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Int. J. Mol. Sci., Volume 11, Issue 2 (February 2010), Pages 386-788

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Research

Jump to: Review

Open AccessArticle Electrostatic Interactions of Fluorescent Molecules with Dielectric Interfaces Studied by Total Internal Reflection Fluorescence Correlation Spectroscopy
Int. J. Mol. Sci. 2010, 11(2), 386-406; doi:10.3390/ijms11020386
Received: 23 November 2009 / Revised: 17 January 2010 / Accepted: 21 January 2010 / Published: 28 January 2010
Cited by 7 | PDF Full-text (355 KB) | HTML Full-text | XML Full-text
Abstract
Electrostatic interactions between dielectric surfaces and different fluorophores used in ultrasensitive fluorescence microscopy are investigated using objective-based Total Internal Reflection Fluorescence Correlation Spectroscopy (TIR-FCS). The interfacial dynamics of cationic rhodamine 123 and rhodamine 6G, anionic/dianionic fluorescein, zwitterionic rhodamine 110 and neutral ATTO [...] Read more.
Electrostatic interactions between dielectric surfaces and different fluorophores used in ultrasensitive fluorescence microscopy are investigated using objective-based Total Internal Reflection Fluorescence Correlation Spectroscopy (TIR-FCS). The interfacial dynamics of cationic rhodamine 123 and rhodamine 6G, anionic/dianionic fluorescein, zwitterionic rhodamine 110 and neutral ATTO 488 are monitored at various ionic strengths at physiological pH. As analyzed by means of the amplitude and time-evolution of the autocorrelation function, the fluorescent molecules experience electrostatic attraction or repulsion at the glass surface depending on their charges. Influences of the electrostatic interactions are also monitored through the triplet-state population and triplet relaxation time, including the amount of detected fluorescence or the count-rate-per-molecule parameter. These TIR-FCS results provide an increased understanding of how fluorophores are influenced by the microenvironment of a glass surface, and show a promising approach for characterizing electrostatic interactions at interfaces. Full article
(This article belongs to the Special Issue Single Molecules)
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Open AccessArticle Bioactivity of Isoflavones: Assessment through a Theoretical Model as a Way to Obtain a “Theoretical Efficacy Related to Estradiol (TERE)”
Int. J. Mol. Sci. 2010, 11(2), 480-491; doi:10.3390/ijms11020480
Received: 30 November 2009 / Revised: 13 January 2010 / Accepted: 20 January 2010 / Published: 2 February 2010
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Abstract
The increase of human life span will have profound implications in Public Health in decades to come. By 2030, there will be an estimated 1.2 billion women in post-menopause. Hormone Replacement Therapy with synthetic hormones is still full of risks and according [...] Read more.
The increase of human life span will have profound implications in Public Health in decades to come. By 2030, there will be an estimated 1.2 billion women in post-menopause. Hormone Replacement Therapy with synthetic hormones is still full of risks and according to the latest developments, should be used for the shortest time possible. Searching for alternative drugs is inevitable in this scenario and science must provide physicians with other substances that can be used to treat the same symptoms with less side effects. Systematic research carried out on this field of study is focusing now on isoflavones but the randomised controlled trials and reviews of meta-analysis concerning post-menopause therapy, that could have an important impact on human health, are very controversial. The aim of the present work was to establish a theoretical calculation suitable for use as a way to estimate the “Theoretical Efficacy (TE)” of a mixture with different bioactive compounds as a way to obtain a “Theoretical Efficacy Related to Estradiol (TERE)”. The theoretical calculation that we propose in this paper integrates different knowledge about this subject and sets methodological boundaries that can be used to analyse already published data. The outcome should set some consensus for new clinical trials using isoflavones (isolated or included in mixtures) that will be evaluated to assess their therapeutically activity. This theoretical method for evaluation of a possible efficacy could probably also be applied to other herbal drug extracts when a synergistic or contradictory bio-effect is not verified. In this way, it we may contribute to enlighten and to the development of new therapeutic approaches. Full article
(This article belongs to the Special Issue Phenolics and Polyphenolics)
Open AccessArticle Effective Population Size, Gene Flow, and Species Status in a Narrow Endemic Sunflower, Helianthus neglectus, Compared to Its Widespread Sister Species, H. petiolaris
Int. J. Mol. Sci. 2010, 11(2), 492-506; doi:10.3390/ijms11020492
Received: 25 November 2009 / Revised: 17 January 2010 / Accepted: 21 January 2010 / Published: 2 February 2010
Cited by 11 | PDF Full-text (900 KB) | HTML Full-text | XML Full-text | Supplementary Files
Abstract
Species delimitation has long been a difficult and controversial process, and different operational criteria often lead to different results. In particular, investigators using phenotypic vs. molecular data to delineate species may recognize different boundaries, especially if morphologically or ecologically differentiated populations have [...] Read more.
Species delimitation has long been a difficult and controversial process, and different operational criteria often lead to different results. In particular, investigators using phenotypic vs. molecular data to delineate species may recognize different boundaries, especially if morphologically or ecologically differentiated populations have only recently diverged. Here we examine the genetic relationship between the widespread sunflower species Helianthus petiolaris and its narrowly distributed sand dune endemic sister species H. neglectus using sequence data from nine nuclear loci. The two species were initially described as distinct based on a number of minor morphological differences, somewhat different ecological tolerances, and at least one chromosomal rearrangement distinguishing them; but detailed molecular data has not been available until now. We find that, consistent with previous work, H. petiolaris is exceptionally genetically diverse. Surprisingly, H. neglectus harbors very similar levels of genetic diversity (average diversity across loci is actually slightly higher in H. neglectus). It is extremely unlikely that such a geographically restricted species could maintain these levels of genetic variation in isolation. In addition, the two species show very little evidence of any genetic divergence, and estimates of interspecific gene flow are comparable to gene flow estimates among regions within H. petiolaris. These results indicate that H. petiolaris and H. neglectus likely do not represent two distinct, isolated gene pools; H. neglectus is probably more accurately thought of as a geographically restricted, morphologically and ecologically distinct subspecies of H. petiolaris rather than a separate species. Full article
(This article belongs to the Special Issue Cladistic Analysis and Molecular Evolution)
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Open AccessArticle Bacillus marcorestinctum sp. nov., a Novel Soil Acylhomoserine Lactone Quorum-Sensing Signal Quenching Bacterium
Int. J. Mol. Sci. 2010, 11(2), 507-520; doi:10.3390/ijms11020507
Received: 7 December 2009 / Revised: 18 January 2010 / Accepted: 20 January 2010 / Published: 3 February 2010
Cited by 8 | PDF Full-text (319 KB) | HTML Full-text | XML Full-text
Abstract
A Gram-positive, facultatively anaerobic, endospore-forming and rod-shaped bacterium was isolated from soil samples and designated strain LQQ. This organism strongly quenches the acylhomoserine lactone quorum-sensing signal. The LQQ strain exhibits phenotypic characteristics consistent with its classification in the genus Bacillus. It [...] Read more.
A Gram-positive, facultatively anaerobic, endospore-forming and rod-shaped bacterium was isolated from soil samples and designated strain LQQ. This organism strongly quenches the acylhomoserine lactone quorum-sensing signal. The LQQ strain exhibits phenotypic characteristics consistent with its classification in the genus Bacillus. It is positive in catalase and no special growth factor is needed. It uses glucose as sole carbon source. The DNA G + C content is 39.8 mol %. The closest relatives based on the 16S rRNA gene sequence are Bacillus anthracis, Bacillus thuringiensis, and Brevibacillus brevis (syn. Bacillus brevis) with the similarity of 96.5%. The DNA–DNA hybridization data indicates a low level of genomic relatedness with the relative type strains of Bacillus thuringiensis (6.1%), Bacillus anthracis (10.5%) and Brevibacillus brevis (8.7%). On the basis of the phenotypic and phylogenetic data together with the genomic distinctiveness, the LQQ strain represents a novel species of the genus Bacillus, for which the name Bacillus marcorestinctum sp. nov. is proposed. The type strain is LQQT. Full article
(This article belongs to the Special Issue Cladistic Analysis and Molecular Evolution)
Open AccessArticle Nuclear Translocation of Nuclear Factor Kappa B in First Trimester Deciduas and Chorionic Villi in Early Spontaneous Miscarriage Women
Int. J. Mol. Sci. 2010, 11(2), 521-531; doi:10.3390/ijms11020521
Received: 24 December 2009 / Revised: 20 January 2010 / Accepted: 21 January 2010 / Published: 3 February 2010
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Abstract
The nuclear factor kappa B is widely expressed in the distinct subpopulations of chorionic villi and deciduas of first-trimester pregnancies. We examined the cellular distribution and expression of nuclear factor kappa B in the human first-trimester chorionic villi and deciduas of women [...] Read more.
The nuclear factor kappa B is widely expressed in the distinct subpopulations of chorionic villi and deciduas of first-trimester pregnancies. We examined the cellular distribution and expression of nuclear factor kappa B in the human first-trimester chorionic villi and deciduas of women with early spontaneous miscarriage and viable pregnancy by confocal laser scanning microscope and immunohistochemistry. There is a greater nuclear translocation of nuclear factor kappa B is restricted to villous stromal cells, decidual stromal cells, glandular epithelial cells and vessel endothelial cells in early spontaneous miscarriage than in viable pregnancies. Collectively these observations suggest that over-activation of nuclear factor kappa B has a relationship with early spontaneous miscarriages. Full article
(This article belongs to the Section Biochemistry, Molecular Biology and Biophysics)
Open AccessArticle The Measurement of Polymer Swelling Processes by an Interferometric Method and Evaluation of Diffusion Coefficients
Int. J. Mol. Sci. 2010, 11(2), 532-543; doi:10.3390/ijms11020532
Received: 3 December 2009 / Revised: 13 January 2010 / Accepted: 26 January 2010 / Published: 3 February 2010
Cited by 4 | PDF Full-text (616 KB) | HTML Full-text | XML Full-text
Abstract
The amorphous polymer film swelling in a liquid solvent below the glass transition temperature was characterized by a few kinetic parameters (especially the mutual diffusion coefficient of swelling and its mean value) obtained by interference of monochromatic light in the wedge arrangement. [...] Read more.
The amorphous polymer film swelling in a liquid solvent below the glass transition temperature was characterized by a few kinetic parameters (especially the mutual diffusion coefficient of swelling and its mean value) obtained by interference of monochromatic light in the wedge arrangement. This interferometric method allows one to determine the concentration field in the swollen surface layer and consequently to compute the concentration-dependent diffusion coefficient. A software system developed at the Department of Physics and Material Engineering at TBU in Zlin has been used for the evaluation of the main kinetic parameters of the swelling process. The software can be used for the on-line analyses of interferograms during the swelling process. The main application outputs are the computation of the concentration profile, the concentration gradient, the mutual diffusion coefficient of the swelling by the solvent and its mean value. Full article
(This article belongs to the Section Biochemistry, Molecular Biology and Biophysics)
Open AccessArticle Isolation of Sulfur Reducing and Oxidizing Bacteria Found in Contaminated Drywall
Int. J. Mol. Sci. 2010, 11(2), 647-655; doi:10.3390/ijms11020647
Received: 22 January 2010 / Accepted: 29 January 2010 / Published: 5 February 2010
Cited by 4 | PDF Full-text (505 KB) | HTML Full-text | XML Full-text
Abstract
Drywall from China has been reported to release sulfur producing products which are corrosive to metals, result in noxious odors, and represent a significant health risk. It has been reported that these emissions produce medical symptoms such as respiratory or asthma type [...] Read more.
Drywall from China has been reported to release sulfur producing products which are corrosive to metals, result in noxious odors, and represent a significant health risk. It has been reported that these emissions produce medical symptoms such as respiratory or asthma type problems, sinusitis, gastrointestinal disorders, and vision problems in home owners and their household pets. We report here a method of identifying a causative agent for these emissions by sampling affected gypsum wallboard and subjecting those samples to Real Time Polymerase Chain Reaction [RT-PCR] studies. Specific DNA probes and primers have been designed and patented that detect a specific iron and sulfur reducing bacterium (i.e., Thiobacillus ferrooxidans). One hundred percent of affected drywall samples obtained from homes located in the southeastern United States tested positive for the presence of T. ferrooxidans. All negative controls consisting of unaffected wallboard and internal controls, Geotrichum sp., tested negative within our limits of detection. Full article
(This article belongs to the Section Biochemistry, Molecular Biology and Biophysics)
Open AccessArticle Concentration of Rutin Model Solutions from Their Mixtures with Glucose Using Ultrafiltration
Int. J. Mol. Sci. 2010, 11(2), 672-690; doi:10.3390/ijms11020672
Received: 19 December 2009 / Revised: 26 January 2010 / Accepted: 26 January 2010 / Published: 9 February 2010
Cited by 2 | PDF Full-text (280 KB) | HTML Full-text | XML Full-text
Abstract
Separation of polyphenolic phytochemical compounds from their mixtures with sugars is necessary to produce an added-value sugar-reduced extract with high biological activity from fruit juice processing industry waste streams. The separation characteristics of a binary mixture of rutin and glucose using a [...] Read more.
Separation of polyphenolic phytochemical compounds from their mixtures with sugars is necessary to produce an added-value sugar-reduced extract with high biological activity from fruit juice processing industry waste streams. The separation characteristics of a binary mixture of rutin and glucose using a Pellicon-2 regenerated cellulose ultrafiltration membrane with an area of 0.1 m2 having nominal MWCO of 1,000 Da were investigated, to demonstrate the separation of phenolic compounds from sugars. The effects of the operating variables–transmembrane pressure, feed solution temperature and pH, initial feed concentration and feed flow rate–on the permeate flux and enrichment of rutin, were determined. The permeate flux increased with the increase in transmembrane pressure up to a certain limit and after that the flux remained more or less constant. The optimum transmembrane pressure was within 4–5 bar. The flux increased with the increase in feed solution temperature because of reduced feed viscosity, and better solubility. The concentration of rutin was optimum at lower temperature (30ºC), with an enrichment factor of 1.3. The effect of pH on permeate flux was less obvious. Lowering the feed solution pH increased the retention of rutin and the optimum separation was obtained within pH 3–4. The permeate flux decreased with the increase in feed concentration of rutin (concentration range 0.1–0.5 g/L). The enrichment of rutin was significant in the glucose concentration range 0.35–0.5 g/L. The feed flow rate had a significant effect on the flux and separation characteristics. Higher cross-flow through the membrane reduced the fouling by providing a shear force to sweep away deposited materials from the membrane surface. At high feed flow rate, more rutin was retained by the membrane with less sugar permeating through. The optimum feed flow rate was 1.5 L/min. For the separation of rutin (in the retentate) and glucose (in the permeate), the best results were obtained at rutin enrichment of 2.9 and recovery 72.5%, respectively. The performance of this system was further improved by operating it in a diafiltration mode, in which only approx. 11% of glucose remained in the retentate. Full article
(This article belongs to the Special Issue Phenolics and Polyphenolics)
Open AccessArticle Temporal and Spatial Regulation of miR-320 in the Uterus during Embryo Implantation in the Rat
Int. J. Mol. Sci. 2010, 11(2), 719-730; doi:10.3390/ijms11020719
Received: 2 December 2009 / Accepted: 10 February 2010 / Published: 11 February 2010
Cited by 29 | PDF Full-text (1442 KB) | HTML Full-text | XML Full-text
Abstract
The implantation process is complex, requiring reciprocal interactions between implantation-competent blastocysts and the receptive uterus. There were reports to show that some microRNAs (miRNAs) may play a key role during embryo implantation in mouse. However, the miR-320 expression profiles in the rat [...] Read more.
The implantation process is complex, requiring reciprocal interactions between implantation-competent blastocysts and the receptive uterus. There were reports to show that some microRNAs (miRNAs) may play a key role during embryo implantation in mouse. However, the miR-320 expression profiles in the rat uterus during peri-implantation are unknown. In the present study, we found that the expression level of miR-320 was lower on day 5 of gestation (g.d. 5) in rats than g.d.3 and g.d.4 and restored gradually from g.d.6. MiR-320 was specifically localized in glandular and luminal epithelia and decidua. The expression of miR-320 was not significantly different in the pseudopregnant uterus and decreased in the uteri of rats subjected to activation of delayed implantation. Artificial decidualization and treatment with progesterone increased the miR-320 expression. Thus, miR-320 was differentially expressed in the rat uterus during implantation. The expression level was affected by active blastocysts and decidualization during the window of implantation. Steroid hormones, progesterone stimulated miR-320 expression. Full article
(This article belongs to the Section Biochemistry, Molecular Biology and Biophysics)
Open AccessArticle Cytotoxic Effects of 2-Bromopropane on Embryonic Development in Mouse Blastocysts
Int. J. Mol. Sci. 2010, 11(2), 731-744; doi:10.3390/ijms11020731
Received: 2 January 2010 / Accepted: 10 February 2010 / Published: 11 February 2010
Cited by 3 | PDF Full-text (192 KB) | HTML Full-text | XML Full-text
Abstract
2-Bromopropane (2-BP), an alternative to ozone-depleting solvents, is used as a cleaning solvent. Here, we examined the cytotoxic effects of 2-bromopropane (2-BP) on mouse embryos at the blastocyst stage, subsequent embryonic attachment and outgrowth in vitro, and in vivo implantation via [...] Read more.
2-Bromopropane (2-BP), an alternative to ozone-depleting solvents, is used as a cleaning solvent. Here, we examined the cytotoxic effects of 2-bromopropane (2-BP) on mouse embryos at the blastocyst stage, subsequent embryonic attachment and outgrowth in vitro, and in vivo implantation via embryo transfer. Mouse blastocysts were incubated in medium with or without 2-BP (2.5, 5 or 10 μM) for 24 h. Cell proliferation and growth were investigated with dual differential staining, apoptosis was analyzed by terminal deoxynucleotidyl transferase-mediated dUTP nick-end labeling (TUNEL) analysis, and implantation and post-implantation development of embryos were assessed using in vitro development analysis and in vivo embryo transfer, respectively. Blastocysts treated with 5 or 10 μM 2-BP displayed significantly increased apoptosis, and decreased inner cell mass (ICM) and trophectoderm (TE) cell number. Additionally, the implantation success rates of 2-BP-pretreated blastocysts were lower than those of untreated controls. In vitro treatment with 5 or 10 μM 2-BP was associated with increased resorption of postimplantation embryos, and decreased placental and fetal weights. Our results collectively indicate that in vitro exposure to 2-BP induces apoptosis, suppresses implantation rates after transfer to host mice, and retards early postimplantation development. Full article
(This article belongs to the Section Biochemistry, Molecular Biology and Biophysics)
Open AccessArticle Bacterial Expression of Mouse Argonaute 2 for Functional and Mutational Studies
Int. J. Mol. Sci. 2010, 11(2), 745-753; doi:10.3390/ijms11020745
Received: 13 January 2010 / Accepted: 10 February 2010 / Published: 12 February 2010
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Abstract
RNA interference (RNAi) is a post-transcriptional gene-silencing process that occurs in many eukaryotic organisms upon intracellular exposure to double-stranded RNA. Argonaute 2 (Ago2) protein is the catalytic engine of mammalian RNAi. It contains a PIWI domain that is structurally related to RNases [...] Read more.
RNA interference (RNAi) is a post-transcriptional gene-silencing process that occurs in many eukaryotic organisms upon intracellular exposure to double-stranded RNA. Argonaute 2 (Ago2) protein is the catalytic engine of mammalian RNAi. It contains a PIWI domain that is structurally related to RNases H and possibly shares with them a two-metal-ion catalysis mechanism. Here we describe the expression in E. coli of mouse Ago2 and testing of its enzymatic activity in a RISC assay, i.e., for the ability to cleave a target RNA in a single position specified by a complementary small interfering RNA (siRNA). The results show that the enzyme can load the siRNA and cleave the complementary RNA in absence of other cellular factors, as described for human Ago2. It was also found that mutation of Arg669, a residue previously proposed to be involved in substrate and/or B metal ion binding, doesn’t affect the enzymatic activity, suggesting that this residue doesn’t belong to the active site. Full article
(This article belongs to the Section Biochemistry, Molecular Biology and Biophysics)
Open AccessArticle Lipid Vesicle Aggregation Induced by Cooling
Int. J. Mol. Sci. 2010, 11(2), 754-761; doi:10.3390/ijms11020754
Received: 6 January 2010 / Accepted: 10 February 2010 / Published: 21 February 2010
PDF Full-text (109 KB) | HTML Full-text | XML Full-text
Abstract
Lipid bilayer fusion is a complex process requiring several intermediate steps. Initially, the two bilayers are brought into close contact following removal of intervening water layers and overcoming electrostatic repulsions between opposing bilayer head groups. In this study we monitor by light [...] Read more.
Lipid bilayer fusion is a complex process requiring several intermediate steps. Initially, the two bilayers are brought into close contact following removal of intervening water layers and overcoming electrostatic repulsions between opposing bilayer head groups. In this study we monitor by light scattering the reversible aggregation of phosphatidylcholine single shell vesicles during which adhesion occurs but stops prior to a fusion process. Light scattering measurements of dimyristoyl-sn-glycero-3-phosphocholine (DMPC), dipalmitoyl-sn-glycero-3-phosphocholine (DPPC) and 1,2-distearoyl-sn-glycero-3-phosphocholine (DSPC) in water show that lowering the temperature of about 0.14 micron single shell vesicles of DPPC (from 20 °C to 5 °C) and about 2 micron vesicles of DSPC (from 20 °C to 15 °C), but not of 1 micron vesicles of DMPC, results in extensive aggregation within 24 hours that is reversible by an increase in temperature. Aggregation of DSPC vesicles was confirmed by direct visual observation. Orientation of lipid head groups parallel to the plane of the bilayer and consequent reduction of the negative surface charge can account for the ability of DPPC and DSPC vesicles to aggregate. Retention of negatively charged phosphates on the surface and the burial of positively charged cholines within the bilayer offer an explanation for the failure of DMPC vesicles to aggregate. Lowering the temperature of 1,2-dipalmitoyl-sn-glycero-3-phosphoserine (DPPS) vesicles from 20 °C to 5 °C failed to increase aggregation within 24 hours at Mg++/DPPS ratios that begin to initiate aggregation and fusion. Full article
(This article belongs to the Special Issue Molecular Self-Assembly)
Open AccessArticle Covalent Anchoring of Chloroperoxidase and Glucose Oxidase on the Mesoporous Molecular Sieve SBA-15
Int. J. Mol. Sci. 2010, 11(2), 762-778; doi:10.3390/ijms11020762
Received: 4 January 2010 / Revised: 9 February 2010 / Accepted: 9 February 2010 / Published: 24 February 2010
Cited by 28 | PDF Full-text (375 KB) | HTML Full-text | XML Full-text
Abstract
Functionalization of porous solids plays an important role in many areas, including heterogeneous catalysis and enzyme immobilization. In this study, large-pore ordered mesoporous SBA-15 molecular sieves were synthesized with tetraethyl orthosilicate (TEOS) in the presence of the non-ionic triblock co-polymer Pluronic P123 [...] Read more.
Functionalization of porous solids plays an important role in many areas, including heterogeneous catalysis and enzyme immobilization. In this study, large-pore ordered mesoporous SBA-15 molecular sieves were synthesized with tetraethyl orthosilicate (TEOS) in the presence of the non-ionic triblock co-polymer Pluronic P123 under acidic conditions. These materials were grafted with 3 aminopropyltrimethoxysilane (ATS), 3-glycidoxypropyltrimethoxysilane (GTS) and with 3 aminopropyltrimethoxysilane and glutaraldehyde (GA-ATS) in order to provide covalent anchoring points for enzymes. The samples were characterized by nitrogen adsorption, powder X-ray diffraction, solid-state NMR spectroscopy, elemental analysis, diffuse reflectance fourier transform infrared spectroscopy and diffuse reflectance UV/Vis spectroscopy. The obtained grafted materials were then used for the immobilization of chloroperoxidase (CPO) and glucose oxidase (GOx) and the resulting biocatalysts were tested in the oxidation of indole. It is found that enzymes anchored to the mesoporous host by the organic moieties can be stored for weeks without losing their activity. Furthermore, the covalently linked enzymes are shown to be less prone to leaching than the physically adsorbed enzymes, as tested in a fixed-bed reactor under continuous operation conditions. Full article
(This article belongs to the Special Issue Biocatalysis)
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Open AccessCommunication Mutagenicity of New Lead Compounds to Treat Sickle Cell Disease Symptoms in a Salmonella/Microsome Assay
Int. J. Mol. Sci. 2010, 11(2), 779-788; doi:10.3390/ijms11020779
Received: 15 January 2010 / Accepted: 10 February 2010 / Published: 25 February 2010
Cited by 9 | PDF Full-text (191 KB) | HTML Full-text | XML Full-text
Abstract
A series of phthalimide derivatives planned as drugs candidates to treat the symptoms of sickle cell anemia were evaluated in a mutagenicity test using strains of Salmonella typhimurium TA100 and TA102, without and with addition of S9 mixture, with the aim to [...] Read more.
A series of phthalimide derivatives planned as drugs candidates to treat the symptoms of sickle cell anemia were evaluated in a mutagenicity test using strains of Salmonella typhimurium TA100 and TA102, without and with addition of S9 mixture, with the aim to identify the best structural requirements for a drug candidate without genotoxic activity. The compounds (1,3-dioxo-1,3-dihydro-2H-isoindol-2-yl)methyl nitrate (1); (1,3-dioxo-1,3-dihydro-2H-isoindol-2-yl)ethyl nitrate (2); 3-(1,3-dioxo-1,3-dihydro-2H-iso-indol-2-yl)benzyl nitrate (3); 4-(1,3-dioxo-1,3-dihydro-2H-isoindol-2-yl)-N-hydroxy-benzenesulfonamide (4); 4-(1,3-dioxo-1,3-dihydro-2H-isoindol-2-yl)benzyl nitrate (5) and 2-[4-(1,3-dioxo-1,3-dihydro-2H-isoindol-2-yl)phenyl]ethyl nitrate (6) presented mutagenic potency ranging between 0-4,803 revertants/μmol. These results allowed us to propose that a methyl spacer linked to a nitrate ester subunit associated to meta aromatic substitution decreases mutagenicity. Full article
(This article belongs to the Section Biochemistry, Molecular Biology and Biophysics)
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Review

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Open AccessReview The Fibrillar Collagen Family
Int. J. Mol. Sci. 2010, 11(2), 407-426; doi:10.3390/ijms11020407
Received: 30 December 2009 / Revised: 22 January 2010 / Accepted: 23 January 2010 / Published: 28 January 2010
Cited by 46 | PDF Full-text (872 KB) | HTML Full-text | XML Full-text
Abstract
Collagens, or more precisely collagen-based extracellular matrices, are often considered as a metazoan hallmark. Among the collagens, fibrillar collagens are present from sponges to humans, and are involved in the formation of the well-known striated fibrils. In this review we discuss the [...] Read more.
Collagens, or more precisely collagen-based extracellular matrices, are often considered as a metazoan hallmark. Among the collagens, fibrillar collagens are present from sponges to humans, and are involved in the formation of the well-known striated fibrils. In this review we discuss the different steps in the evolution of this protein family, from the formation of an ancestral fibrillar collagen gene to the formation of different clades. Genomic data from the choanoflagellate (sister group of Metazoa) Monosiga brevicollis, and from diploblast animals, have suggested that the formation of an ancestral α chain occurred before the metazoan radiation. Phylogenetic studies have suggested an early emergence of the three clades that were first described in mammals. Hence the duplication events leading to the formation of the A, B and C clades occurred before the eumetazoan radiation. Another important event has been the two rounds of “whole genome duplication” leading to the amplification of fibrillar collagen gene numbers, and the importance of this diversification in developmental processes. We will also discuss some other aspects of fibrillar collagen evolution such as the development of the molecular mechanisms involved in the formation of procollagen molecules and of striated fibrils. Full article
(This article belongs to the Special Issue Cladistic Analysis and Molecular Evolution)
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Open AccessReview Recent Developments in Fluorescence Correlation Spectroscopy for Diffusion Measurements in Planar Lipid Membranes
Int. J. Mol. Sci. 2010, 11(2), 427-457; doi:10.3390/ijms11020427
Received: 3 December 2009 / Revised: 11 January 2010 / Accepted: 15 January 2010 / Published: 28 January 2010
Cited by 21 | PDF Full-text (712 KB) | HTML Full-text | XML Full-text
Abstract
Fluorescence correlation spectroscopy (FCS) is a single molecule technique used mainly for determination of mobility and local concentration of molecules. This review describes the specific problems of FCS in planar systems and reviews the state of the art experimental approaches such as [...] Read more.
Fluorescence correlation spectroscopy (FCS) is a single molecule technique used mainly for determination of mobility and local concentration of molecules. This review describes the specific problems of FCS in planar systems and reviews the state of the art experimental approaches such as 2-focus, Z-scan or scanning FCS, which overcome most of the artefacts and limitations of standard FCS. We focus on diffusion measurements of lipids and proteins in planar lipid membranes and review the contributions of FCS to elucidating membrane dynamics and the factors influencing it, such as membrane composition, ionic strength, presence of membrane proteins or frictional coupling with solid support. Full article
(This article belongs to the Special Issue Single Molecules)
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Open AccessReview Biological Activities of Phenolic Compounds Present in Virgin Olive Oil
Int. J. Mol. Sci. 2010, 11(2), 458-479; doi:10.3390/ijms11020458
Received: 1 December 2009 / Revised: 19 January 2010 / Accepted: 22 January 2010 / Published: 2 February 2010
Cited by 113 | PDF Full-text (195 KB) | HTML Full-text | XML Full-text
Abstract
The Mediterranean diet is associated with a lower incidence of atherosclerosis, cardiovascular disease, neurodegenerative diseases and certain types of cancer. The apparent health benefits have been partially ascribed to the dietary consumption of virgin olive oil by Mediterranean populations. Much research has [...] Read more.
The Mediterranean diet is associated with a lower incidence of atherosclerosis, cardiovascular disease, neurodegenerative diseases and certain types of cancer. The apparent health benefits have been partially ascribed to the dietary consumption of virgin olive oil by Mediterranean populations. Much research has focused on the biologically active phenolic compounds naturally present in virgin olive oils to aid in explaining reduced mortality and morbidity experienced by people consuming a traditional Mediterranean diet. Studies (human, animal, in vivo and in vitro) have demonstrated that olive oil phenolic compounds have positive effects on certain physiological parameters, such as plasma lipoproteins, oxidative damage, inflammatory markers, platelet and cellular function, antimicrobial activity and bone health. This paper summarizes current knowledge on the bioavailability and biological activities of olive oil phenolic compounds. Full article
(This article belongs to the Special Issue Phenolics and Polyphenolics)
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Open AccessReview Novel Neuroprotective Strategies in Ischemic Retinal Lesions
Int. J. Mol. Sci. 2010, 11(2), 544-561; doi:10.3390/ijms11020544
Received: 7 January 2010 / Revised: 27 January 2010 / Accepted: 27 January 2010 / Published: 3 February 2010
Cited by 15 | PDF Full-text (430 KB) | HTML Full-text | XML Full-text
Abstract
Retinal ischemia can be effectively modeled by permanent bilateral common carotid artery occlusion, which leads to chronic hypoperfusion-induced degeneration in the entire rat retina. The complex pathways leading to retinal cell death offer a complex approach of neuroprotective strategies. In the present [...] Read more.
Retinal ischemia can be effectively modeled by permanent bilateral common carotid artery occlusion, which leads to chronic hypoperfusion-induced degeneration in the entire rat retina. The complex pathways leading to retinal cell death offer a complex approach of neuroprotective strategies. In the present review we summarize recent findings with different neuroprotective candidate molecules. We describe the protective effects of intravitreal treatment with: (i) urocortin 2; (ii) a mitochondrial ATP-sensitive K+ channel opener, diazoxide; (iii) a neurotrophic factor, pituitary adenylate cyclase activating polypeptide; and (iv) a novel poly(ADP-ribose) polymerase inhibitor (HO3089). The retinoprotective effects are demonstrated with morphological description and effects on apoptotic pathways using molecular biological techniques. Full article
(This article belongs to the Special Issue Neuroprotective Strategies (special issue))
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Open AccessReview Hypericins as Potential Leads for New Therapeutics
Int. J. Mol. Sci. 2010, 11(2), 562-594; doi:10.3390/ijms11020562
Received: 3 December 2009 / Revised: 27 January 2010 / Accepted: 28 January 2010 / Published: 4 February 2010
Cited by 96 | PDF Full-text (568 KB) | HTML Full-text | XML Full-text
Abstract
70 years have passed since the first isolation of the naphthodianthrones hypericin and pseudohypericin from Hypericum perforatum L. Today, they continue to be one of the most promising group of polyphenols, as they fascinate with their physical, chemical and important biological properties which derive from their unique chemical structure. Hypericins and their derivatives have been extensively studied mainly for their antitumor, antiviral and antidepressant properties. Notably, hypericin is one of the most potent naturally occurring photodynamic agents. It is able to generate the superoxide anion and a high quantum yield of singlet oxygen that are considered to be primarily responsible for its biological effects. The prooxidant photodynamic properties of hypericin have been exploited for the photodynamic therapy of cancer (PDT), as hypericin, in combination with light, very effectively induces apoptosis and/or necrosis of cancer cells. The mechanism by which these activities are expressed continues to be a main topic of discussion, but according to scientific data, different modes of action (generation of ROS & singlet oxygen species, antiangiogenesis, immune responces) and multiple molecular pathways (intrinsic/extrinsic apoptotic pathway, ERK inhibition) possibly interrelating are implicated. The aim of this review is to analyse the most recent advances (from 2005 and thereof) in the chemistry and biological activities (in vitro and in vivo) of the pure naphthodianthrones, hypericin and pseudohypericin from H. perforatum. Extracts from H. perforatum were not considered, nor pharmakokinetic or clinical data. Computerised literature searches were performed using the Medline (PubMed), ChemSciFinder and Scirus Library databases. No language restrictions were imposed. Full article
(This article belongs to the Special Issue Phenolics and Polyphenolics)
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Open AccessReview The Creation and Physiological Relevance of Divergent Hydroxylation Patterns in the Flavonoid Pathway
Int. J. Mol. Sci. 2010, 11(2), 595-621; doi:10.3390/ijms11020595
Received: 11 December 2009 / Revised: 27 January 2010 / Accepted: 28 January 2010 / Published: 4 February 2010
Cited by 28 | PDF Full-text (300 KB) | HTML Full-text | XML Full-text
Abstract
Flavonoids and biochemically-related chalcones are important secondary metabolites, which are ubiquitously present in plants and therefore also in human food. They fulfill a broad range of physiological functions in planta and there are numerous reports about their physiological relevance for humans. Flavonoids [...] Read more.
Flavonoids and biochemically-related chalcones are important secondary metabolites, which are ubiquitously present in plants and therefore also in human food. They fulfill a broad range of physiological functions in planta and there are numerous reports about their physiological relevance for humans. Flavonoids have in common a basic C6-C3-C6 skeleton structure consisting of two aromatic rings (A and B) and a heterocyclic ring (C) containing one oxygen atom, whereas chalcones, as the intermediates in the formation of flavonoids, have not yet established the heterocyclic C-ring. Flavonoids are grouped into eight different classes, according to the oxidative status of the C-ring. The large number of divergent chalcones and flavonoid structures is from the extensive modification of the basic molecules. The hydroxylation pattern influences physiological properties such as light absorption and antioxidative activity, which is the base for many beneficial health effects of flavonoids. In some cases antiinfective properties are also effected. Full article
(This article belongs to the Special Issue Phenolics and Polyphenolics)
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Open AccessReview Biological Activities of Polyphenols from Grapes
Int. J. Mol. Sci. 2010, 11(2), 622-646; doi:10.3390/ijms11020622
Received: 1 December 2009 / Revised: 26 January 2010 / Accepted: 29 January 2010 / Published: 4 February 2010
Cited by 226 | PDF Full-text (157 KB) | HTML Full-text | XML Full-text
Abstract
The dietary consumption of grape and its products is associated with a lower incidence of degenerative diseases such as cardiovascular disease and certain types of cancers. Most recent interest has focused on the bioactive phenolic compounds in grape. Anthocyanins, flavanols, flavonols and [...] Read more.
The dietary consumption of grape and its products is associated with a lower incidence of degenerative diseases such as cardiovascular disease and certain types of cancers. Most recent interest has focused on the bioactive phenolic compounds in grape. Anthocyanins, flavanols, flavonols and resveratrol are the most important grape polyphenols because they possess many biological activities, such as antioxidant, cardioprotective, anticancer, anti-inflammation, antiaging and antimicrobial properties. This review summarizes current knowledge on the bioactivities of grape phenolics. The extraction, isolation and identification methods of polyphenols from grape as well as their bioavailability and potential toxicity also are included. Full article
(This article belongs to the Special Issue Phenolics and Polyphenolics)
Open AccessReview Anchoring of a Single Molecular Rotor and Its Array on Metal Surfaces using Molecular Design and Self-Assembly
Int. J. Mol. Sci. 2010, 11(2), 656-671; doi:10.3390/ijms11020656
Received: 14 January 2010 / Revised: 26 January 2010 / Accepted: 1 February 2010 / Published: 9 February 2010
Cited by 4 | PDF Full-text (3632 KB) | HTML Full-text | XML Full-text
Abstract
Functionalizing of single molecules on surfaces has manifested great potential for bottom-up construction of complex devices on a molecular scale. We discuss the growth mechanism for the initial layers of polycyclic aromatic hydrocarbons on metal surfaces and we review our recent progress [...] Read more.
Functionalizing of single molecules on surfaces has manifested great potential for bottom-up construction of complex devices on a molecular scale. We discuss the growth mechanism for the initial layers of polycyclic aromatic hydrocarbons on metal surfaces and we review our recent progress on molecular machines, and present a molecular rotor with a fixed off-center axis formed by chemical bonding. These results represent important advances in molecular-based nanotechnology. Full article
(This article belongs to the Special Issue Single Molecules)
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Open AccessReview Role of Dehydrodiferulates in Maize Resistance to Pests and Diseases
Int. J. Mol. Sci. 2010, 11(2), 691-703; doi:10.3390/ijms11020691
Received: 15 January 2010 / Accepted: 4 February 2010 / Published: 9 February 2010
Cited by 22 | PDF Full-text (157 KB) | HTML Full-text | XML Full-text
Abstract
Phenolic esters have attracted considerable interest due to the potential they offer for peroxidase catalysed cross-linking of cell wall polysaccharides. Particularly, feruloyl residues undergo radical coupling reactions that result in cross-linking (intra-/intermolecular) between polysaccharides, between polysaccharides and lignin and, between polysaccharides and [...] Read more.
Phenolic esters have attracted considerable interest due to the potential they offer for peroxidase catalysed cross-linking of cell wall polysaccharides. Particularly, feruloyl residues undergo radical coupling reactions that result in cross-linking (intra-/intermolecular) between polysaccharides, between polysaccharides and lignin and, between polysaccharides and proteins. This review addresses for the first time different studies in which it is established that cross-linking by dehydrodiferulates contributes to maize’s defences to pests and diseases. Dehydrodiferulate cross-links are involved in maize defence mechanisms against insects such as the European, Mediterranean, and tropical corn borers and, storage pest as the maize weevil. In addition, cross-links are also discussed to be involved in genetic resistance of maize to fungus diseases as Gibberella ear and stalk rot. Resistance against insects and fungus attending dehydrodiferulates could go hand in hand. Quantitative trait loci mapping for these cell wall components could be a useful tool for enhancing resistance to pest and diseases in future breeding programs. Full article
(This article belongs to the Special Issue Phenolics and Polyphenolics)
Open AccessReview Molecular Design and Functional Control of Novel Self-Oscillating Polymers
Int. J. Mol. Sci. 2010, 11(2), 704-718; doi:10.3390/ijms11020704
Received: 31 December 2009 / Accepted: 24 January 2010 / Published: 10 February 2010
Cited by 16 | PDF Full-text (763 KB) | HTML Full-text | XML Full-text
Abstract
If we could realize an autonomous polymer system driven under biological conditions by a tailor-made molecular design, human beings could create unprecedented biomimetic functions and materials such as heartbeats, autonomous peristaltic pumps, etc. In order to achieve this objective, we have investigated [...] Read more.
If we could realize an autonomous polymer system driven under biological conditions by a tailor-made molecular design, human beings could create unprecedented biomimetic functions and materials such as heartbeats, autonomous peristaltic pumps, etc. In order to achieve this objective, we have investigated the molecular design of such a polymer system. As a result, we were the first to demonstrate a self-oscillating polymer system driven in a solution where only malonic acid existed, which could convert the chemical energy of the Belousov-Zhabotinsky (BZ) reaction into a change in the conformation of the polymer chain. To cause the self-oscillation in solution, we have attempted to construct a built-in system where the required BZ system substrates other than the organic acid are incorporated into the polymer itself. That is, the novel polymer chain incorporated the metal catalyst of the BZ reaction, a pH-control site and an oxidant supply site at the same time. As a result of introducing the pH control and oxidant supply sites into the conventional-type self-oscillating polymer chain, the novel polymer chain caused aggregation-disaggregation self-oscillations in the solution. We clarified that the period of the self-oscillation of the novel self-oscillating polymer chain was proportional to the concentration of the malonic acid. Therefore, the concentration of the malonic acid can be determined by measuring the period of the novel self-oscillating polymer solution. In this review, we introduce the detailed molecular design of the novel self-oscillating polymer chain and its self-oscillating behavior. Moreover, we report an autonomous self-oscillating polymer gel actuator that causes a bending-stretching motion under the constant conditions. Full article
(This article belongs to the Special Issue Molecular Biomimetics and Materials Design)

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