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Int. J. Mol. Sci., Volume 11, Issue 9 (September 2010) – 35 articles , Pages 3039-3622

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Open AccessArticle
Exposure to Sodium Fluoride Produces Signs of Apoptosis in Rat Leukocytes
Int. J. Mol. Sci. 2010, 11(9), 3610-3622; https://doi.org/10.3390/ijms11093610 - 27 Sep 2010
Cited by 14 | Viewed by 6430
Abstract
Fluoride is naturally present in the earth's crust and can be found in rocks, coal, and clay; thus, it can be found in small quantities in water, air, plants, and animals. Therefore, humans are exposed to fluoride through food, drinking water, and in [...] Read more.
Fluoride is naturally present in the earth's crust and can be found in rocks, coal, and clay; thus, it can be found in small quantities in water, air, plants, and animals. Therefore, humans are exposed to fluoride through food, drinking water, and in the air they breathe. Flouride is essential to maintain bone strength and to protect against dental decay, but if it is absorbed too frequently, it can cause tooth decay, osteoporosis, and damage to kidneys, bones, nerves, and muscles. Therefore, the present work was aimed at determining the effect of intake of sodium fluoride (NaF) as an apoptosis inducer in leukocytes of rats treated for eight weeks with 1 or 50 parts per million (ppm) NaF. Expression of p53, bcl-2, and caspade-3 were used as apoptotic and general metabolism indicators of leukocyte-like indicators of the (INT) oxidation system. Male rats were exposed to NaF (1 and 500 ppm) for eight weeks, and then sacrificed weekly to obtain blood samples. Expression of p53, bcl-2, and caspase-3 were determined in leukocytes by Western blot, and general metabolism of leukocytes was analyzed with a commercial kit. We found changes in the expression of the proteins described, especially when the animals received 50 ppm of NaF. These results indicate that NaF intoxication can be an apoptosis inducer in rat leukocytes treated with the compound for eight weeks. Full article
(This article belongs to the Section Biochemistry)
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Open AccessArticle
Model Free Approach for Non-Isothermal Decomposition of Un-Irradiated and g-Irradiated Silver Acetate: New Route for Synthesis of Ag2O Nanoparticles
Int. J. Mol. Sci. 2010, 11(9), 3600-3609; https://doi.org/10.3390/ijms11093600 - 27 Sep 2010
Cited by 6 | Viewed by 6377
Abstract
Kinetic studies for the non-isothermal decomposition of unirradiated and γ‑irradiated silver acetate with 103 kGy total γ-ray doses were carried out in air. The results showed that the decomposition proceeds in one major step in the temperature range of (180–270 °C) with [...] Read more.
Kinetic studies for the non-isothermal decomposition of unirradiated and γ‑irradiated silver acetate with 103 kGy total γ-ray doses were carried out in air. The results showed that the decomposition proceeds in one major step in the temperature range of (180–270 °C) with the formation of Ag2O as solid residue. The non-isothermal data for un‑irradiated and γ-irradiated silver acetate were analyzed using Flynn-Wall-Ozawa (FWO) and nonlinear Vyazovkin (VYZ) iso-conversional methods. These free models on the investigated data showed a systematic dependence of Ea on a indicating a simple decomposition process. No significant changes in the thermal decomposition behavior of silver acetate were recorded as a result of γ-irradiation. Calcinations of γ-irradiated silver acetate (CH3COOAg) at 200 °C for 2 hours only led to the formation of pure Ag2O mono-dispersed nanoparticles. X-ray diffraction, FTIR and SEM techniques were employed for characterization of the synthesized nanoparticles. Full article
(This article belongs to the Section Physical Chemistry, Theoretical and Computational Chemistry)
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Open AccessReview
Quantitative Analysis of Cellular Metabolic Dissipative, Self-Organized Structures
Int. J. Mol. Sci. 2010, 11(9), 3540-3599; https://doi.org/10.3390/ijms11093540 - 27 Sep 2010
Cited by 18 | Viewed by 9344
Abstract
One of the most important goals of the postgenomic era is understanding the metabolic dynamic processes and the functional structures generated by them. Extensive studies during the last three decades have shown that the dissipative self-organization of the functional enzymatic associations, the catalytic [...] Read more.
One of the most important goals of the postgenomic era is understanding the metabolic dynamic processes and the functional structures generated by them. Extensive studies during the last three decades have shown that the dissipative self-organization of the functional enzymatic associations, the catalytic reactions produced during the metabolite channeling, the microcompartmentalization of these metabolic processes and the emergence of dissipative networks are the fundamental elements of the dynamical organization of cell metabolism. Here we present an overview of how mathematical models can be used to address the properties of dissipative metabolic structures at different organizational levels, both for individual enzymatic associations and for enzymatic networks. Recent analyses performed with dissipative metabolic networks have shown that unicellular organisms display a singular global enzymatic structure common to all living cellular organisms, which seems to be an intrinsic property of the functional metabolism as a whole. Mathematical models firmly based on experiments and their corresponding computational approaches are needed to fully grasp the molecular mechanisms of metabolic dynamical processes. They are necessary to enable the quantitative and qualitative analysis of the cellular catalytic reactions and also to help comprehend the conditions under which the structural dynamical phenomena and biological rhythms arise. Understanding the molecular mechanisms responsible for the metabolic dissipative structures is crucial for unraveling the dynamics of cellular life. Full article
(This article belongs to the Special Issue Quantitative Modelling in Molecular System Bioenergetics)
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Open AccessArticle
Fabrication of Chitosan/Silk Fibroin Composite Nanofibers for Wound-dressing Applications
Int. J. Mol. Sci. 2010, 11(9), 3529-3539; https://doi.org/10.3390/ijms11093529 - 21 Sep 2010
Cited by 211 | Viewed by 10445
Abstract
Chitosan, a naturally occurring polysaccharide with abundant resources, has been extensively exploited for various biomedical applications, typically as wound dressings owing to its unique biocompatibility, good biodegradability and excellent antibacterial properties. In this work, composite nanofibrous membranes of chitosan (CS) and silk fibroin [...] Read more.
Chitosan, a naturally occurring polysaccharide with abundant resources, has been extensively exploited for various biomedical applications, typically as wound dressings owing to its unique biocompatibility, good biodegradability and excellent antibacterial properties. In this work, composite nanofibrous membranes of chitosan (CS) and silk fibroin (SF) were successfully fabricated by electrospinning. The morphology of electrospun blend nanofibers was observed by scanning electron microscopy (SEM) and the fiber diameters decreased with the increasing percentage of chitosan. Further, the mechanical test illustrated that the addition of silk fibroin enhanced the mechanical properties of CS/SF nanofibers. The antibacterial activities against Escherichia coli (Gram negative) and Staphylococcus aureus (Gram positive) were evaluated by the turbidity measurement method; and results suggest that the antibacterial effect of composite nanofibers varied on the type of bacteria. Furthermore, the biocompatibility of murine fibroblast on as-prepared nanofibrous membranes was investigated by hematoxylin and eosin (H&E) staining and MTT assays in vitro, and the membranes were found to promote the cell attachment and proliferation. These results suggest that as-prepared chitosan/silk fibroin (CS/SF) composite nanofibrous membranes could be a promising candidate for wound healing applications. Full article
(This article belongs to the Special Issue Chitins)
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Open AccessReview
Human Umbilical Cord Blood Stem Cells: Rational for Use as a Neuroprotectant in Ischemic Brain Disease
Int. J. Mol. Sci. 2010, 11(9), 3513-3528; https://doi.org/10.3390/ijms11093513 - 21 Sep 2010
Cited by 20 | Viewed by 6883
Abstract
The use of stem cells for reparative medicine was first proposed more than three decades ago. Hematopoietic stem cells from bone marrow, peripheral blood and human umbilical cord blood (CB) have gained major use for treatment of hematological indications. CB, however, is also [...] Read more.
The use of stem cells for reparative medicine was first proposed more than three decades ago. Hematopoietic stem cells from bone marrow, peripheral blood and human umbilical cord blood (CB) have gained major use for treatment of hematological indications. CB, however, is also a source of cells capable of differentiating into various non-hematopoietic cell types, including neural cells. Several animal model reports have shown that CB cells may be used for treatment of neurological injuries. This review summarizes the information available on the origin of CB-derived neuronal cells and the mechanisms proposed to explain their action. The potential use of stem/progenitor cells for treatment of ischemic brain injuries is discussed. Issues that remain to be resolved at the present stage of preclinical trials are addressed. Full article
(This article belongs to the Special Issue Neuroprotective Strategies (special issue))
Open AccessArticle
Interferon-alpha Induces High Expression of APOBEC3G and STAT-1 in Vitro and in Vivo
Int. J. Mol. Sci. 2010, 11(9), 3501-3512; https://doi.org/10.3390/ijms11093501 - 20 Sep 2010
Cited by 19 | Viewed by 6551
Abstract
To investigate whether the JAK-STAT (Janus kinase-signal transducers and activators of transcription) pathway participates in the regulation of APOBEC3G (Apolipoprotein B mRNA-editing enzyme, catalytic polypeptide-like 3G) gene transcription and to study the molecular mechanisms of interferon resistance in patients with chronic hepatitis B [...] Read more.
To investigate whether the JAK-STAT (Janus kinase-signal transducers and activators of transcription) pathway participates in the regulation of APOBEC3G (Apolipoprotein B mRNA-editing enzyme, catalytic polypeptide-like 3G) gene transcription and to study the molecular mechanisms of interferon resistance in patients with chronic hepatitis B (CHB), changes in APOBEC3G and STAT-1 expression levels in HepG2.2.15 cells after treatment with various concentrations of IFN-a, were detected using real-time RT-PCR and Western-blot. In addition, the differences in STAT-1 and APOBEC3G expression in liver tissues were also observed in patients with different anti-viral responses to IFN-a. It is found that IFN-a suppressed HBV replication and expression markedly in HepG2.2.15 cells, and simultaneously enhanced APOBEC3G expression in a dose- or time-dependent manner within a certain range. Moreover, a corresponding gradual increase in STAT-1 expression levels was also observed. The expression levels of STAT-1 and APOBEC3G in the liver of CHB patients with a complete response to IFN-a are significantly higher than that of the patients with non-response to IFN-a treatment. It is suggested that inducing intracellular APOBEC3G expression may be one of anti-HBV mechanisms of IFN-a, and IFN-a-induced APOBEC3G expression may be via the JAK-STAT signaling pathway. Moreover, interferon resistance may be related to the down-regulation of STAT-1 expression in the patients who had non-response to IFN-a treatment. Full article
(This article belongs to the Section Biochemistry)
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Open AccessReview
The Chemical Master Equation Approach to Nonequilibrium Steady-State of Open Biochemical Systems: Linear Single-Molecule Enzyme Kinetics and Nonlinear Biochemical Reaction Networks
Int. J. Mol. Sci. 2010, 11(9), 3472-3500; https://doi.org/10.3390/ijms11093472 - 20 Sep 2010
Cited by 45 | Viewed by 8401
Abstract
We develop the stochastic, chemical master equation as a unifying approach to the dynamics of biochemical reaction systems in a mesoscopic volume under a living environment. A living environment provides a continuous chemical energy input that sustains the reaction system in a nonequilibrium [...] Read more.
We develop the stochastic, chemical master equation as a unifying approach to the dynamics of biochemical reaction systems in a mesoscopic volume under a living environment. A living environment provides a continuous chemical energy input that sustains the reaction system in a nonequilibrium steady state with concentration fluctuations. We discuss the linear, unimolecular single-molecule enzyme kinetics, phosphorylation-dephosphorylation cycle (PdPC) with bistability, and network exhibiting oscillations. Emphasis is paid to the comparison between the stochastic dynamics and the prediction based on the traditional approach based on the Law of Mass Action. We introduce the difference between nonlinear bistability and stochastic bistability, the latter has no deterministic counterpart. For systems with nonlinear bistability, there are three different time scales: (a) individual biochemical reactions, (b) nonlinear network dynamics approaching to attractors, and (c) cellular evolution. For mesoscopic systems with size of a living cell, dynamics in (a) and (c) are stochastic while that with (b) is dominantly deterministic. Both (b) and (c) are emergent properties of a dynamic biochemical network; We suggest that the (c) is most relevant to major cellular biochemical processes such as epi-genetic regulation, apoptosis, and cancer immunoediting. The cellular evolution proceeds with transitions among the attractors of (b) in a “punctuated equilibrium” manner. Full article
(This article belongs to the Special Issue Quantitative Modelling in Molecular System Bioenergetics)
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Open AccessArticle
Removal of Parabens from Aqueous Solution Using β-Cyclodextrin Cross-Linked Polymer
Int. J. Mol. Sci. 2010, 11(9), 3459-3471; https://doi.org/10.3390/ijms11092459 - 20 Sep 2010
Cited by 50 | Viewed by 5871
Abstract
The removal of four parabens, methyl-, ethyl-, propyl-, and benzyl-paraben, by β-cyclodextrin (β-CD) polymer from aqueous solution was studied. Different β-CD polymers were prepared by using two cross-linkers, i.e., hexamethylene diisocyanate (HMDI) and toluene-2,6-diisocyanate (TDI), with various molar ratios of cross-linker. β-CD-HMDI [...] Read more.
The removal of four parabens, methyl-, ethyl-, propyl-, and benzyl-paraben, by β-cyclodextrin (β-CD) polymer from aqueous solution was studied. Different β-CD polymers were prepared by using two cross-linkers, i.e., hexamethylene diisocyanate (HMDI) and toluene-2,6-diisocyanate (TDI), with various molar ratios of cross-linker. β-CD-HMDI polymer with molar ratio of 1:7 and β-CD-TDI polymer with ratio 1:4 gave the highest adsorption of parabens among the β-CD-HMDI and β-CD-TDI series, and were subsequently used for further studies. The adsorption capacity of β-CD-HMDI is 0.0305, 0.0376, 0.1854 and 0.3026 mmol/g for methyl-, ethyl-, propyl-, and benzyl-paraben, respectively. β-CD-TDI have higher adsorption capacities compared with β-CD-HMDI, the adsorption capacity are 0.1019, 0.1286, 0.2551, and 0.3699 mmol/g methyl-, ethyl-, propyl-, and benzyl-paraben respectively. The parameters studied were adsorption capacity, water retention, and reusability. Role of both cross-linker in adsorption, hydrophobicity of polymers, and adsorption capacity of different parabens were compared and discussed. All experiments were conducted in batch adsorption technique. These polymers were applied to real samples and showed positive results. Full article
(This article belongs to the Section Biochemistry)
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Open AccessArticle
In Silico Prediction of Estrogen Receptor Subtype Binding Affinity and Selectivity Using Statistical Methods and Molecular Docking with 2-Arylnaphthalenes and 2-Arylquinolines
Int. J. Mol. Sci. 2010, 11(9), 3434-3458; https://doi.org/10.3390/ijms11093434 - 20 Sep 2010
Cited by 30 | Viewed by 6230
Abstract
Over the years development of selective estrogen receptor (ER) ligands has been of great concern to researchers involved in the chemistry and pharmacology of anticancer drugs, resulting in numerous synthesized selective ER subtype inhibitors. In this work, a data set of 82 ER [...] Read more.
Over the years development of selective estrogen receptor (ER) ligands has been of great concern to researchers involved in the chemistry and pharmacology of anticancer drugs, resulting in numerous synthesized selective ER subtype inhibitors. In this work, a data set of 82 ER ligands with ERα and ERβ inhibitory activities was built, and quantitative structure-activity relationship (QSAR) methods based on the two linear (multiple linear regression, MLR, partial least squares regression, PLSR) and a nonlinear statistical method (Bayesian regularized neural network, BRNN) were applied to investigate the potential relationship of molecular structural features related to the activity and selectivity of these ligands. For ERα and ERβ, the performances of the MLR and PLSR models are superior to the BRNN model, giving more reasonable statistical properties (ERα: for MLR, Rtr2 = 0.72, Qte2 = 0.63; for PLSR, Rtr2 = 0.92, Qte2 = 0.84. ERβ: for MLR, Rtr2 = 0.75, Qte2 = 0.75; for PLSR, Rtr2 = 0.98, Qte2 = 0.80). The MLR method is also more powerful than other two methods for generating the subtype selectivity models, resulting in Rtr2 = 0.74 and Qte2 = 0.80. In addition, the molecular docking method was also used to explore the possible binding modes of the ligands and a relationship between the 3D-binding modes and the 2D-molecular structural features of ligands was further explored. The results show that the binding affinity strength for both ERα and ERβ is more correlated with the atom fragment type, polarity, electronegativites and hydrophobicity. The substitutent in position 8 of the naphthalene or the quinoline plane and the space orientation of these two planes contribute the most to the subtype selectivity on the basis of similar hydrogen bond interactions between binding ligands and both ER subtypes. The QSAR models built together with the docking procedure should be of great advantage for screening and designing ER ligands with improved affinity and subtype selectivity property. Full article
(This article belongs to the Special Issue Recent Advances in QSAR/QSPR Theory)
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Open AccessArticle
Prediction of PKCθ Inhibitory Activity Using the Random Forest Algorithm
Int. J. Mol. Sci. 2010, 11(9), 3413-3433; https://doi.org/10.3390/ijms11093413 - 20 Sep 2010
Cited by 8 | Viewed by 6422
Abstract
This work is devoted to the prediction of a series of 208 structurally diverse PKCθ inhibitors using the Random Forest (RF) based on the Mold2 molecular descriptors. The RF model was established and identified as a robust predictor of the experimental pIC [...] Read more.
This work is devoted to the prediction of a series of 208 structurally diverse PKCθ inhibitors using the Random Forest (RF) based on the Mold2 molecular descriptors. The RF model was established and identified as a robust predictor of the experimental pIC50 values, producing good external R2pred of 0.72, a standard error of prediction (SEP) of 0.45, for an external prediction set of 51 inhibitors which were not used in the development of QSAR models. By using the RF built-in measure of the relative importance of the descriptors, an important predictor—the number of group donor atoms for H-bonds (with N and O)―has been identified to play a crucial role in PKCθ inhibitory activity. We hope that the developed RF model will be helpful in the screening and prediction of novel unknown PKCθ inhibitory activity. Full article
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Open AccessReview
Practical Application of Toxicogenomics for Profiling Toxicant-Induced Biological Perturbations
Int. J. Mol. Sci. 2010, 11(9), 3397-3412; https://doi.org/10.3390/ijms11093397 - 20 Sep 2010
Cited by 21 | Viewed by 7191
Abstract
A systems-level understanding of molecular perturbations is crucial for evaluating chemical-induced toxicity risks appropriately, and for this purpose comprehensive gene expression analysis or toxicogenomics investigation is highly advantageous. The recent accumulation of toxicity-associated gene sets (toxicogenomic biomarkers), enrichment in public or commercial large-scale [...] Read more.
A systems-level understanding of molecular perturbations is crucial for evaluating chemical-induced toxicity risks appropriately, and for this purpose comprehensive gene expression analysis or toxicogenomics investigation is highly advantageous. The recent accumulation of toxicity-associated gene sets (toxicogenomic biomarkers), enrichment in public or commercial large-scale microarray database and availability of open-source software resources facilitate our utilization of the toxicogenomic data. However, toxicologists, who are usually not experts in computational sciences, tend to be overwhelmed by the gigantic amount of data. In this paper we present practical applications of toxicogenomics by utilizing biomarker gene sets and a simple scoring method by which overall gene set-level expression changes can be evaluated efficiently. Results from the gene set-level analysis are not only an easy interpretation of toxicological significance compared with individual gene-level profiling, but also are thought to be suitable for cross-platform or cross-institutional toxicogenomics data analysis. Enrichment in toxicogenomics databases, refinements of biomarker gene sets and scoring algorithms and the development of user-friendly integrative software will lead to better evaluation of toxicant-elicited biological perturbations. Full article
(This article belongs to the Special Issue Advances in Molecular Toxicology)
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Open AccessArticle
Inhibitory Activities of Cyanidin and Its Glycosides and Synergistic Effect with Acarbose against Intestinal α-Glucosidase and Pancreatic α-Amylase
Int. J. Mol. Sci. 2010, 11(9), 3387-3396; https://doi.org/10.3390/ijms11093387 - 20 Sep 2010
Cited by 146 | Viewed by 8558
Abstract
Cyanidin and its glycosides are naturally dietary pigments which have been indicated as promising candidates to have potential benefits to humans, especially in the prevention and treatment of diabetes mellitus. We investigated the structure activity relationships of cyanidin and its glycosides to inhibit [...] Read more.
Cyanidin and its glycosides are naturally dietary pigments which have been indicated as promising candidates to have potential benefits to humans, especially in the prevention and treatment of diabetes mellitus. We investigated the structure activity relationships of cyanidin and its glycosides to inhibit intestinal a-glucosidases and pancreatic a-amylase in vitro. The results found that cyanidin and its glycosides are more specific inhibitors of intestinal sucrase than intestinal maltase. Cyanidin-3-galactoside and cyanidin-3-glucoside were the most potent inhibitors against intestinal sucrase and pancreatic a-amylase with IC50 values of 0.50 ± 0.05 and 0.30 ± 0.01 mM, respectively. Our findings indicate that the structural difference between glucose and galactose at the 3-O-position of cyanidin was an important factor for modulating the inhibition of intestinal sucrase and pancreatic a-amylase. The combination of cyandin-3-glucoside, cyanidin-3-galactoside or cyanidin-3,5-diglucosides with a low concentration of acarbose showed synergistic inhibition on intestinal maltase and sucrase. The synergistic inhibition was also found for a combination of cyanidin or cyanidin-3-glucoside with a low concentration of acarbose. The findings could provide a new insight into a use for the naturally occurring intestinal a-glucosidase and pancreatic a-amylase inhibitors for the prevention and treatment of diabetes and its complications. Full article
(This article belongs to the Section Biochemistry)
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Open AccessArticle
Cigarette Smoke Affects ABCAl Expression via Liver X Receptor Nuclear Translocation in Human Keratinocytes
Int. J. Mol. Sci. 2010, 11(9), 3375-3386; https://doi.org/10.3390/ijms11093375 - 17 Sep 2010
Cited by 25 | Viewed by 7166
Abstract
Cutaneous tissue is the first barrier against outdoor insults. The outer most layer of the skin, the stratum corneum (SC), is formed by corneocytes embedded in a lipid matrix (cholesterol, ceramide and fatty acids). Therefore, the regulation of lipids and, in particular, of [...] Read more.
Cutaneous tissue is the first barrier against outdoor insults. The outer most layer of the skin, the stratum corneum (SC), is formed by corneocytes embedded in a lipid matrix (cholesterol, ceramide and fatty acids). Therefore, the regulation of lipids and, in particular, of cholesterol homeostasis in the skin is of great importance. ABCA1 is a membrane transporter responsible for cholesterol efflux and plays a key role in maintaining cellular cholesterol levels. Among the many factors that have been associated with skin diseases, the environmental stressor cigarette smoke has been recently studied. In the present study, we demonstrate that ABCA1 expression in human cells (HaCaT) was increased (both mRNA and protein levels) after CS exposure. This effect was mediated by the inhibition of NFkB (aldehydes adducts formation) that allows the translocation of liver X receptor (LXR). These findings suggest that passive smoking may play a role in skin cholesterol levels and thus affect cutaneous tissues functions. Full article
(This article belongs to the Special Issue Advances in Molecular Toxicology)
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Open AccessArticle
3D-QSAR and Molecular Docking Studies on Fused Pyrazoles as p38α Mitogen-Activated Protein Kinase Inhibitors
Int. J. Mol. Sci. 2010, 11(9), 3357-3374; https://doi.org/10.3390/ijms11093357 - 17 Sep 2010
Cited by 29 | Viewed by 6783
Abstract
The p38α mitogen-activated protein kinase (MAPK) has become an attractive target for the treatment of many diseases such as rheumatoid arthritis, inflammatory bowel disease and Crohn’s disease. In this paper, 3D-QSAR and molecular docking studies were performed on 59 p38α MAPK inhibitors. Comparative [...] Read more.
The p38α mitogen-activated protein kinase (MAPK) has become an attractive target for the treatment of many diseases such as rheumatoid arthritis, inflammatory bowel disease and Crohn’s disease. In this paper, 3D-QSAR and molecular docking studies were performed on 59 p38α MAPK inhibitors. Comparative molecular field analysis (CoMFA) and comparative molecular similarity indices analysis (CoMSIA) were applied to determine the structural requirements for potency in inhibiting p38α MAPK. The resulting model of CoMFA and CoMSIA exhibited good r2cv values of 0.725 and 0.609, and r2 values of 0.961 and 0.905, respectively. Molecular docking was used to explore the binding mode between the inhibitors and p38α MAPK. We have accordingly designed a series of novel p38α MAPK inhibitors by utilizing the structure-activity relationship (SAR) results revealed in the present study, which were predicted with excellent potencies in the developed models. The results provided a useful guide to design new compounds for p38α MAPK inhibitors. Full article
(This article belongs to the Special Issue Recent Advances in QSAR/QSPR Theory)
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Open AccessArticle
Microbial Contamination of Orthodontic Buccal Tubes from Manufacturers
Int. J. Mol. Sci. 2010, 11(9), 3349-3356; https://doi.org/10.3390/ijms11093349 - 16 Sep 2010
Cited by 10 | Viewed by 5300
Abstract
This study aimed to test the sterility of new unused orthodontic buccal tubes received from manufacturers. Four different types of buccal tubes were used straight from the manufactures package without any additional sterilizing step. Of these buccal tubes tested, three genera of bacteria, [...] Read more.
This study aimed to test the sterility of new unused orthodontic buccal tubes received from manufacturers. Four different types of buccal tubes were used straight from the manufactures package without any additional sterilizing step. Of these buccal tubes tested, three genera of bacteria, implicated as opportunistic pathogens, namely Micrococcus luteus, Staphylococcus haemolyticus and Acinetobacter calcoaceticus were recovered from these buccal tubes. Our data showing microbial contamination on buccal tubes highlights the need of sterilization before clinical use. We also suggest that manufacturers should list the sterility state of orthodontic buccal tubes on their packaging or instructions stating the need for sterilization. Full article
(This article belongs to the Section Biochemistry)
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Graphical abstract

Open AccessReview
Recognition of Chiral Carboxylic Anions by Artificial Receptors
Int. J. Mol. Sci. 2010, 11(9), 3334-3348; https://doi.org/10.3390/ijms11093334 - 15 Sep 2010
Cited by 28 | Viewed by 5987
Abstract
Many carboxylic molecules, ranging from drugs to flavors and fragrances, contain chiral centers. As a consequence, research has been carried out in order to design and synthesize artificial receptors for carboxylic anions. Many problems have to be solved for binding anions. The results [...] Read more.
Many carboxylic molecules, ranging from drugs to flavors and fragrances, contain chiral centers. As a consequence, research has been carried out in order to design and synthesize artificial receptors for carboxylic anions. Many problems have to be solved for binding anions. The results obtained in the binding of carboxylic anions by guanidine, secondary ammonium and metal-center have been selected. The last part of this review focuses on chiral recognition of carboxylic anions by organic and metal-based chiral receptors. Full article
(This article belongs to the Special Issue Advances in Molecular Recognition)
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Open AccessArticle
The Mechanism of (R,R) ZX-5 on Increasing NO Release
Int. J. Mol. Sci. 2010, 11(9), 3323-3333; https://doi.org/10.3390/ijms11093323 - 15 Sep 2010
Cited by 2 | Viewed by 6289
Abstract
(R,R) ZX-5 has been proven to have positive effects on choroidal blood flow without affecting the sclera and ciliary bodies in New Zealand white rabbits. This study was designed to investigate the mechanisms of (R,R) ZX-5 on improving the choroidal blood flow and [...] Read more.
(R,R) ZX-5 has been proven to have positive effects on choroidal blood flow without affecting the sclera and ciliary bodies in New Zealand white rabbits. This study was designed to investigate the mechanisms of (R,R) ZX-5 on improving the choroidal blood flow and promoting NO production. HUVECs (human umbilical vein endothelial cells) were used to determine the production of eNOS, p-eNOS, AKT and Erk1/2 by Western blot analysis. iNOS and eNOS mRNA levels were investigated by RT-PCR and the effect of (R,R) ZX-5 on NO production were determined by eNOS activity assay. We found (R,R) ZX-5 upregulated protein expression of eNOS and iNOS, increased NO production, and reduced ERK and Akt protein level. Therefore, (R,R) ZX-5 may promote the choroidal blood flow in New Zealand white rabbits without affecting the blood flow in the iris or ciliary bodies via increasing NO production. These results suggest that (R,R) ZX-5 may function to cure and prevent Age-related macular degeneration (AMD). Full article
(This article belongs to the Section Biochemistry)
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Open AccessReview
Materials for Pharmaceutical Dosage Forms: Molecular Pharmaceutics and Controlled Release Drug Delivery Aspects
Int. J. Mol. Sci. 2010, 11(9), 3298-3322; https://doi.org/10.3390/ijms11093298 - 15 Sep 2010
Cited by 132 | Viewed by 9153
Abstract
Controlled release delivery is available for many routes of administration and offers many advantages (as microparticles and nanoparticles) over immediate release delivery. These advantages include reduced dosing frequency, better therapeutic control, fewer side effects, and, consequently, these dosage forms are well accepted by [...] Read more.
Controlled release delivery is available for many routes of administration and offers many advantages (as microparticles and nanoparticles) over immediate release delivery. These advantages include reduced dosing frequency, better therapeutic control, fewer side effects, and, consequently, these dosage forms are well accepted by patients. Advances in polymer material science, particle engineering design, manufacture, and nanotechnology have led the way to the introduction of several marketed controlled release products and several more are in pre-clinical and clinical development. Full article
(This article belongs to the Special Issue Biodegradability of Materials in Biomedical Applications 2011)
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Open AccessReview
Stem Cells and Neuroprotection: Understanding the Players
Int. J. Mol. Sci. 2010, 11(9), 3288-3297; https://doi.org/10.3390/ijms11093288 - 15 Sep 2010
Cited by 4 | Viewed by 5372
Abstract
The use of neuroprotective therapies begs the question of how such therapies could affect preexisting stem cell populations within the host, as well as those introduced through cell-replacement therapy. Multiple mechanisms may mediate stem cell responses to neuroprotectants such as host/donor age and [...] Read more.
The use of neuroprotective therapies begs the question of how such therapies could affect preexisting stem cell populations within the host, as well as those introduced through cell-replacement therapy. Multiple mechanisms may mediate stem cell responses to neuroprotectants such as host/donor age and gender, cellular lineage/differentiation status, and mitochondrial dynamics. Current therapeutic sources for stem cells are embryonic, somatic, or induced pluripotent, with very little known about the effects of gender, age, cell type, and mitochondrial dynamics. With the advent of therapies to stimulate and recruit endogenous stem cells or transplant donor cells into damage areas in the hopes of recuperative regeneration of lost neurons, it is important to discuss mechanisms that dictate the winning players in the neuroprotection game. This review will focus on our current understanding of the characteristics of renewing stem cells that may affect neuroprotection. Full article
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Open AccessArticle
Effects of Time of Initial Exposure to MSV Sarcoma on Bone Induction by Dentine Matrix Implants and on Orthotopic Femora
Int. J. Mol. Sci. 2010, 11(9), 3277-3287; https://doi.org/10.3390/ijms11093277 - 15 Sep 2010
Cited by 2 | Viewed by 4376
Abstract
HCl-demineralized murine lower incisors were implanted intramuscularly into syngeneic BALB/c mice to induce heterotopic osteogenesis. Implants were exposed at the early, preosteogenic stage (4), or at the later, osteogenic stage (12) to the Moloney sarcoma virus (MSV), which within 3–4 days results in [...] Read more.
HCl-demineralized murine lower incisors were implanted intramuscularly into syngeneic BALB/c mice to induce heterotopic osteogenesis. Implants were exposed at the early, preosteogenic stage (4), or at the later, osteogenic stage (12) to the Moloney sarcoma virus (MSV), which within 3–4 days results in a sarcoma. The yield of bone induction was determined by weight of dry bone mass following NaOH hydrolysis of soft tissues. To verify the effect of this sarcoma on orthotopic local femoral bone, the dry mass of the tumor-exposed femora was measured and compared with the weight of MSV-unexposed contralateral controls. MSV-sarcoma or cells involved with their spontaneous rejection have a stimulatory effect on the periosteal membrane of the tumor-adjacent femoral bones, increasing their dry mass on average by 18%. No stimulatory effect on heterotopic bone induction was observed when the MSV sarcoma grew during the early, preosteogenic stage (4 onward), but when the tooth matrix had been exposed to such tumor at the already bone-forming stage, (12 onward), the yield of bone induction was enhanced. Thus, it is postulated that lesions induced by MSV during the early, preosteogenic stage inhibit recruitment of osteoprogenitor cells or degrade Bone Morphogenetic Proteins (BMPs) released by matrix resorbing inflammatory cells, whereas when acting on already existing bone they have a stimulatory effect. Full article
(This article belongs to the Special Issue Composite Materials in Skeletal Engineering)
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Open AccessArticle
Molecular Modeling of Peroxidase and Polyphenol Oxidase: Substrate Specificity and Active Site Comparison
Int. J. Mol. Sci. 2010, 11(9), 3266-3276; https://doi.org/10.3390/ijms11093266 - 14 Sep 2010
Cited by 40 | Viewed by 8169
Abstract
Peroxidases (POD) and polyphenol oxidase (PPO) are enzymes that are well known to be involved in the enzymatic browning reaction of fruits and vegetables with different catalytic mechanisms. Both enzymes have some common substrates, but each also has its specific substrates. In our [...] Read more.
Peroxidases (POD) and polyphenol oxidase (PPO) are enzymes that are well known to be involved in the enzymatic browning reaction of fruits and vegetables with different catalytic mechanisms. Both enzymes have some common substrates, but each also has its specific substrates. In our computational study, the amino acid sequence of grape peroxidase (ABX) was used for the construction of models employing homology modeling method based on the X-ray structure of cytosolic ascorbate peroxidase from pea (PDB ID:1APX), whereas the model of grape polyphenol oxidase was obtained directly from the available X-ray structure (PDB ID:2P3X). Molecular docking of common substrates of these two enzymes was subsequently studied. It was found that epicatechin and catechin exhibited high affinity with both enzymes, even though POD and PPO have different binding pockets regarding the size and the key amino acids involved in binding. Predicted binding modes of substrates with both enzymes were also compared. The calculated docking interaction energy of trihydroxybenzoic acid related compounds shows high affinity, suggesting specificity and potential use as common inhibitor to grape ascorbate peroxidase and polyphenol oxidase. Full article
(This article belongs to the Section Biochemistry)
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Open AccessArticle
A Computational Simulation Study of Benzamidine Derivatives Binding to Arginine-Specific Gingipain (HRgpA) from Periodontopathogen Porphyromonas gingivalis
Int. J. Mol. Sci. 2010, 11(9), 3252-3265; https://doi.org/10.3390/ijms11093252 - 13 Sep 2010
Viewed by 4978
Abstract
We have shown that the binding free energy calculation from molecular dynamics can be adapted successfully to cysteine proteinases, such as arginine-specific gingipain (HRgpA) from Porphyromonas gingivalis. The binding free energy obtained is in good agreement with the available experimental data for [...] Read more.
We have shown that the binding free energy calculation from molecular dynamics can be adapted successfully to cysteine proteinases, such as arginine-specific gingipain (HRgpA) from Porphyromonas gingivalis. The binding free energy obtained is in good agreement with the available experimental data for eight benzamidine derivatives including urea and ether linker. The calculations showed that the electrostatic energies between HRgpA and inhibitors were important in determining the relative affinities of the inhibitors to the HRgpA, with an average binding free energy of about −5 kcal/mol. The average structures of the eight complexes suggest that benzamidine inhibitors interact with Asp387, His435, and Cys468 by hydrogen bonding and with Trp508 by hydrophilic interactions that are essential for the activities of benzamidine inhibitors. It can therefore be expected that the method provides a reliable tool for the investigation of new HRgpA inhibitors. This finding could significantly benefit the future design of HRgpA inhibitors. Full article
(This article belongs to the Section Physical Chemistry, Theoretical and Computational Chemistry)
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Open AccessReview
Synthesis, Characterization, and Application of 1-D Cerium Oxide Nanomaterials: A Review
Int. J. Mol. Sci. 2010, 11(9), 3226-3251; https://doi.org/10.3390/ijms11093226 - 13 Sep 2010
Cited by 110 | Viewed by 9125
Abstract
The present work provides a comprehensive overview of the recent progress of research work toward developing new one dimensional (1-D) ceria (CeO2) nanomaterials. The review has been classified into three parts: the preparation procedures with identification of the existing different dimensional [...] Read more.
The present work provides a comprehensive overview of the recent progress of research work toward developing new one dimensional (1-D) ceria (CeO2) nanomaterials. The review has been classified into three parts: the preparation procedures with identification of the existing different dimensional ceria nanomaterials, the formation mechanisms, and an analysis of their applications. From literature survey, it is inaugurated that the fundamental structures of the ceria nanomaterials constructively dominate their properties and applications. In addition, this work will also provide a perspective on the future technical trends for the development of different dimensional CeO2 nanomaterials. Full article
(This article belongs to the Section Biochemistry)
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Open AccessReview
Biomarkers for Colorectal Cancer
Int. J. Mol. Sci. 2010, 11(9), 3209-3225; https://doi.org/10.3390/ijms11093209 - 13 Sep 2010
Cited by 78 | Viewed by 8347
Abstract
Colorectal cancer (CRC) is the third most common epithelial malignancy in the world. Since CRC develops slowly from removable precancerous lesions, detection of the lesion at an early stage by regular health examinations can reduce the incidence and mortality of this malignancy. Colonoscopy [...] Read more.
Colorectal cancer (CRC) is the third most common epithelial malignancy in the world. Since CRC develops slowly from removable precancerous lesions, detection of the lesion at an early stage by regular health examinations can reduce the incidence and mortality of this malignancy. Colonoscopy significantly improves the detection rate of CRC, but the examination is expensive and inconvenient. Therefore, we need novel biomarkers that are non-invasive to enable us to detect CRC quite early. A number of validation studies have been conducted to evaluate genetic, epigenetic or protein markers for identification in the stool and/or serum. Currently, the fecal occult blood test is the most widely used method of screening for CRC. However, advances in genomics and proteomics will lead to the discovery of novel non-invasive biomarkers. Full article
(This article belongs to the Special Issue Biomarkers)
Open AccessArticle
Expression of an Organic Solvent Stable Lipase from Staphylococcus epidermidis AT2
Int. J. Mol. Sci. 2010, 11(9), 3195-3208; https://doi.org/10.3390/ijms11093195 - 13 Sep 2010
Cited by 20 | Viewed by 5051
Abstract
An organic solvent tolerant lipase gene from Staphylococcus epidermidis AT2 was successfully cloned and expressed with pTrcHis2 in E. coli TOP10. Sequence analysis revealed an open reading frame (ORF) of 1,933 bp in length which coded for a polypeptide of 643 amino acid [...] Read more.
An organic solvent tolerant lipase gene from Staphylococcus epidermidis AT2 was successfully cloned and expressed with pTrcHis2 in E. coli TOP10. Sequence analysis revealed an open reading frame (ORF) of 1,933 bp in length which coded for a polypeptide of 643 amino acid residues. The polypeptide comprised of a signal peptide (37 amino acids), pro-peptide and a mature protein of 390 amino acids. Expression of AT2 lipase resulted in an 18-fold increase in activity, upon the induction of 0.6 mM IPTG after a 10 h incubation period. Interestingly, this lipase was stable in various organic solvents (25% (v/v), mainly toluene, octanol, p-xylene and n-hexane). Literature shows that most of the organic solvent stable bacterial lipases were produced by Pseudomonas sp. and Bacillus sp., but very few from Staphylococcus sp. This lipase demonstrates great potential to be employed in various industrial applications. Full article
(This article belongs to the Section Biochemistry)
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Open AccessArticle
Dimerization of Protegrin-1 in Different Environments
Int. J. Mol. Sci. 2010, 11(9), 3177-3194; https://doi.org/10.3390/ijms11093177 - 09 Sep 2010
Cited by 14 | Viewed by 5020
Abstract
The dimerization of the cationic β-hairpin antimicrobial peptide protegrin-1 (PG1) is investigated in three different environments: water, the surface of a lipid bilayer membrane, and the core of the membrane. PG1 is known to kill bacteria by forming oligomeric membrane pores, which permeabilize [...] Read more.
The dimerization of the cationic β-hairpin antimicrobial peptide protegrin-1 (PG1) is investigated in three different environments: water, the surface of a lipid bilayer membrane, and the core of the membrane. PG1 is known to kill bacteria by forming oligomeric membrane pores, which permeabilize the cells. PG1 dimers are found in two distinct, parallel and antiparallel, conformations, known as important intermediate structural units of the active pore oligomers. What is not clear is the sequence of events from PG1 monomers in solution to pores inside membranes. The step we focus on in this work is the dimerization of PG1. In particular, we are interested in determining where PG1 dimerization is most favorable. We use extensive molecular dynamics simulations to determine the potential of mean force as a function of distance between two PG1 monomers in the aqueous subphase, the surface of model lipid bilayers and the interior of these bilayers. We investigate the two known distinct modes of dimerization that result in either a parallel or an antiparallel β-sheet orientation. The model bilayer membranes are composed of anionic palmitoyl-oleoyl-phosphatidylglycerol (POPG) and palmitoyl-oleoyl-phosphatidylethanolamine (POPE) in a 1:3 ratio (POPG:POPE). We find the parallel PG1 dimer association to be more favorable than the antiparallel one in water and inside the membrane. However, we observe that the antiparallel PG1 β-sheet dimer conformation is somewhat more stable than the parallel dimer association at the surface of the membrane. We explore the role of hydrogen bonds and ionic bridges in peptide dimerization in the three environments. Detailed knowledge of how networks of ionic bridges and hydrogen bonds contribute to peptide stability is essential for the purpose of understanding the mechanism of action for membrane-active peptides as well as for designing peptides which can modulate membrane properties. The findings are suggestive of the dominant pathways leading from individual PG1 molecules in solution to functional pores in bacterial membranes. Full article
(This article belongs to the Special Issue Advances in Molecular Recognition)
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Open AccessArticle
Synthesis and Characterization of a Heteroleptic Ru(II) Complex of Phenanthroline Containing Oligo-Anthracenyl Carboxylic Acid Moieties
Int. J. Mol. Sci. 2010, 11(9), 3158-3176; https://doi.org/10.3390/ijms11093158 - 08 Sep 2010
Cited by 16 | Viewed by 7062
Abstract
In an effort to develop new ruthenium(II) complexes, this work describes the design, synthesis and characterization of a ruthenium(II) functionalized phenanthroline complex with extended π-conjugation. The ligand were L1 (4,7-bis(2,3-dimethylacrylic acid)-1,10-phenanthroline), synthesized by a direct aromatic substitution reaction, and L2 (4,7-bis(trianthracenyl-2,3-dimethylacrylic [...] Read more.
In an effort to develop new ruthenium(II) complexes, this work describes the design, synthesis and characterization of a ruthenium(II) functionalized phenanthroline complex with extended π-conjugation. The ligand were L1 (4,7-bis(2,3-dimethylacrylic acid)-1,10-phenanthroline), synthesized by a direct aromatic substitution reaction, and L2 (4,7-bis(trianthracenyl-2,3-dimethylacrylic acid)-1,10-phenanthroline), which was synthesized by the dehalogenation of halogenated aromatic compounds using a zero-valent palladium cross-catalyzed reaction in the absence of magnesium-diene complexes and/or cyclooctadienyl nickel (0) catalysts to generate a new carbon-carbon bond (C-C bond) polymerized hydrocarbon units. The ruthenium complex [RuL1L2(NCS)2] showed improved photophysical properties (red-shifted metal-to-ligand charge-transfer transition absorptions and enhanced molar extinction coefficients), luminescence and interesting electrochemical properties. Cyclic and square wave voltammetry revealed five major redox processes. The number of electron(s) transferred by the ruthenium complex was determined by chronocoulometry in each case. The results show that processes I, II and III are multi-electron transfer reactions while processes IV and V involved one-electron transfer reaction. The photophysical property of the complex makes it a promising candidate in the design of chemosensors and photosensitizers, while its redox-active nature makes the complex a potential mediator of electron transfer in photochemical processes. Full article
(This article belongs to the Section Biochemistry)
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Open AccessArticle
A Simple Method for DNA Extraction from Mature Date Palm Leaves: Impact of Sand Grinding and Composition of Lysis Buffer
Int. J. Mol. Sci. 2010, 11(9), 3149-3157; https://doi.org/10.3390/ijms11093149 - 08 Sep 2010
Cited by 14 | Viewed by 9557
Abstract
Molecular marker techniques have been widely used for cultivar identification of inbred date palms (Phoenix dactylifera L.; Arecaceae) and biodiversity conservation. Isolation of highly pure DNA is the prerequisite for PCR amplification and subsequent use such as DNA fingerprinting and sequencing [...] Read more.
Molecular marker techniques have been widely used for cultivar identification of inbred date palms (Phoenix dactylifera L.; Arecaceae) and biodiversity conservation. Isolation of highly pure DNA is the prerequisite for PCR amplification and subsequent use such as DNA fingerprinting and sequencing of genes that have recently been developed for barcoding. To avoid problems related to the preservation and use of liquid nitrogen, we examined sterile sand for grinding the date palm leaves. Individual and combined effects of sodium chloride (NaCl), polyvinylpyrrolidone (PVP) and lithium chloride (LiCl) with the cetyltrimethylammonium bromide (CTAB) method for a DNA yield of sufficient purity and PCR amplification were evaluated in this study. Presence of LiCl and PVP alone or together in the lysis buffer did not significantly improve the DNA yield and purity compared with the addition of NaCl. Our study suggested that grinding of date palm leaf with sterile sand and inclusion of NaCl (1.4 M) in the lysis buffer without the costly use of liquid nitrogen, PVP and LiCl, provides a DNA yield of sufficient purity, suitable for PCR amplification. Full article
(This article belongs to the Section Biochemistry)
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Open AccessArticle
Rapid and Accurate Detection of Plant miRNAs by Liquid Northern Hybridization
Int. J. Mol. Sci. 2010, 11(9), 3138-3148; https://doi.org/10.3390/ijms11093138 - 07 Sep 2010
Cited by 14 | Viewed by 5041
Abstract
Northern blot analysis is a powerful research tool for discovery, validation and expression of genes, and is currently widely used to detect microRNA (miRNA) accumulation. However, the traditional Northern blot procedure, which is based on a support membrane, is overly elaborate and time-consuming, [...] Read more.
Northern blot analysis is a powerful research tool for discovery, validation and expression of genes, and is currently widely used to detect microRNA (miRNA) accumulation. However, the traditional Northern blot procedure, which is based on a support membrane, is overly elaborate and time-consuming, although it is unsurpassed in accuracy for determining the sizes and amounts of multiple small RNAs sharing high sequence identity. Here we present an alternative method derived from plant miRNAs, liquid Northern hybridization, using fluorescently labeled oligonucleotide probes and characterized by simple and specific miRNA determination and quantitation. The entire detection process is completed within a few hours, and multiple miRNAs can be simultaneously detected in a single experiment. Full article
(This article belongs to the Section Biochemistry)
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Open AccessArticle
A Selective Assay to Detect Chitin and Biologically Active Nano-Machineries for Chitin-Biosynthesis with Their Intrinsic Chitin-Synthase Molecules
Int. J. Mol. Sci. 2010, 11(9), 3122-3137; https://doi.org/10.3390/ijms11093122 - 07 Sep 2010
Cited by 5 | Viewed by 6327
Abstract
A new assay system for chitin has been developed. It comprises the chitin-binding protein ChbB in fusion with a His-tag as well as with a Strep-tag, the latter of which was chemically coupled to horseradish peroxidase. With the resulting complex, minimal quantities of [...] Read more.
A new assay system for chitin has been developed. It comprises the chitin-binding protein ChbB in fusion with a His-tag as well as with a Strep-tag, the latter of which was chemically coupled to horseradish peroxidase. With the resulting complex, minimal quantities of chitin are photometrically detectable. In addition, the assay allows rapid scoring of the activity of chitin-synthases. As a result, a refined procedure for the rapid purification of yeast chitosomes (nano-machineries for chitin biosynthesis) has been established. Immuno-electronmicroscopical studies of purified chitosomes, gained from a yeast strain carrying a chitin-synthase gene fused to that for GFP (green-fluorescence protein), has led to the in situ localization of chitin-synthase-GFP molecules within chitosomes. Full article
(This article belongs to the Special Issue Chitins)
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