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Int. J. Mol. Sci., Volume 9, Issue 10 (October 2008), Pages 1893-2061

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Research

Jump to: Review

Open AccessArticle Performance of a Yeast-mediated Biological Fuel Cell
Int. J. Mol. Sci. 2008, 9(10), 1893-1907; doi:10.3390/ijms9101893
Received: 12 June 2008 / Revised: 30 August 2008 / Accepted: 24 September 2008 / Published: 8 October 2008
Cited by 29 | PDF Full-text (594 KB) | HTML Full-text | XML Full-text
Abstract
Saccharomyces cerevisiae present in common Baker’s yeast was used in a microbial fuel cell in which glucose was the carbon source. Methylene blue was used as the electronophore in the anode compartment, while potassium ferricyanide and methylene blue were tested as electron [...] Read more.
Saccharomyces cerevisiae present in common Baker’s yeast was used in a microbial fuel cell in which glucose was the carbon source. Methylene blue was used as the electronophore in the anode compartment, while potassium ferricyanide and methylene blue were tested as electron acceptors in the cathode compartment. Microbes in a mediator-free environment were used as the control. The experiment was performed in both open and closed circuit configurations under different loads ranging from 100 kΩ to 400Ω. The eukaryotic S. cerevisiae-based fuel cell showed improved performance when methylene blue and ferricyanide were used as electron mediators, rendering a maximum power generation of 146.71±7.7 mW/m3. The fuel cell generated a maximum open circuit voltage of 383.6±1.5 mV and recorded a maximum efficiency of 28±1.8 % under 100 kΩ of external load. Full article
(This article belongs to the Special Issue Energy Technology for the 21st Century - Materials and Devices)
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Open AccessArticle A DFT Study on Deactivation of Triplet Excited State Riboflavin by Polyphenols
Int. J. Mol. Sci. 2008, 9(10), 1908-1914; doi:10.3390/ijms9101908
Received: 30 July 2008 / Revised: 7 September 2008 / Accepted: 27 September 2008 / Published: 8 October 2008
Cited by 6 | PDF Full-text (209 KB) | HTML Full-text | XML Full-text
Abstract
The deactivation of triplet excited state riboflavin by polyphenols, e.g. rutin and catechin, was studied on the basis of density functional theory calculations. The results show that the H-atom transfer pathway is more feasible on thermodynamic grounds in comparison with the direct [...] Read more.
The deactivation of triplet excited state riboflavin by polyphenols, e.g. rutin and catechin, was studied on the basis of density functional theory calculations. The results show that the H-atom transfer pathway is more feasible on thermodynamic grounds in comparison with the direct energy transfer or direct electron transfer pathways involved in the triplet excited state riboflavin deactivation by rutin/catechin. The findings are helpful to understand the protective effect of polyphenols against the riboflavin induced photosensitizing damage. Full article
(This article belongs to the Section Physical Chemistry, Theoretical and Computational Chemistry)
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Open AccessArticle Actomyosin Interaction: Mechanical and Energetic Properties in Different Nucleotide Binding States
Int. J. Mol. Sci. 2008, 9(10), 1927-1943; doi:10.3390/ijms9101927
Received: 21 May 2008 / Revised: 8 October 2008 / Accepted: 10 October 2008 / Published: 13 October 2008
Cited by 2 | PDF Full-text (387 KB) | HTML Full-text | XML Full-text
Abstract
The mechanics of the actomyosin interaction is central in muscle contraction and intracellular trafficking. A better understanding of the events occurring in the actomyosin complex requires the examination of all nucleotide-dependent states and of the energetic features associated with the dynamics of [...] Read more.
The mechanics of the actomyosin interaction is central in muscle contraction and intracellular trafficking. A better understanding of the events occurring in the actomyosin complex requires the examination of all nucleotide-dependent states and of the energetic features associated with the dynamics of the cross-bridge cycle. The aim of the present study is to estimate the interaction strength between myosin in nucleotide-free, ATP, ADP·Pi and ADP states and actin monomer. The molecular models of the complexes were constructed based on cryo-electron microscopy maps and the interaction properties were estimated by means of a molecular dynamics approach, which simulate the unbinding of the complex applying a virtual spring to the core of myosin protein. Our results suggest that during an ATP hydrolysis cycle the affinity of myosin for actin is modulated by the presence and nature of the nucleotide in the active site of the myosin motor domain. When performing unbinding simulations with a pulling rate of 0.001 nm/ps, the maximum pulling force applied to the myosin during the experiment is about 1nN. Under these conditions the interaction force between myosin and actin monomer decreases from 0.83 nN in the nucleotide-free state to 0.27 nN in the ATP state, and increases to 0.60 nN after ATP hydrolysis and Pi release from the complex (ADP state). Full article
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Open AccessArticle Prediction of Human Intestinal Absorption by GA Feature Selection and Support Vector Machine Regression
Int. J. Mol. Sci. 2008, 9(10), 1961-1976; doi:10.3390/ijms9101961
Received: 2 July 2008 / Revised: 5 September 2008 / Accepted: 15 October 2008 / Published: 20 October 2008
Cited by 26 | PDF Full-text (262 KB) | HTML Full-text | XML Full-text | Supplementary Files
Abstract
QSAR (Quantitative Structure Activity Relationships) models for the prediction of human intestinal absorption (HIA) were built with molecular descriptors calculated by ADRIANA.Code, Cerius2 and a combination of them. A dataset of 552 compounds covering a wide range of current drugs with [...] Read more.
QSAR (Quantitative Structure Activity Relationships) models for the prediction of human intestinal absorption (HIA) were built with molecular descriptors calculated by ADRIANA.Code, Cerius2 and a combination of them. A dataset of 552 compounds covering a wide range of current drugs with experimental HIA values was investigated. A Genetic Algorithm feature selection method was applied to select proper descriptors. A Kohonen's self-organizing Neural Network (KohNN) map was used to split the whole dataset into a training set including 380 compounds and a test set consisting of 172 compounds. First, the six selected descriptors from ADRIANA.Code and the six selected descriptors from Cerius2 were used as the input descriptors for building quantitative models using Partial Least Square (PLS) analysis and Support Vector Machine (SVM) Regression. Then, another two models were built based on nine descriptors selected by a combination of ADRIANA.Code and Cerius2 descriptors using PLS and SVM, respectively. For the three SVM models, correlation coefficients (r) of 0.87, 0.89 and 0.88 were achieved; and standard deviations (s) of 10.98, 9.72 and 9.14 were obtained for the test set. Full article
(This article belongs to the Section Physical Chemistry, Theoretical and Computational Chemistry)
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Open AccessArticle Elevation of Inducible Nitric Oxide Synthase and Cyclooxygenase-2 Expression in the Mouse Brain after Chronic Nonylphenol Exposure
Int. J. Mol. Sci. 2008, 9(10), 1977-1988; doi:10.3390/ijms9101977
Received: 21 March 2008 / Revised: 9 October 2008 / Accepted: 13 October 2008 / Published: 24 October 2008
Cited by 14 | PDF Full-text (246 KB) | HTML Full-text | XML Full-text
Abstract
The present study was performed to investigate the effects of chronic administration of nonylphenol (NP) on the expression of inflammation-related genes in the brains of mice. NP was given orally by gavages at 0, 50, 100, and 200 mg/kg/d. The expression of [...] Read more.
The present study was performed to investigate the effects of chronic administration of nonylphenol (NP) on the expression of inflammation-related genes in the brains of mice. NP was given orally by gavages at 0, 50, 100, and 200 mg/kg/d. The expression of inflammatory enzymes, inducible nitric oxide synthase (iNOS) and cyclooxygenase-2 (COX-2), was evaluated by immunohistochemistry and immunoblotting assays. The nitric oxide (NO) level and nitric oxide synthase (NOS) activity were also measured by biochemical analyses. The results showed that NP at a high dose (200 mg/kg/d) significantly increased the expression of iNOS and COX-2 in both the hippocampus and cortex. In parallel with the increase in iNOS expression, the NO level was significantly greater at the dose of 200 mg/kg/d, compared to the control. The activity of NOS was also increased in the brain of mice at the dose of 100 and 200 mg/kg/d. These findings demonstrate that NP may have the potential to induce the chronic inflammation or cause neurotoxicity in the mouse brain. Full article
(This article belongs to the Section Biochemistry, Molecular Biology and Biophysics)
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Open AccessArticle Accelerator Analysis of Tributyltin Adsorbed onto the Surface of a Tributyltin Resistant Marine Pseudoalteromonas sp. Cell
Int. J. Mol. Sci. 2008, 9(10), 1989-2002; doi:10.3390/ijms9101989
Received: 28 August 2008 / Revised: 16 October 2008 / Accepted: 20 October 2008 / Published: 24 October 2008
Cited by 6 | PDF Full-text (1155 KB) | HTML Full-text | XML Full-text
Abstract
Tributyltin (TBT) released into seawater from ship hulls is a stable marine pollutant and obviously remains in marine environments. We isolated a TBT resistant marine Pseudoalteromonas sp. TBT1 from sediment of a ship’s ballast water. The isolate (109.3 ± 0.2 colony-forming [...] Read more.
Tributyltin (TBT) released into seawater from ship hulls is a stable marine pollutant and obviously remains in marine environments. We isolated a TBT resistant marine Pseudoalteromonas sp. TBT1 from sediment of a ship’s ballast water. The isolate (109.3 ± 0.2 colony-forming units mL-1) adsorbed TBT in proportion to the concentrations of TBTCl externally added up to 3 mM, where the number of TBT adsorbed by a single cell was estimated to be 108.2. The value was reduced to about one-fifth when the lysozyme-treated cells were used. The surface of ethanol treated cells became rough, but the capacity of TBT adsorption was the same as that for native cells. These results indicate that the function of the cell surface, rather than that structure, plays an important role to the adsorption of TBT. The adsorption state of TBT seems to be multi-layer when the number of more than 106.8 TBT molecules is adsorbed by a single cell. Full article
(This article belongs to the Special Issue Green Antifouling)
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Open AccessArticle The Effect of the Argon Carrier Gas in the Multiphoton Dissociation-Ionization of Tetracene
Int. J. Mol. Sci. 2008, 9(10), 2003-2015; doi:10.3390/ijms9102003
Received: 12 August 2008 / Revised: 10 October 2008 / Accepted: 15 October 2008 / Published: 28 October 2008
Cited by 4 | PDF Full-text (336 KB) | HTML Full-text | XML Full-text
Abstract
The multiphoton dissociation-ionization of tetracene at 355 nm using 6.5 nanosecond laser pulses, with and without argon as a carrier gas (CG), has been studied and compared. Ion fragments were analyzed in a time-of-flight mass spectrometer and separated according to their mass-to-charge [...] Read more.
The multiphoton dissociation-ionization of tetracene at 355 nm using 6.5 nanosecond laser pulses, with and without argon as a carrier gas (CG), has been studied and compared. Ion fragments were analyzed in a time-of-flight mass spectrometer and separated according to their mass-to-charge ratio (m/z). The results show that the dynamic of photodissociation at ~1010 W⋅cm-2 intensities is strongly influenced by the CG. The suppression of fragmentation channels primarily those relating to the formation of the CHm+ (m = 2, 4), C2H4+ and C5H4+2 ions. CH5+ and CH6+ were observed which have not been reported before in photodissociation tetracene experiments. Full article
(This article belongs to the Section Biochemistry, Molecular Biology and Biophysics)
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Open AccessArticle Schultz Index of Armchair Polyhex Nanotubes
Int. J. Mol. Sci. 2008, 9(10), 2016-2026; doi:10.3390/ijms9102016
Received: 3 July 2008 / Revised: 23 August 2008 / Accepted: 14 October 2008 / Published: 29 October 2008
Cited by 9 | PDF Full-text (182 KB) | HTML Full-text | XML Full-text
Abstract
The study of topological indices – graph invariants that can be used for describing and predicting physicochemical or pharmacological properties of organic compounds – is currently one of the most active research fields in chemical graph theory. In this paper we study [...] Read more.
The study of topological indices – graph invariants that can be used for describing and predicting physicochemical or pharmacological properties of organic compounds – is currently one of the most active research fields in chemical graph theory. In this paper we study the Schultz index and find a relation with the Wiener index of the armchair polyhex nanotubes TUV C6[2p; q]. An exact expression for Schultz index of this molecule is also found. Full article
(This article belongs to the Section Physical Chemistry, Theoretical and Computational Chemistry)
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Open AccessArticle Aspergillus parasiticus crzA, Which Encodes Calcineurin Response Zinc-Finger Protein, Is Required for Aflatoxin Production under Calcium Stress
Int. J. Mol. Sci. 2008, 9(10), 2027-2043; doi:10.3390/ijms9102027
Received: 16 September 2008 / Revised: 27 October 2008 / Accepted: 28 October 2008 / Published: 29 October 2008
Cited by 9 | PDF Full-text (737 KB) | HTML Full-text | XML Full-text
Abstract
Two morphologically different Aspergillus parasiticus strains, one producing aflatoxins, abundant conidia but few sclerotia (BN9) and the other producing O-methylsterimatocystin (OMST), copious sclerotia but a low number of conidia (RH), were used to assess the role of crzA which encodes a putative [...] Read more.
Two morphologically different Aspergillus parasiticus strains, one producing aflatoxins, abundant conidia but few sclerotia (BN9) and the other producing O-methylsterimatocystin (OMST), copious sclerotia but a low number of conidia (RH), were used to assess the role of crzA which encodes a putative calcium-signaling pathway regulatory protein. Under standard culture conditions, BN9ΔcrzA mutants conidiated normally but decreased slightly in radial growth, regardless of illumination conditions. RHΔcrzA mutants produced only conidia under light and showed decreased conidiation and delayed sclerotial formation in the dark. Regulation of conidiation of both A. parasiticus strains by light was independent of crzA. Increased concentrations of lithium, sodium, and potassium impaired conidiation and sclerotial formation of the RHΔcrzA mutants but they did not affect conidiation of the BN9ΔcrzA mutants. Vegetative growth and asexual development of both ΔcrzA mutants were hypersensitive to increased calcium concentrations. Calcium supplementation (10 mM) resulted in 3-fold and 2-fold decreases in the relative expression of the endoplasmic reticulum calcium ATPase 2 gene in the BN9 and RH parental strains, respectively, but changes in both ΔcrzA mutants were less significant. Compared to the parental strains, the ΔcrzA mutants barely produced aflatoxins or OMST after the calcium supplementation. The relative expression levels of aflatoxin biosynthesis genes, nor1, ver1, and omtA, in both ΔcrzA mutants were decreased significantly, but the decreases in the parental strains were at much lower extents. CrzA is required for growth and development and for aflatoxin biosynthesis under calcium stress conditions. Full article
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Open AccessArticle Preparation and Characterization of Highly Fluorescent, Glutathione-coated Near Infrared Quantum Dots for in Vivo Fluorescence Imaging
Int. J. Mol. Sci. 2008, 9(10), 2044-2061; doi:10.3390/ijms9102044
Received: 23 August 2008 / Revised: 23 October 2008 / Accepted: 28 October 2008 / Published: 29 October 2008
Cited by 57 | PDF Full-text (632 KB) | HTML Full-text | XML Full-text
Abstract
Fluorescent probes that emit in the near-infrared (NIR, 700-1,300 nm) region are suitable as optical contrast agents for in vivo fluorescence imaging because of low scattering and absorption of the NIR light in tissues. Recently, NIR quantum dots (QDs) have become a [...] Read more.
Fluorescent probes that emit in the near-infrared (NIR, 700-1,300 nm) region are suitable as optical contrast agents for in vivo fluorescence imaging because of low scattering and absorption of the NIR light in tissues. Recently, NIR quantum dots (QDs) have become a new class of fluorescent materials that can be used for in vivo imaging. Compared with traditional organic fluorescent dyes, QDs have several unique advantages such as size- and composition-tunable emission, high brightness, narrow emission bands, large Stokes shifts, and high resistance to photobleaching. In this paper, we report a facile method for the preparation of highly fluorescent, water-soluble glutathione (GSH)-coated NIR QDs for in vivo imaging. GSH-coated NIR QDs (GSH-QDs) were prepared by surface modification of hydrophobic CdSeTe/CdS (core/shell) QDs. The hydrophobic surface of the CdSeTe/CdS QDs was exchanged with GSH in tetrahydrofuran-water. The resulting GSH-QDs were monodisperse particles and stable in PBS (phosphate buffered saline, pH = 7.4). The GSH-QDs (800 nm emission) were highly fluorescent in aqueous solutions (quantum yield = 22% in PBS buffer), and their hydrodynamic diameter was less than 10 nm, which is comparable to the size of proteins. The cellular uptake and viability for the GSH-QDs were examined using HeLa and HEK 293 cells. When the cells were incubated with aqueous solutions of the GSH-QDs (10 nM), the QDs were taken into the cells and distributed in the perinuclear region of both cells. After 12 hrs incubation of 4 nM of GSH-QDs, the viabilities of HeLa and HEK 293 cells were ca. 80 and 50%, respectively. As a biomedical utility of the GSH-QDs, in vivo NIRfluorescence imaging of a lymph node in a mouse is presented. Full article
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Review

Jump to: Research

Open AccessReview Antibody-mediated Prevention of Fusarium Mycotoxins in the Field
Int. J. Mol. Sci. 2008, 9(10), 1915-1926; doi:10.3390/ijms9101915
Received: 21 August 2008 / Revised: 26 September 2008 / Accepted: 6 October 2008 / Published: 9 October 2008
Cited by 7 | PDF Full-text (71 KB) | HTML Full-text | XML Full-text
Abstract
Fusarium mycotoxins directly accumulated in grains during the infection of wheat and other cereal crops by Fusarium head blight (FHB) pathogens are detrimental to humans and domesticated animals. Prevention of the mycotoxins via the development of FHB-resistant varieties has been a challenge [...] Read more.
Fusarium mycotoxins directly accumulated in grains during the infection of wheat and other cereal crops by Fusarium head blight (FHB) pathogens are detrimental to humans and domesticated animals. Prevention of the mycotoxins via the development of FHB-resistant varieties has been a challenge due to the scarcity of natural resistance against FHB pathogens. Various antibodies specific to Fusarium fungi and mycotoxins are widely used in immunoassays and antibody-mediated resistance in planta against Fusarium pathogens has been demonstrated. Antibodies fused to antifungal proteins have been shown to confer a very significantly enhanced Fusarium resistance in transgenic plants. Thus, antibody fusions hold great promise as an effective tool for the prevention of mycotoxin contaminations in cereal grains. This review highlights the utilization of protective antibodies derived from phage display to increase endogenous resistance of wheat to FHB pathogens and consequently to reduce mycotoxins in field. The role played by Fusarium-specific antibody in the resistance is also discussed. Full article
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Open AccessReview DNA Mimics for the Rapid Identification of Microorganisms by Fluorescence in situ Hybridization (FISH)
Int. J. Mol. Sci. 2008, 9(10), 1944-1960; doi:10.3390/ijms9101944
Received: 2 April 2008 / Revised: 24 September 2008 / Accepted: 6 October 2008 / Published: 20 October 2008
Cited by 38 | PDF Full-text (128 KB) | HTML Full-text | XML Full-text
Abstract
Fluorescence in situ hybridization (FISH) is a well-established technique that is used for a variety of purposes, ranging from pathogen detection in clinical diagnostics to the determination of chromosomal stability in stem cell research. The key step of FISH involves the detection [...] Read more.
Fluorescence in situ hybridization (FISH) is a well-established technique that is used for a variety of purposes, ranging from pathogen detection in clinical diagnostics to the determination of chromosomal stability in stem cell research. The key step of FISH involves the detection of a nucleic acid region and as such, DNA molecules have typically been used to probe for the sequences of interest. However, since the turn of the century, an increasing number of laboratories have started to move on to the more robust DNA mimics methods, most notably peptide and locked nucleic acids (PNA and LNA). In this review, we will cover the state-of-the-art of the different DNA mimics in regard to their application as efficient markers for the presence of individual microbial cells, and consider their potential advantages and pitfalls. Available PNA probes are then reassessed in terms of sensitivity and specificity using rRNA databases. In addition, we also attempt to predict the applicability of DNA mimics in well-known techniques attempting to detect in situ low number of copies of specific nucleic acid sequences such as catalyzed reporter deposition (CARD) and recognition of individual genes (RING) FISH. Full article
(This article belongs to the Special Issue Nucleic Acid Derivatives in Emerging Technologies)
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