scores and interactions with key active site amino acids are identified as potent chymase hits. Moreover, DFT study is performed which confirms very clear trends between electronic properties and inhibitory activity (IC50) data thus successfully validating “Hypo1” by DFT method. Therefore, this research exertion can be helpful in the development of new potent hits for chymase. In addition, the combinational use of docking, orbital energies and molecular electrostatic potential analysis is also demonstrated as a good endeavor to gain an insight into the interaction between chymase and inhibitors. Full article
(This article belongs to the Section Biochemistry, Molecular Biology and Biophysics)
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Open AccessArticle Inference of Gene Regulation via miRNAs During ES Cell Differentiation Using MiRaGE Method
Int. J. Mol. Sci. 2011, 12(12), 9265-9276; doi:10.3390/ijms12129265
Received: 24 October 2011 / Revised: 22 November 2011 / Accepted: 29 November 2011 / Published: 12 December 2011
Cited by 6 | PDF Full-text (321 KB) | HTML Full-text | XML Full-text
Abstract
MicroRNA (miRNA) is a critical regulator of cell growth, differentiation, and development. To identify important miRNAs in a biological process, many bioinformatical tools have been developed. We have developed MiRaGE (MiRNA Ranking by Gene Expression) method to infer the regulation of gene expression
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MicroRNA (miRNA) is a critical regulator of cell growth, differentiation, and development. To identify important miRNAs in a biological process, many bioinformatical tools have been developed. We have developed MiRaGE (MiRNA Ranking by Gene Expression) method to infer the regulation of gene expression by miRNAs from changes of gene expression profiles. The method does not require precedent array normalization. We applied the method to elucidate possibly important miRNAs during embryonic stem (ES) cell differentiation to neuronal cells and we infer that certain miRNAs, including miR-200 family, miR-429, miR-302 family, and miR-17-92 cluster members may be important to the maintenance of undifferentiated status in ES cells. Full article
(This article belongs to the Special Issue Non-Coding RNAs)
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Open AccessArticle Combined Extraction Processes of Lipid from Chlorella vulgaris Microalgae: Microwave Prior to Supercritical Carbon Dioxide Extraction
Int. J. Mol. Sci. 2011, 12(12), 9332-9341; doi:10.3390/ijms12129332
Received: 1 September 2011 / Revised: 21 October 2011 / Accepted: 2 December 2011 / Published: 13 December 2011
Cited by 30 | PDF Full-text (1401 KB) | HTML Full-text | XML Full-text
Abstract
Extraction yields and fatty acid profiles from freeze-dried Chlorella vulgaris by microwave pretreatment followed by supercritical carbon dioxide (MW-SCCO2) extraction were compared with those obtained by supercritical carbon dioxide extraction alone (SCCO2). Work performed with pressure range of 20–28
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Extraction yields and fatty acid profiles from freeze-dried Chlorella vulgaris by microwave pretreatment followed by supercritical carbon dioxide (MW-SCCO2) extraction were compared with those obtained by supercritical carbon dioxide extraction alone (SCCO2). Work performed with pressure range of 20–28 Mpa and temperature interval of 40–70 °C, gave the highest extraction yield (w/w dry weight) at 28 MPa/40 °C. MW-SCCO2 allowed to obtain the highest extraction yield (4.73%) compared to SCCO2 extraction alone (1.81%). Qualitative and quantitative analyses of microalgae oil showed that palmitic, oleic, linoleic and α-linolenic acid were the most abundant identified fatty acids. Oils obtained by MW-SCCO2 extraction had the highest concentrations of fatty acids compared to SCCO2 extraction without pretreatment. Native form, and microwave pretreated and untreated microalgae were observed by scanning electronic microscopy (SEM). SEM micrographs of pretreated microalgae present tearing wall agglomerates. After SCCO2, microwave pretreated microalgae presented several micro cracks; while native form microalgae wall was slightly damaged. Full article
(This article belongs to the Section Green Chemistry)
Open AccessArticle The Relationships Between Biological Activities and Structure of Flavan-3-Ols
Int. J. Mol. Sci. 2011, 12(12), 9342-9353; doi:10.3390/ijms12129342
Received: 27 October 2011 / Revised: 23 November 2011 / Accepted: 5 December 2011 / Published: 13 December 2011
Cited by 15 | PDF Full-text (405 KB) | HTML Full-text | XML Full-text
Abstract
Flavan-3-ols are involved in multiple metabolic pathways that induce inhibition of cell proliferation. We studied the structure-activity relationship of gallic acid (GA) and four flavan-3-ols: epigallocatechin gallate (EGCG), epigallocatechin (EGC), catechin (C), and epicatechin (EC). We measured the cell viability by the MTT
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Flavan-3-ols are involved in multiple metabolic pathways that induce inhibition of cell proliferation. We studied the structure-activity relationship of gallic acid (GA) and four flavan-3-ols: epigallocatechin gallate (EGCG), epigallocatechin (EGC), catechin (C), and epicatechin (EC). We measured the cell viability by the MTT assay and we determined the concentration of testing compound required to reduce cell viability by 50% (IC50). All tested compounds showed a dose-dependent and time-dependent inhibitory antiproliferative effect on Hs578T cells; IC50 values varying from the 15.81 to 326.8 µM. Intracellular ROS (reactive oxygen species) were quantified using a fluorescent probe 2’,7’-dichlorofluorescin diacetate (DCFH-DA). Only the treatment with 10 µM EGC and EGCG was able to induce a significant decrease of ROS concentration and increased levels of ROS were registered for 100 µM EGCG, EGC and GA. Flavans-3-ols and GA induced apoptosis in a dose- and time-dependent manner, which indicated that the induction of apoptosis mediated their cytotoxic activity at least partially. The galloylated catechins have shown a stronger antiproliferative activity and apoptotic effect than the one produced by non galloylated catechins. The galloylated flavan-3-ols are potential therapeutic agents for patients with triple negative breast cancer via induction of apoptosis. Full article
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Open AccessArticle QSAR Study and Molecular Design of Open-Chain Enaminones as Anticonvulsant Agents
Int. J. Mol. Sci. 2011, 12(12), 9354-9368; doi:10.3390/ijms12129354
Received: 15 September 2011 / Revised: 7 November 2011 / Accepted: 24 November 2011 / Published: 14 December 2011
Cited by 35 | PDF Full-text (262 KB) | HTML Full-text | XML Full-text | Supplementary Files
Abstract
Present work employs the QSAR formalism to predict the ED50 anticonvulsant activity of ringed-enaminones, in order to apply these relationships for the prediction of unknown open-chain compounds containing the same types of functional groups in their molecular structure. Two different modeling approaches
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Present work employs the QSAR formalism to predict the ED50 anticonvulsant activity of ringed-enaminones, in order to apply these relationships for the prediction of unknown open-chain compounds containing the same types of functional groups in their molecular structure. Two different modeling approaches are applied with the purpose of comparing the consistency of our results: (a) the search of molecular descriptors via multivariable linear regressions; and (b) the calculation of flexible descriptors with the CORAL (CORrelation And Logic) program. Among the results found, we propose some potent candidate open-chain enaminones having ED50 values lower than 10 mg·kg−1 for corresponding pharmacological studies. These compounds are classified as Class 1 and Class 2 according to the Anticonvulsant Selection Project. Full article
(This article belongs to the Special Issue Atoms in Molecules and in Nanostructures)
Open AccessArticle Monitoring Insulin Aggregation via Capillary Electrophoresis
Int. J. Mol. Sci. 2011, 12(12), 9369-9388; doi:10.3390/ijms12129369
Received: 22 October 2011 / Revised: 6 December 2011 / Accepted: 12 December 2011 / Published: 14 December 2011
Cited by 7 | PDF Full-text (621 KB) | HTML Full-text | XML Full-text | Supplementary Files
Abstract
Early stages of insulin aggregation, which involve the transient formation of oligomeric aggregates, are an important aspect in the progression of Type II diabetes and in the quality control of pharmaceutical insulin production. This study is the first to utilize capillary electrophoresis (CE)
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Early stages of insulin aggregation, which involve the transient formation of oligomeric aggregates, are an important aspect in the progression of Type II diabetes and in the quality control of pharmaceutical insulin production. This study is the first to utilize capillary electrophoresis (CE) with ultraviolet (UV) detection to monitor insulin oligomer formation at pH 8.0 and physiological ionic strength. The lag time to formation of the first detected species in the aggregation process was evaluated by UV-CE and thioflavin T (ThT) binding for salt concentrations from 100 mM to 250 mM. UV-CE had a significantly shorter (5–8 h) lag time than ThT binding (15–19 h). In addition, the lag time to detection of the first aggregated species via UV-CE was unaffected by salt concentration, while a trend toward an increased lag time with increased salt concentration was observed with ThT binding. This result indicates that solution ionic strength impacts early stages of aggregation and β-sheet aggregate formation differently. To observe whether CE may be applied for the analysis of biological samples containing low insulin concentrations, the limit of detection using UV and laser induced fluorescence (LIF) detection modes was determined. The limit of detection using LIF-CE, 48.4 pM, was lower than the physiological insulin concentration, verifying the utility of this technique for monitoring biological samples. LIF-CE was subsequently used to analyze the time course for fluorescein isothiocyanate (FITC)-labeled insulin oligomer formation. This study is the first to report that the FITC label prevented incorporation of insulin into oligomers, cautioning against the use of this fluorescent label as a tag for following early stages of insulin aggregation. Full article
(This article belongs to the Special Issue Protein Aggregation)
Open AccessArticle Identification of (−)(E)-N-[2(S)-Hydroxy-2-(4-hydroxyphenyl) ethyl]ferulamide, a Natural Product Isolated from Croton Pullei: Theoretical and Experimental Analysis
Int. J. Mol. Sci. 2011, 12(12), 9389-9403; doi:10.3390/ijms12129389
Received: 31 August 2011 / Revised: 23 November 2011 / Accepted: 5 December 2011 / Published: 15 December 2011
Cited by 4 | PDF Full-text (652 KB) | HTML Full-text | XML Full-text
Abstract
Ferulic acid (FA) and its derivatives (FADs) are known for a variety of biological activities, such as photo-protective agent, antioxidant, antiatherogenic and antiplasmodial activities. During structural definition of a FAD isolated from Croton pullei, the possibility of a heterologous series made this
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Ferulic acid (FA) and its derivatives (FADs) are known for a variety of biological activities, such as photo-protective agent, antioxidant, antiatherogenic and antiplasmodial activities. During structural definition of a FAD isolated from Croton pullei, the possibility of a heterologous series made this definition difficult. In this regard, computational simulations were performed using theoretical calculations at DFT level to predict Infrared (IR) and Nuclear Magnetic Resonance (NMR) data. The IR and NMR 13C and 1H data were compared with the theoretical calculations performed for three structural possibilities of a heterologous series. The theoretical results were compared with the experimental data through linear regression in order to define the most probable structure and showed satisfactory values. Full article
(This article belongs to the Section Physical Chemistry, Theoretical and Computational Chemistry)
Open AccessArticle Dynamic Structure-Based Pharmacophore Model Development: A New and Effective Addition in the Histone Deacetylase 8 (HDAC8) Inhibitor Discovery
Int. J. Mol. Sci. 2011, 12(12), 9440-9462; doi:10.3390/ijms12129440
Received: 29 August 2011 / Revised: 15 November 2011 / Accepted: 8 December 2011 / Published: 19 December 2011
Cited by 10 | PDF Full-text (1041 KB) | HTML Full-text | XML Full-text | Supplementary Files
Abstract
Histone deacetylase 8 (HDAC8) is an enzyme involved in deacetylating the amino groups of terminal lysine residues, thereby repressing the transcription of various genes including tumor suppressor gene. The over expression of HDAC8 was observed in many cancers and thus inhibition of this
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Histone deacetylase 8 (HDAC8) is an enzyme involved in deacetylating the amino groups of terminal lysine residues, thereby repressing the transcription of various genes including tumor suppressor gene. The over expression of HDAC8 was observed in many cancers and thus inhibition of this enzyme has emerged as an efficient cancer therapeutic strategy. In an effort to facilitate the future discovery of HDAC8 inhibitors, we developed two pharmacophore models containing six and five pharmacophoric features, respectively, using the representative structures from two molecular dynamic (MD) simulations performed in Gromacs 4.0.5 package. Various analyses of trajectories obtained from MD simulations have displayed the changes upon inhibitor binding. Thus utilization of the dynamically-responded protein structures in pharmacophore development has the added advantage of considering the conformational flexibility of protein. The MD trajectories were clustered based on single-linkage method and representative structures were taken to be used in the pharmacophore model development. Active site complimenting structure-based pharmacophore models were developed using Discovery Studio 2.5 program and validated using a dataset of known HDAC8 inhibitors. Virtual screening of chemical database coupled with drug-like filter has identified drug-like hit compounds that match the pharmacophore models. Molecular docking of these hits reduced the false positives and identified two potential compounds to be used in future HDAC8 inhibitor design. Full article
(This article belongs to the Section Physical Chemistry, Theoretical and Computational Chemistry)
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Open AccessArticle Use of Peroxyacetic Acid as Green Chemical on Yield and Sensorial Quality in Watercress (Nasturtium officinale R. Br.) Under Soilless Culture
Int. J. Mol. Sci. 2011, 12(12), 9463-9470; doi:10.3390/ijms12129463
Received: 26 October 2011 / Revised: 8 December 2011 / Accepted: 12 December 2011 / Published: 19 December 2011
Cited by 2 | PDF Full-text (103 KB) | HTML Full-text | XML Full-text
Abstract
The goal of this research was to evaluate the effect of different doses of peroxyacetic acid on the productivity of watercress (Nasturtium officinale R. Br.) cultivated hydroponically using a constant nutritive solution. Green chemistry in protected horticulture seeks compatibility with the environment
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The goal of this research was to evaluate the effect of different doses of peroxyacetic acid on the productivity of watercress (Nasturtium officinale R. Br.) cultivated hydroponically using a constant nutritive solution. Green chemistry in protected horticulture seeks compatibility with the environment through the creation of biodegradable byproducts. In hydroponics, appropriate doses of peroxyacetic mixtures deliver these byproducts while also oxygenating the roots. Watercress producers who recirculate the nutritive solution can use these mixtures in order to increase oxygenation in the hydroponic system. The experiment took place between August and December 2009, beginning with the planting of the watercress seeds and concluding with the completion of the sensory panels. A completely random design was used, including three treatments and four repetitions, with applications of 0, 20 and 40 mg L−1 of the peroxyacetic mixture. Measured variables were growth (plant height, leaf length and stem diameter), yield (weight per plant and dry matter) and organoleptic quality (color and sensory panel). The application of 40 mg L−1 of the peroxyacetic mixture had a greater effect on the growth and development of the plants, which reached an average height of 29.3 cm, stem diameter of 3.3 mm and leaf length of 7.6 cm, whereas the control group reached an average height of only 20.2 cm, stem diameter of 1.9 mm and leaf length of 5.7 cm. The application of the peroxyacetic mixtures resulted in an improvement in growth parameters as well as in yield. Individual weights achieved using the 40 mg L−1 dose were 1.3 g plant−1 in the control group and 3.4 g plant−1 in the experimental group (62% yield increase). Sensory analysis revealed no differences in organoleptic quality. Full article
(This article belongs to the Special Issue Advances in Green Chemistry and Sustainable Chemistry 2011)
Open AccessArticle Molecular Diagnosis of 5α-Reductase Type II Deficiency in Brazilian Siblings with 46,XY Disorder of Sex Development
Int. J. Mol. Sci. 2011, 12(12), 9471-9480; doi:10.3390/ijms12129471
Received: 2 September 2011 / Revised: 28 November 2011 / Accepted: 13 December 2011 / Published: 19 December 2011
PDF Full-text (1297 KB) | HTML Full-text | XML Full-text
Abstract
The steroid 5α-reductase type II enzyme catalyzes the conversion of testosterone (T) to dihydrotestosterone (DHT), and its deficiency leads to undervirilization in 46,XY individuals, due to an impairment of this conversion in genital tissues. Molecular analysis in the steroid 5α-reductase type II gene
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The steroid 5α-reductase type II enzyme catalyzes the conversion of testosterone (T) to dihydrotestosterone (DHT), and its deficiency leads to undervirilization in 46,XY individuals, due to an impairment of this conversion in genital tissues. Molecular analysis in the steroid 5α-reductase type II gene (SRD5A2) was performed in two 46,XY female siblings. SRD5A2 gene sequencing revealed that the patients were homozygous for p.Gln126Arg missense mutation, which results from the CGA > CAA nucleotide substitution. The molecular result confirmed clinical diagnosis of 46,XY disorder of sex development (DSD) for the older sister and directed the investigation to other family members. Studies on SRD5A2 protein structure showed severe changes at NADPH binding region indicating that structural modeling analysis can be useful to evaluate the deleterious role of a mutation as causing 5α-reductase type II enzyme deficiency. Full article
(This article belongs to the Special Issue Advances in Molecular Diagnostics)
Open AccessArticle Modeling Natural Anti-Inflammatory Compounds by Molecular Topology
Int. J. Mol. Sci. 2011, 12(12), 9481-9503; doi:10.3390/ijms12129481
Received: 8 November 2011 / Revised: 8 December 2011 / Accepted: 9 December 2011 / Published: 20 December 2011
Cited by 16 | PDF Full-text (269 KB) | HTML Full-text | XML Full-text | Supplementary Files
Abstract
One of the main pharmacological problems today in the treatment of chronic inflammation diseases consists of the fact that anti-inflammatory drugs usually exhibit side effects. The natural products offer a great hope in the identification of bioactive lead compounds and their development into
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One of the main pharmacological problems today in the treatment of chronic inflammation diseases consists of the fact that anti-inflammatory drugs usually exhibit side effects. The natural products offer a great hope in the identification of bioactive lead compounds and their development into drugs for treating inflammatory diseases. Computer-aided drug design has proved to be a very useful tool for discovering new drugs and, specifically, Molecular Topology has become a good technique for such a goal. A topological-mathematical model, obtained by linear discriminant analysis, has been developed for the search of new anti-inflammatory natural compounds. An external validation obtained with the remaining compounds (those not used in building up the model), has been carried out. Finally, a virtual screening on natural products was performed and 74 compounds showed actual anti-inflammatory activity. From them, 54 had been previously described as anti-inflammatory in the literature. This can be seen as a plus in the model validation and as a reinforcement of the role of Molecular Topology as an efficient tool for the discovery of new anti-inflammatory natural compounds. Full article
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Open AccessArticle Q Fever Endocarditis in Romania: The First Cases Confirmed by Direct Sequencing
Int. J. Mol. Sci. 2011, 12(12), 9504-9513; doi:10.3390/ijms12129504
Received: 18 November 2011 / Revised: 9 December 2011 / Accepted: 12 December 2011 / Published: 20 December 2011
PDF Full-text (215 KB) | HTML Full-text | XML Full-text
Abstract
Infective endocarditis (IE) is a serious, life-threatening disease with highly variable clinical signs, making its diagnostic a real challenge. A diagnosis is readily made if blood cultures are positive, but in 2.5 to 31% of all infective endocarditis cases, routine blood cultures are
[...] Read more.
Infective endocarditis (IE) is a serious, life-threatening disease with highly variable clinical signs, making its diagnostic a real challenge. A diagnosis is readily made if blood cultures are positive, but in 2.5 to 31% of all infective endocarditis cases, routine blood cultures are negative. In such situations, alternative diagnostic approaches are necessary. Coxiella burnetii and Bartonella spp. are the etiological agents of blood culture-negative endocarditis (BCNE) most frequently identified by serology. The purpose of this study is to investigate the usefulness of molecular assays, as complementary methods to the conventional serologic methods for the rapid confirmatory diagnostic of Q fever endocarditis in patients with BCNE. Currently, detection of C. burnetii by culture or an antiphase I IgG antibody titers >800 represents a major Duke criterion for defining IE, while a titers of >800 for IgG antibodies to either B. henselae or B. quintana is used for the diagnosis of endocarditis due to Bartonella spp. We used indirect immunofluorescence assays for the detection of IgG titers for C. burnetii, B. henselae and B. quintana in 57 serum samples from patients with clinical suspicion of IE. Thirty three samples originated from BCNE patients, whereas 24 were tested before obtaining the blood cultures results, which finally were positive. The results of serologic testing showed that nine out of 33 BCNE cases exhibited antiphase I C. burnetii IgG antibody titer >800, whereas none has IgG for B. henselae or B. quintana. Subsequently, we used nested-PCR assay for the amplification of C. burnetii DNA in the nine positive serum samples, and we obtained positive PCR results for all analyzed cases. Afterwards we used the DNA sequencing of amplicons for the repetitive element associated to htpAB gene to confirm the results of nested-PCR. The results of sequencing allowed us to confirm that C. burnetii is the causative microorganism responsible for BCNE. In conclusion, the nested PCR amplification followed by direct sequencing is a reliable and accurate method when applied to serum samples, and it may be used as an additional test to the serological methods for the confirmatory diagnosis of BCNE cases determined by C. burnetii. Full article
(This article belongs to the Section Molecular Diagnostics)
Open AccessArticle Introducing Catastrophe-QSAR. Application on Modeling Molecular Mechanisms of Pyridinone Derivative-Type HIV Non-Nucleoside Reverse Transcriptase Inhibitors
Int. J. Mol. Sci. 2011, 12(12), 9533-9569; doi:10.3390/ijms12129533
Received: 27 October 2011 / Revised: 28 November 2011 / Accepted: 12 December 2011 / Published: 20 December 2011
Cited by 10 | PDF Full-text (602 KB) | HTML Full-text | XML Full-text
Abstract
The classical method of quantitative structure-activity relationships (QSAR) is enriched using non-linear models, as Thom’s polynomials allow either uni- or bi-variate structural parameters. In this context, catastrophe QSAR algorithms are applied to the anti-HIV-1 activity of pyridinone derivatives. This requires calculation of the
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The classical method of quantitative structure-activity relationships (QSAR) is enriched using non-linear models, as Thom’s polynomials allow either uni- or bi-variate structural parameters. In this context, catastrophe QSAR algorithms are applied to the anti-HIV-1 activity of pyridinone derivatives. This requires calculation of the so-called relative statistical power and of its minimum principle in various QSAR models. A new index, known as a statistical relative power, is constructed as an Euclidian measure for the combined ratio of the Pearson correlation to algebraic correlation, with normalized t-Student and the Fisher tests. First and second order inter-model paths are considered for mono-variate catastrophes, whereas for bi-variate catastrophes the direct minimum path is provided, allowing the QSAR models to be tested for predictive purposes. At this stage, the max-to-min hierarchies of the tested models allow the interaction mechanism to be identified using structural parameter succession and the typical catastrophes involved. Minimized differences between these catastrophe models in the common structurally influential domains that span both the trial and tested compounds identify the “optimal molecular structural domains” and the molecules with the best output with respect to the modeled activity, which in this case is human immunodeficiency virus type 1 HIV-1 inhibition. The best molecules are characterized by hydrophobic interactions with the HIV-1 p66 subunit protein, and they concur with those identified in other 3D-QSAR analyses. Moreover, the importance of aromatic ring stacking interactions for increasing the binding affinity of the inhibitor-reverse transcriptase ligand-substrate complex is highlighted. Full article
(This article belongs to the Special Issue Advances in Molecular Electronic Structure Calculations)
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Open AccessArticle Synthesis and Insecticidal Activities of New Ester-Derivatives of Celangulin-V
Int. J. Mol. Sci. 2011, 12(12), 9596-9604; doi:10.3390/ijms12129596
Received: 17 August 2011 / Revised: 28 October 2011 / Accepted: 15 December 2011 / Published: 20 December 2011
Cited by 8 | PDF Full-text (188 KB) | HTML Full-text | XML Full-text
Abstract
In order to develop new biorational pesticides, ten new 6-substituted ester derivatives of Celangulin-V were designed and synthesized. The structures of the new derivatives were confirmed by IR, 1H-NMR, 13C-NMR and ESI-MS spectral analysis. Insecticidal activities of these compounds were tested
[...] Read more.
In order to develop new biorational pesticides, ten new 6-substituted ester derivatives of Celangulin-V were designed and synthesized. The structures of the new derivatives were confirmed by IR, 1H-NMR, 13C-NMR and ESI-MS spectral analysis. Insecticidal activities of these compounds were tested against the third-instar larvae of Mythimna separata. Two derivatives (1.1, 1.2) showed higher insecticidal activities than Celangulin-V, with mortality of 75.0% and 83.3%, respectively. While four compounds (1.3, 1.4, 1.7, 1.8) denoted lower insecticidal activities, the others (1.5, 1.6, 1.9, 1.10) revealed no activities at a concentration of 10 mg.mL−1. The results suggest that C-6 substitutions of Celangulin-V are very important in determining the insecticidal activities of its ester-derivatives. That the acetyl (1.1) and propionyl (1.2) derivatives possessed much higher insecticidal activities than Celangulin-V itself supported the view that Celangulin-V has the potential to be a lead structure of semi-synthetic green insecticides. Full article
(This article belongs to the Section Green Chemistry)

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Open AccessReview A Greatly Under-Appreciated Fundamental Principle of Physical Organic Chemistry
Int. J. Mol. Sci. 2011, 12(12), 8316-8332; doi:10.3390/ijms12128316
Received: 19 October 2011 / Revised: 10 November 2011 / Accepted: 14 November 2011 / Published: 28 November 2011
Cited by 17 | PDF Full-text (379 KB) | HTML Full-text | XML Full-text
Abstract
If a species does not have a finite lifetime in the reaction medium, it cannot be a mechanistic intermediate. This principle was first enunciated by Jencks, as the concept of an enforced mechanism. For instance, neither primary nor secondary carbocations have long enough
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If a species does not have a finite lifetime in the reaction medium, it cannot be a mechanistic intermediate. This principle was first enunciated by Jencks, as the concept of an enforced mechanism. For instance, neither primary nor secondary carbocations have long enough lifetimes to exist in an aqueous medium, so SN1 reactions involving these substrates are not possible, and an SN2 mechanism is enforced. Only tertiary carbocations and those stabilized by resonance (benzyl cations, acylium ions) are stable enough to be reaction intermediates. More importantly, it is now known that neither H3O+ nor HO exist as such in dilute aqueous solution. Several recent high-level calculations on large proton clusters are unable to localize the positive charge; it is found to be simply “on the cluster” as a whole. The lifetime of any ionized water species is exceedingly short, a few molecular vibrations at most; the best experimental study, using modern IR instrumentation, has the most probable hydrated proton structure as H13O6+, but only an estimated quarter of the protons are present even in this form at any given instant. Thanks to the Grotthuss mechanism of chain transfer along hydrogen bonds, in reality a proton or a hydroxide ion is simply instantly available anywhere it is needed for reaction. Important mechanistic consequences result. Any charged oxygen species (e.g., a tetrahedral intermediate) is also not going to exist long enough to be a reaction intermediate, unless the charge is stabilized in some way, usually by resonance. General acid catalysis is the rule in reactions in concentrated aqueous acids. The Grotthuss mechanism also means that reactions involving neutral water are favored; the solvent is already highly structured, so the entropy involved in bringing several solvent molecules to the reaction center is unimportant. Examples are given. Full article
(This article belongs to the Special Issue Correlation Analysis Applied to Solvolysis Reactions)
Open AccessReview Fernblock, a Nutriceutical with Photoprotective Properties and Potential Preventive Agent for Skin Photoaging and Photoinduced Skin Cancers
Int. J. Mol. Sci. 2011, 12(12), 8466-8475; doi:10.3390/ijms12128466
Received: 27 September 2011 / Revised: 31 October 2011 / Accepted: 21 November 2011 / Published: 29 November 2011
Cited by 18 | PDF Full-text (114 KB) | HTML Full-text | XML Full-text
Abstract
Many phytochemicals are endowed with photoprotective properties, i.e., the capability to prevent the harmful effects of excessive exposure to ultraviolet (UV) light. These effects include photoaging and skin cancer, and immunosuppression. Photoprotection is endowed through two major modes of action: UV absorption
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Many phytochemicals are endowed with photoprotective properties, i.e., the capability to prevent the harmful effects of excessive exposure to ultraviolet (UV) light. These effects include photoaging and skin cancer, and immunosuppression. Photoprotection is endowed through two major modes of action: UV absorption or reflection/scattering; and tissue repair post-exposure. We and others have uncovered the photoprotective properties of an extract of the fern Polypodium leucotomos (commercial name Fernblock). Fernblock is an all-natural antioxidant extract, administered both topically (on the skin) or orally. It inhibits generation of reactive oxygen species (ROS) production induced by UV including superoxide anion. It also prevents damage to the DNA, inhibits UV-induced AP1 and NF-κB, and protects endogenous skin natural antioxidant systems, i.e., CAT, GSH, and GSSR. Its photoprotective effects at a cellular level include a marked decrease of UV-mediated cellular apoptosis and necrosis and a profound inhibition of extracellular matrix remodeling. These molecular and cellular effects translate into long-term inhibition of photoaging and carcinogenesis that, together with its lack of toxicity, postulate its use as a novel-generation photoprotective nutriceutical of phytochemical origin. Full article
(This article belongs to the Special Issue Advances in Nutraceutical Research)
Open AccessReview Crossing the Border: Molecular Control of Motor Axon Exit
Int. J. Mol. Sci. 2011, 12(12), 8539-8561; doi:10.3390/ijms12128539
Received: 17 October 2011 / Revised: 5 November 2011 / Accepted: 8 November 2011 / Published: 29 November 2011
Cited by 8 | PDF Full-text (1101 KB) | HTML Full-text | XML Full-text
Abstract
Living organisms heavily rely on the function of motor circuits for their survival and for adapting to ever-changing environments. Unique among central nervous system (CNS) neurons, motor neurons (MNs) project their axons out of the CNS. Once in the periphery, motor axons navigate
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Living organisms heavily rely on the function of motor circuits for their survival and for adapting to ever-changing environments. Unique among central nervous system (CNS) neurons, motor neurons (MNs) project their axons out of the CNS. Once in the periphery, motor axons navigate along highly stereotyped trajectories, often at considerable distances from their cell bodies, to innervate appropriate muscle targets. A key decision made by pathfinding motor axons is whether to exit the CNS through dorsal or ventral motor exit points (MEPs). In contrast to the major advances made in understanding the mechanisms that regulate the specification of MN subtypes and the innervation of limb muscles, remarkably little is known about how MN axons project out of the CNS. Nevertheless, a limited number of studies, mainly in Drosophila, have identified transcription factors, and in some cases candidate downstream effector molecules, that are required for motor axons to exit the spinal cord. Notably, specialized neural crest cell derivatives, referred to as Boundary Cap (BC) cells, pre-figure and demarcate MEPs in vertebrates. Surprisingly, however, BC cells are not required for MN axon exit, but rather restrict MN cell bodies from ectopically migrating along their axons out of the CNS. Here, we describe the small set of studies that have addressed motor axon exit in Drosophila and vertebrates, and discuss our fragmentary knowledge of the mechanisms, which guide motor axons out of the CNS. Full article
(This article belongs to the Special Issue Studies of Motor Molecules)
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Open AccessReview Approaches to Manipulating the Dimensionality and Physicochemical Properties of Common Cellular Scaffolds
Int. J. Mol. Sci. 2011, 12(12), 8596-8609; doi:10.3390/ijms12128596
Received: 14 November 2011 / Accepted: 18 November 2011 / Published: 29 November 2011
PDF Full-text (581 KB) | HTML Full-text | XML Full-text
Abstract
A major hurdle in studying biological systems and administering effective tissue engineered therapies is the lack of suitable cell culture models that replicate the dynamic nature of cell-microenvironment interactions. Advances in the field of surface chemistry and polymer science have allowed researchers to
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A major hurdle in studying biological systems and administering effective tissue engineered therapies is the lack of suitable cell culture models that replicate the dynamic nature of cell-microenvironment interactions. Advances in the field of surface chemistry and polymer science have allowed researchers to develop novel methodologies to manipulate materials to be extrinsically tunable. Usage of such materials in modeling tissues in vitro has offered valuable insights into numerous cellular processes including motility, invasion, and alterations in cell morphology. Here, we discuss novel techniques devised to more closely mimic cell-tissue interactions and to study cell response to distinct physico-chemical changes in biomaterials, with an emphasis on the manipulation of collagen scaffolds. The benefits and pitfalls associated with using collagen are discussed in the context of strategies proposed to control the engineered microenvironment. Tunable systems such as these offer the ability to alter individual features of the microenvironment in vitro, with the promise that the molecular basis of mechanotransduction in vivo may be laid out in future. Full article
(This article belongs to the Special Issue Programmable Materials for Mechanobiology)
Open AccessReview A Concise Review on Epigenetic Regulation: Insight into Molecular Mechanisms
Int. J. Mol. Sci. 2011, 12(12), 8661-8694; doi:10.3390/ijms12128661
Received: 9 August 2011 / Revised: 7 November 2011 / Accepted: 10 November 2011 / Published: 30 November 2011
Cited by 13 | PDF Full-text (299 KB) | HTML Full-text | XML Full-text
Abstract
Epigenetic mechanisms are responsible for the regulation of transcription of imprinted genes and those that induce a totipotent state. Starting just after fertilization, DNA methylation pattern undergoes establishment, reestablishment and maintenance. These modifications are important for normal embryo and placental developments. Throughout life
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Epigenetic mechanisms are responsible for the regulation of transcription of imprinted genes and those that induce a totipotent state. Starting just after fertilization, DNA methylation pattern undergoes establishment, reestablishment and maintenance. These modifications are important for normal embryo and placental developments. Throughout life and passing to the next generation, epigenetic events establish, maintain, erase and reestablish. In the context of differentiated cell reprogramming, demethylation and activation of genes whose expressions contribute to the pluripotent state is the crux of the matter. In this review, firstly, regulatory epigenetic mechanisms related to somatic cell nuclear transfer (SCNT) reprogramming are discussed, followed by embryonic development, and placental epigenetic issues. Full article
(This article belongs to the Special Issue Non-Coding RNAs)
Open AccessReview X-Ray Detected Magnetic Resonance: A Unique Probe of the Precession Dynamics of Orbital Magnetization Components
Int. J. Mol. Sci. 2011, 12(12), 8797-8835; doi:10.3390/ijms12128797
Received: 11 October 2011 / Revised: 12 November 2011 / Accepted: 15 November 2011 / Published: 2 December 2011
Cited by 5 | PDF Full-text (608 KB) | HTML Full-text | XML Full-text
Abstract
X-ray Detected Magnetic Resonance (XDMR) is a novel spectroscopy in which X-ray Magnetic Circular Dichroism (XMCD) is used to probe the resonant precession of local magnetization components in a strong microwave pump field. We review the conceptual bases of XDMR and recast them
[...] Read more.
X-ray Detected Magnetic Resonance (XDMR) is a novel spectroscopy in which X-ray Magnetic Circular Dichroism (XMCD) is used to probe the resonant precession of local magnetization components in a strong microwave pump field. We review the conceptual bases of XDMR and recast them in the general framework of the linear and nonlinear theories of ferromagnetic resonance (FMR). Emphasis is laid on the information content of XDMR spectra which offer a unique opportunity to disentangle the precession dynamics of spin and orbital magnetization components at given absorbing sites. For the sake of illustration, we focus on selected examples in which marked differences were found between FMR and XDMR spectra simultaneously recorded on ferrimagnetically ordered iron garnets. With pumping capabilities extended up to sub-THz frequencies, high-field XDMR should allow us to probe the precession of orbital magnetization components in paramagnetic organometallic complexes with large zero-field splitting. Even more challenging, we suggest that XDMR spectra might be recorded on selected antiferromagnetic crystals for which orbital magnetism is most often ignored in the absence of any supporting experimental evidence. Full article
(This article belongs to the Special Issue Applications of Circular Dichroism)
Open AccessReview The Wnt and BMP Families of Signaling Morphogens at the Vertebrate Neuromuscular Junction
Int. J. Mol. Sci. 2011, 12(12), 8924-8946; doi:10.3390/ijms12128924
Received: 18 October 2011 / Revised: 18 November 2011 / Accepted: 22 November 2011 / Published: 5 December 2011
Cited by 11 | PDF Full-text (1371 KB) | HTML Full-text | XML Full-text
Abstract
The neuromuscular junction has been extensively employed in order to identify crucial determinants of synaptogenesis. At the vertebrate neuromuscular synapse, extracellular matrix and signaling proteins play stimulatory and inhibitory roles on the assembly of functional synapses. Studies in invertebrate species have revealed crucial
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The neuromuscular junction has been extensively employed in order to identify crucial determinants of synaptogenesis. At the vertebrate neuromuscular synapse, extracellular matrix and signaling proteins play stimulatory and inhibitory roles on the assembly of functional synapses. Studies in invertebrate species have revealed crucial functions of early morphogens during the assembly and maturation of the neuromuscular junction. Here, we discuss growing evidence addressing the function of Wnt and Bone morphogenetic protein (BMP) signaling pathways at the vertebrate neuromuscular synapse. We focus on the emerging role of Wnt proteins as positive and negative regulators of postsynaptic differentiation. We also address the possible involvement of BMP pathways on motor neuron behavior for the assembly and/or regeneration of the neuromuscular junction. Full article
(This article belongs to the Section Biochemistry, Molecular Biology and Biophysics)
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Open AccessReview The Role of the E2F Transcription Factor Family in UV-Induced Apoptosis
Int. J. Mol. Sci. 2011, 12(12), 8947-8960; doi:10.3390/ijms12128947
Received: 11 October 2011 / Revised: 15 November 2011 / Accepted: 30 November 2011 / Published: 6 December 2011
Cited by 10 | PDF Full-text (327 KB) | HTML Full-text | XML Full-text
Abstract
The E2F transcription factor family is traditionally associated with cell cycle control. However, recent data has shown that activating E2Fs (E2F1-3a) are potent activators of apoptosis. In contrast, the recently cloned inhibitory E2Fs (E2F7 and 8) appear to antagonize E2F-induced cell death. In
[...] Read more.
The E2F transcription factor family is traditionally associated with cell cycle control. However, recent data has shown that activating E2Fs (E2F1-3a) are potent activators of apoptosis. In contrast, the recently cloned inhibitory E2Fs (E2F7 and 8) appear to antagonize E2F-induced cell death. In this review we will discuss (i) the potential role of E2Fs in UV-induced cell death and (ii) the implications of this to the development of UV-induced cutaneous malignancies. Full article
(This article belongs to the Special Issue UV-Induced Cell Death)
Open AccessReview Mechanobiology of Platelets: Techniques to Study the Role of Fluid Flow and Platelet Retraction Forces at the Micro- and Nano-Scale
Int. J. Mol. Sci. 2011, 12(12), 9009-9030; doi:10.3390/ijms12129009
Received: 14 October 2011 / Revised: 24 November 2011 / Accepted: 28 November 2011 / Published: 7 December 2011
Cited by 8 | PDF Full-text (1668 KB) | HTML Full-text | XML Full-text
Abstract
Coagulation involves a complex set of events that are important in maintaining hemostasis. Biochemical interactions are classically known to regulate the hemostatic process, but recent evidence has revealed that mechanical interactions between platelets and their surroundings can also play a substantial role. Investigations
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Coagulation involves a complex set of events that are important in maintaining hemostasis. Biochemical interactions are classically known to regulate the hemostatic process, but recent evidence has revealed that mechanical interactions between platelets and their surroundings can also play a substantial role. Investigations into platelet mechanobiology have been challenging however, due to the small dimensions of platelets and their glycoprotein receptors. Platelet researchers have recently turned to microfabricated devices to control these physical, nanometer-scale interactions with a higher degree of precision. These approaches have enabled exciting, new insights into the molecular and biomechanical factors that affect platelets in clot formation. In this review, we highlight the new tools used to understand platelet mechanobiology and the roles of adhesion, shear flow, and retraction forces in clot formation. Full article
(This article belongs to the Special Issue Programmable Materials for Mechanobiology)
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Open AccessReview Molecular Motor Proteins and Amyotrophic Lateral Sclerosis
Int. J. Mol. Sci. 2011, 12(12), 9057-9082; doi:10.3390/ijms12129057
Received: 11 October 2011 / Revised: 28 November 2011 / Accepted: 30 November 2011 / Published: 7 December 2011
Cited by 10 | PDF Full-text (228 KB) | HTML Full-text | XML Full-text
Abstract
Amyotrophic lateral sclerosis (ALS) is a neurodegenerative disorder affecting motor neurons in the brain, brainstem and spinal cord, which is characterized by motor dysfunction, muscle dystrophy and progressive paralysis. Both inherited and sporadic forms of ALS share common pathological features, however, the initial
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Amyotrophic lateral sclerosis (ALS) is a neurodegenerative disorder affecting motor neurons in the brain, brainstem and spinal cord, which is characterized by motor dysfunction, muscle dystrophy and progressive paralysis. Both inherited and sporadic forms of ALS share common pathological features, however, the initial trigger of neurodegeneration remains unknown. Motor neurons are uniquely targeted by ubiquitously expressed proteins in ALS but the reason for this selectively vulnerability is unclear. However motor neurons have unique characteristics such as very long axons, large cell bodies and high energetic metabolism, therefore placing high demands on cellular transport processes. Defects in cellular trafficking are now widely reported in ALS, including dysfunction to the molecular motors dynein and kinesin. Abnormalities to dynein in particular are linked to ALS, and defects in dynein-mediated axonal transport processes have been reported as one of the earliest pathologies in transgenic SOD1 mice. Furthermore, dynein is very highly expressed in neurons and neurons are particularly sensitive to dynein dysfunction. Hence, unravelling cellular transport processes mediated by molecular motor proteins may help shed light on motor neuron loss in ALS. Full article
(This article belongs to the Special Issue Studies of Motor Molecules)
Open AccessReview RNA Aptamer Evolution: Two Decades of SELEction
Int. J. Mol. Sci. 2011, 12(12), 9155-9171; doi:10.3390/ijms12129155
Received: 24 October 2011 / Revised: 24 November 2011 / Accepted: 28 November 2011 / Published: 8 December 2011
Cited by 28 | PDF Full-text (444 KB) | HTML Full-text | XML Full-text
Abstract
Aptamers are small non-coding RNAs capable of recognizing, with high specificity and affinity, a wide variety of molecules in a manner that resembles antibodies. This class of nucleic acids is the resulting product of applying a well-established screening method known as SELEX. First
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Aptamers are small non-coding RNAs capable of recognizing, with high specificity and affinity, a wide variety of molecules in a manner that resembles antibodies. This class of nucleic acids is the resulting product of applying a well-established screening method known as SELEX. First developed in 1990, the SELEX process has become a powerful tool to select structured oligonucleotides for the recognition of targets, starting with small molecules, going through protein complexes until whole cells. SELEX has also evolved along with new technologies positioning itself as an alternative in the design of a new class of therapeutic agents in modern molecular medicine. This review is an historical follow-up of SELEX method over the two decades since its first appearance. Full article
(This article belongs to the Special Issue Non-Coding RNAs)
Open AccessReview Hormonal Influence on Coenzyme Q10 Levels in Blood Plasma
Int. J. Mol. Sci. 2011, 12(12), 9216-9225; doi:10.3390/ijms12129216
Received: 1 November 2011 / Revised: 19 November 2011 / Accepted: 29 November 2011 / Published: 9 December 2011
Cited by 6 | PDF Full-text (364 KB) | HTML Full-text | XML Full-text
Abstract
Coenzyme Q10 (CoQ10), also known as ubiquinone for its presence in all body cells, is an essential part of the cell energy-producing system. However, it is also a powerful lipophilic antioxidant protecting lipoproteins and cell membranes. Due to these two
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Coenzyme Q10 (CoQ10), also known as ubiquinone for its presence in all body cells, is an essential part of the cell energy-producing system. However, it is also a powerful lipophilic antioxidant protecting lipoproteins and cell membranes. Due to these two actions, CoQ10 is commonly used in clinical practice in chronic heart failure, male infertility, and neurodegenerative disease. However, it is also taken as an anti-aging substance by healthy people aiming for long-term neuroprotection and by sportsmen to improve endurance. Many hormones are known to be involved in body energy regulation, in terms of production, consumption and dissipation, and their influence on CoQ10 body content or blood values may represent an important pathophysiological mechanism. We summarize the main findings of the literature about the link between hormonal systems and circulating CoQ10 levels. In particular the role of thyroid hormones, directly involved in the regulation of energy homeostasis, is discussed. There is also a link with gonadal and adrenal hormones, partially due to the common biosynthetic pathway with CoQ10, but also to the increased oxidative stress found in hypogonadism and hypoadrenalism. Full article
(This article belongs to the Special Issue Molecular System Bioenergetics 2011)
Open AccessReview The Slowly Aggregating Salmon Calcitonin: A Useful Tool for the Study of the Amyloid Oligomers Structure and Activity
Int. J. Mol. Sci. 2011, 12(12), 9277-9295; doi:10.3390/ijms12129277
Received: 28 October 2011 / Revised: 17 November 2011 / Accepted: 24 November 2011 / Published: 13 December 2011
Cited by 9 | PDF Full-text (3581 KB) | HTML Full-text | XML Full-text
Abstract
Amyloid proteins of different aminoacidic composition share the tendency to misfold and aggregate in a similar way, following common aggregation steps. The process includes the formation of dimers, trimers, and low molecular weight prefibrillar oligomers, characterized by the typical morphology of globules less
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Amyloid proteins of different aminoacidic composition share the tendency to misfold and aggregate in a similar way, following common aggregation steps. The process includes the formation of dimers, trimers, and low molecular weight prefibrillar oligomers, characterized by the typical morphology of globules less than 10 nm diameter. The globules spontaneously form linear or annular structures and, eventually, mature fibers. The rate of this process depends on characteristics intrinsic to the different proteins and to environmental conditions (i.e., pH, ionic strength, solvent composition, temperature). In the case of neurodegenerative diseases, it is now generally agreed that the pathogenic aggregates are not the mature fibrils, but the intermediate, soluble oligomers. However, the molecular mechanism by which these oligomers trigger neuronal damage is still unclear. Inparticular, it is not clear if there is a peculiar structure at the basis of the neurotoxic effect and how this structure interacts with neurons. This review will focus on the results we obtained using salmon Calcitonin, an amyloid protein characterized by a very slow aggregation rate, which allowed us to closely monitor the aggregation process. We used it as a tool to investigate the characteristics of amyloid oligomers formation and their interactions with neuronal cells. Our results indicate that small globules of about 6 nm could be the responsible for the neurotoxic effects. Moreover, our data suggest that the rich content in lipid rafts of neuronal cell plasma membrane may render neurons particularly vulnerable to the amyloid protein toxic effect. Full article
(This article belongs to the Special Issue Protein Aggregation)
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Open AccessReview Chiral Vibrational Structures of Proteins at Interfaces Probed by Sum Frequency Generation Spectroscopy
Int. J. Mol. Sci. 2011, 12(12), 9404-9425; doi:10.3390/ijms12129404
Received: 8 November 2011 / Revised: 13 December 2011 / Accepted: 13 December 2011 / Published: 16 December 2011
Cited by 37 | PDF Full-text (963 KB) | HTML Full-text | XML Full-text
Abstract
We review the recent development of chiral sum frequency generation (SFG) spectroscopy and its applications to study chiral vibrational structures at interfaces. This review summarizes observations of chiral SFG signals from various molecular systems and describes the molecular origins of chiral SFG response.
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We review the recent development of chiral sum frequency generation (SFG) spectroscopy and its applications to study chiral vibrational structures at interfaces. This review summarizes observations of chiral SFG signals from various molecular systems and describes the molecular origins of chiral SFG response. It focuses on the chiral vibrational structures of proteins and presents the chiral SFG spectra of proteins at interfaces in the C-H stretch, amide I, and N-H stretch regions. In particular, a combination of chiral amide I and N-H stretches of the peptide backbone provides highly characteristic vibrational signatures, unique to various secondary structures, which demonstrate the capacity of chiral SFG spectroscopy to distinguish protein secondary structures at interfaces. On the basis of these recent developments, we further discuss the advantages of chiral SFG spectroscopy and its potential application in various fields of science and technology. We conclude that chiral SFG spectroscopy can be a new approach to probe chiral vibrational structures of protein at interfaces, providing structural and dynamic information to study in situ and in real time protein structures and dynamics at interfaces. Full article
(This article belongs to the Special Issue Applications of Circular Dichroism)
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Open AccessReview Genetic and Epigenetic Traits as Biomarkers in Colorectal Cancer
Int. J. Mol. Sci. 2011, 12(12), 9426-9439; doi:10.3390/ijms12129426
Received: 17 October 2011 / Revised: 28 November 2011 / Accepted: 7 December 2011 / Published: 16 December 2011
Cited by 19 | PDF Full-text (312 KB) | HTML Full-text | XML Full-text | Supplementary Files
Abstract
Colorectal cancer is a major health burden, and a leading cause of cancer-related deaths in industrialized countries. The steady improvements in surgery and chemotherapy have improved survival, but the ability to identify high- and low-risk patients is still somewhat poor. Molecular biology has,
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Colorectal cancer is a major health burden, and a leading cause of cancer-related deaths in industrialized countries. The steady improvements in surgery and chemotherapy have improved survival, but the ability to identify high- and low-risk patients is still somewhat poor. Molecular biology has, over the years, given insight into basic principles of colorectal cancer initiation and development. These findings include aberrations increasing risk of tumor development, genetic changes associated with the stepwise progression of the disease, and errors predicting response to a specific treatment. Potential biomarkers in colorectal cancer are extensively studied, and how the molecular aberrations relate to clinical features. Yet, little of this knowledge has been possible to transfer into clinical practice. In this review, an overview of colorectal cancer genetics will be given, as well as how aberrations found in this tumor type are proposed as biomarkers for risk prediction, as diagnostic tools, for prognosis or prediction of treatment outcome. Full article
(This article belongs to the Section Biochemistry, Molecular Biology and Biophysics)
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Open AccessReview Volatile Compounds in Honey: A Review on Their Involvement in Aroma, Botanical Origin Determination and Potential Biomedical Activities
Int. J. Mol. Sci. 2011, 12(12), 9514-9532; doi:10.3390/ijms12129514
Received: 2 November 2011 / Revised: 29 November 2011 / Accepted: 12 December 2011 / Published: 20 December 2011
Cited by 32 | PDF Full-text (154 KB) | HTML Full-text | XML Full-text
Abstract
Volatile organic compounds (VOCs) in honey are obtained from diverse biosynthetic pathways and extracted by using various methods associated with varying degrees of selectivity and effectiveness. These compounds are grouped into chemical categories such as aldehyde, ketone, acid, alcohol, hydrocarbon, norisoprenoids, terpenes and
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Volatile organic compounds (VOCs) in honey are obtained from diverse biosynthetic pathways and extracted by using various methods associated with varying degrees of selectivity and effectiveness. These compounds are grouped into chemical categories such as aldehyde, ketone, acid, alcohol, hydrocarbon, norisoprenoids, terpenes and benzene compounds and their derivatives, furan and pyran derivatives. They represent a fingerprint of a specific honey and therefore could be used to differentiate between monofloral honeys from different floral sources, thus providing valuable information concerning the honey’s botanical and geographical origin. However, only plant derived compounds and their metabolites (terpenes, norisoprenoids and benzene compounds and their derivatives) must be employed to discriminate among floral origins of honey. Notwithstanding, many authors have reported different floral markers for honey of the same floral origin, consequently sensory analysis, in conjunction with analysis of VOCs could help to clear this ambiguity. Furthermore, VOCs influence honey’s aroma described as sweet, citrus, floral, almond, rancid, etc. Clearly, the contribution of a volatile compound to honey aroma is determined by its odor activity value. Elucidation of the aroma compounds along with floral origins of a particular honey can help to standardize its quality and avoid fraudulent labeling of the product. Although only present in low concentrations, VOCS could contribute to biomedical activities of honey, especially the antioxidant effect due to their natural radical scavenging potential. Full article
(This article belongs to the Section Biochemistry, Molecular Biology and Biophysics)
Open AccessReview Advances in Carcinogenic Metal Toxicity and Potential Molecular Markers
Int. J. Mol. Sci. 2011, 12(12), 9576-9595; doi:10.3390/ijms12129576
Received: 13 September 2011 / Revised: 28 October 2011 / Accepted: 12 December 2011 / Published: 20 December 2011
Cited by 49 | PDF Full-text (236 KB) | HTML Full-text | XML Full-text
Abstract
Metal compounds such as arsenic, cadmium, chromium, cobalt, lead, mercury, and nickel are classified as carcinogens affecting human health through occupational and environmental exposure. However, the underlying mechanisms involved in tumor formation are not well clarified. Interference of metal homeostasis may result in
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Metal compounds such as arsenic, cadmium, chromium, cobalt, lead, mercury, and nickel are classified as carcinogens affecting human health through occupational and environmental exposure. However, the underlying mechanisms involved in tumor formation are not well clarified. Interference of metal homeostasis may result in oxidative stress which represents an imbalance between production of free radicals and the system’s ability to readily detoxify reactive intermediates. This event consequently causes DNA damage, lipid peroxidation, protein modification, and possibly symptomatic effects for various diseases including cancer. This review discusses predominant modes of action and numerous molecular markers. Attention is paid to metal-induced generation of free radicals, the phenomenon of oxidative stress, damage to DNA, lipid, and proteins, responsive signal transduction pathways with major roles in cell growth and development, and roles of antioxidant enzymatic and DNA repair systems. Interaction of non-enzymatic antioxidants (carotenoids, flavonoids, glutathione, selenium, vitamin C, vitamin E, and others) with cellular oxidative stress markers (catalase, glutathione peroxidase, and superoxide dismutase) as well as certain regulatory factors, including AP-1, NF-κB, Ref-1, and p53 is also reviewed. Dysregulation of protective pathways, including cellular antioxidant network against free radicals as well as DNA repair deficiency is related to oncogenic stimulation. These observations provide evidence that emerging oxidative stress-responsive regulatory factors and DNA repair proteins are putative predictive factors for tumor initiation and progression. Full article
(This article belongs to the Special Issue Biomarkers 2011)

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Open AccessShort Note Seasonal Variation in the Hepatoproteome of the Dehydration- and Freeze-Tolerant Wood Frog, Rana sylvatica
Int. J. Mol. Sci. 2011, 12(12), 8406-8414; doi:10.3390/ijms12128406
Received: 17 October 2011 / Revised: 12 November 2011 / Accepted: 21 November 2011 / Published: 29 November 2011
Cited by 10 | PDF Full-text (125 KB) | HTML Full-text | XML Full-text
Abstract
Winter’s advent invokes physiological adjustments that permit temperate ectotherms to cope with stresses such as food shortage, water deprivation, hypoxia, and hypothermia. We used liquid chromatography (LC) in combination with tandem mass spectrometry (MS/MS) quantitative isobaric (iTRAQ™) peptide mapping to assess variation in
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Winter’s advent invokes physiological adjustments that permit temperate ectotherms to cope with stresses such as food shortage, water deprivation, hypoxia, and hypothermia. We used liquid chromatography (LC) in combination with tandem mass spectrometry (MS/MS) quantitative isobaric (iTRAQ™) peptide mapping to assess variation in the abundance of hepatic proteins in summer- and winter-acclimatized wood frogs (Rana sylvatica), a northerly-distributed species that tolerates extreme dehydration and tissue freezing during hibernation. Thirty-three unique proteins exhibited strong seasonal lability. Livers of winter frogs had relatively high levels of proteins involved in cytoprotection, including heat-shock proteins and an antioxidant, and a reduced abundance of proteins involved in cell proliferation, protein synthesis, and mitochondrial function. They also exhibited altered levels of certain metabolic enzymes that participate in the biochemical reorganization associated with aphagia and reliance on energy reserves, as well as the freezing mobilization and post-thaw recovery of glucose, an important cryoprotective solute in freezing adaptation. Full article
(This article belongs to the Section Biochemistry, Molecular Biology and Biophysics)
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Open AccessTechnical Note Development and Characterization of 20 Microsatellite Markers for Chinese Black Sleeper, Bostrychus sinensis
Int. J. Mol. Sci. 2011, 12(12), 9570-9575; doi:10.3390/ijms12129570
Received: 12 October 2011 / Revised: 30 November 2011 / Accepted: 12 December 2011 / Published: 20 December 2011
Cited by 4 | PDF Full-text (131 KB) | HTML Full-text | XML Full-text
Abstract
Twenty microsatellite markers were isolated and characterized from the Chinese black sleeper, Bostrychus sinensis. Loci were screened in 30 individuals from Taiwan. For each locus, the number of alleles varied from 4 to 22 with mean expected and observed heterozygosity of 0.79
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Twenty microsatellite markers were isolated and characterized from the Chinese black sleeper, Bostrychus sinensis. Loci were screened in 30 individuals from Taiwan. For each locus, the number of alleles varied from 4 to 22 with mean expected and observed heterozygosity of 0.79 and 0.66, respectively. One locus significantly deviated from Hardy-Weinberg equilibrium after Bonferroni correction and no significant linkage disequilibrium was detected. This set of microsatellites will provide a suitable tool for population genetic studies of Chinese black sleeper. Full article
(This article belongs to the Section Biochemistry, Molecular Biology and Biophysics)

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