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Int. J. Mol. Sci., Volume 8, Issue 5 (May 2007), Pages 363-469

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Research

Open AccessArticle Introducing Spectral Structure Activity Relationship (S-SAR) Analysis. Application to Ecotoxicology
Int. J. Mol. Sci. 2007, 8(5), 363-391; doi:10.3390/i8050363
Received: 20 March 2007 / Revised: 4 May 2007 / Accepted: 4 May 2007 / Published: 22 May 2007
Cited by 42 | PDF Full-text (427 KB) | HTML Full-text | XML Full-text
Abstract
A novel quantitative structure-activity (property) relationship model, namelySpectral-SAR, is presented in an exclusive algebraic way replacing the old-fashionedmulti-regression one. The actual S-SAR method interprets structural descriptors as vectorsin a generic data space that is further mapped into a full orthogonal space by means
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A novel quantitative structure-activity (property) relationship model, namelySpectral-SAR, is presented in an exclusive algebraic way replacing the old-fashionedmulti-regression one. The actual S-SAR method interprets structural descriptors as vectorsin a generic data space that is further mapped into a full orthogonal space by means of theGram-Schmidt algorithm. Then, by coordinated transformation between the data andorthogonal spaces, the S-SAR equation is given under simple determinant form for anychemical-biological interactions under study. While proving to give the same analyticalequation and correlation results with standard multivariate statistics, the actual S-SARframe allows the introduction of the spectral norm as a valid substitute for the correlationfactor, while also having the advantage to design the various related SAR models throughthe introduced “minimal spectral path” rule. An application is given performing a completeS-SAR analysis upon the Tetrahymena pyriformis ciliate species employing its reportedeco-toxicity activities among relevant classes of xenobiotics. By representing the spectralnorm of the endpoint models against the concerned structural coordinates, the obtainedS-SAR endpoints hierarchy scheme opens the perspective to further design the eco-toxicological test batteries with organisms from different species. Full article
(This article belongs to the Section Physical Chemistry, Theoretical and Computational Chemistry)
Open AccessArticle Organo-niobate Ionic Liquids: Synthesis, Characterization and Application as Acid Catalyst in Pechmann Reactions
Int. J. Mol. Sci. 2007, 8(5), 392-398; doi:10.3390/i8050392
Received: 27 March 2007 / Accepted: 5 May 2007 / Published: 11 May 2007
Cited by 11 | PDF Full-text (60 KB) | HTML Full-text | XML Full-text
Abstract
The combinations of 1-butyl-3-methylimidazolium chloride with NbCl5 yieldedionic mixtures with different melting point temperatures and acidity depending on theniobium molar fraction. The mixtures were characterized by thermal (DSC) andspectroscopic (FT-IR and 1H NMR) analysis. The Pechmann reactions of different phenolswith ethylacetoacetate,
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The combinations of 1-butyl-3-methylimidazolium chloride with NbCl5 yieldedionic mixtures with different melting point temperatures and acidity depending on theniobium molar fraction. The mixtures were characterized by thermal (DSC) andspectroscopic (FT-IR and 1H NMR) analysis. The Pechmann reactions of different phenolswith ethylacetoacetate, producing coumarins, was used as model to evaluate the catalyticbehavior of these mixtures as acid Lewis catalyst. These reactions were carried out usingacidic mixtures of 60 mol%. Full article
(This article belongs to the Special Issue Ionic Liquids)
Open AccessArticle Functional Analysis of the Drosophila Dnop5 Using Targeted RNA Interference
Int. J. Mol. Sci. 2007, 8(5), 399-406; doi:10.3390/i8050399
Received: 7 March 2007 / Revised: 3 May 2007 / Accepted: 9 May 2007 / Published: 31 May 2007
PDF Full-text (144 KB) | HTML Full-text | XML Full-text
Abstract
Dnop5 is a member of the conserved nop5/sik1 gene family, which encodecomponents of small nucleolar ribonucleoprotein(snoRNP) complexes. To study thefunction of DNop5, we generated the polyclonal antibody and determined its expressionpattern. It is highly expressed in different periods of the Drosophila development. We
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Dnop5 is a member of the conserved nop5/sik1 gene family, which encodecomponents of small nucleolar ribonucleoprotein(snoRNP) complexes. To study thefunction of DNop5, we generated the polyclonal antibody and determined its expressionpattern. It is highly expressed in different periods of the Drosophila development. We usedheritable RNA interference (RNAi) in combination with the yeast GAL4/UAS binarysystem to knock down the DNop5 protein. It resulted in lethality and dramatic somaticanomalies in RNAi mutant fly, in which the DNop5 protein is reduced efficiently. Northernblotting showed that the processing of 18S rRNA was disrupted in DNop5 knock down fly,but 28S rRNA is normal. These results suggest that DNop5 is essential for the Drosophilagrowth and function in the execution of early pre-rRNA processing steps that lead toformation of 18S rRNA. Full article
(This article belongs to the Section Biochemistry, Molecular Biology and Biophysics)
Open AccessArticle Prediction of Standard Enthalpy of Formation by a QSPR Model
Int. J. Mol. Sci. 2007, 8(5), 407-432; doi:10.3390/i8050407
Received: 1 March 2007 / Accepted: 27 March 2007 / Published: 22 May 2007
Cited by 86 | PDF Full-text (161 KB) | HTML Full-text | XML Full-text | Correction
Abstract
The standard enthalpy of formation of 1115 compounds from all chemicalgroups, were predicted using genetic algorithm-based multivariate linear regression (GA-MLR). The obtained multivariate linear five descriptors model by GA-MLR has correlationcoefficient ( R 2 = 0.9830 ). All molecular descriptors which have entered
[...] Read more.
The standard enthalpy of formation of 1115 compounds from all chemicalgroups, were predicted using genetic algorithm-based multivariate linear regression (GA-MLR). The obtained multivariate linear five descriptors model by GA-MLR has correlationcoefficient ( R 2 = 0.9830 ). All molecular descriptors which have entered in this model arecalculated from chemical structure of any molecule. As a result, application of this modelfor any compound is easy and accurate. Full article
(This article belongs to the Section Physical Chemistry, Theoretical and Computational Chemistry)
Open AccessArticle Molecular Cloning and Characterization of a Novel Human Glycine-N-acyltransferase Gene GLYATL1, Which Activates Transcriptional Activity of HSE Pathway
Int. J. Mol. Sci. 2007, 8(5), 433-444; doi:10.3390/i8050433
Received: 18 April 2007 / Revised: 5 May 2007 / Accepted: 10 May 2007 / Published: 25 May 2007
Cited by 4 | PDF Full-text (1681 KB) | HTML Full-text | XML Full-text
Abstract
The glycine-N-acyltransferase (GLYAT) is well known to be involved in thedetoxification of endogenous and exogenous xenobiotic acyl-CoA's in mammals.Unfortunately, the knowledge about the gene encoding GLYAT is very limited. Here wereport a novel gene encoding a GLYAT member, designated as GLYATL1, which was1546
[...] Read more.
The glycine-N-acyltransferase (GLYAT) is well known to be involved in thedetoxification of endogenous and exogenous xenobiotic acyl-CoA's in mammals.Unfortunately, the knowledge about the gene encoding GLYAT is very limited. Here wereport a novel gene encoding a GLYAT member, designated as GLYATL1, which was1546 base pairs in length and contained an open reading frame (ORF) encoding apolypeptide of 302 amino acids. GLYATL1 was a split gene that was consisted of 7 exonsand 6 introns and mapped to chromosome 11q12.1. The expression of GLYATL1 could befound in liver, kidney, pancreas, testis, ovary and stomach among 18 human tissues by RT-PCR analysis. Subcellular localization of myc-tagged GLYATL1 fusion protein revealedthat GLYATL1 was distributed primarily in the cytoplasm of COS-7 cells. Furthermore,through the pathway profiling assay, the GLYATL1 protein was found to activate HSEsignaling pathway in a dose-dependent manner when overexpressed in HEK293T cells. Full article
(This article belongs to the Special Issue Interaction of Biological Molecules)
Open AccessArticle Preparation and Characterization of a Chloroperoxidase-like Catalytic Antibody
Int. J. Mol. Sci. 2007, 8(5), 445-454; doi:10.3390/i8050445
Received: 10 February 2007 / Revised: 12 April 2007 / Accepted: 16 May 2006 / Published: 29 May 2007
PDF Full-text (954 KB) | HTML Full-text | XML Full-text
Abstract
The small molecule, meso-tetra(α,α,α,α-o-phenylacetamidophenyl)porphyrin(Mr1147.0) was used as complete antigen to elicit MAb through the immunization and cellfusion techniques.The MAb 1F2 obtained was demonstrated to be very pure byMALDI/TOFMS.The subtype of MAb 1F2 is IgG2a, which has a relative molecular weightof 156,678.8 Da.No significant
[...] Read more.
The small molecule, meso-tetra(α,α,α,α-o-phenylacetamidophenyl)porphyrin(Mr1147.0) was used as complete antigen to elicit MAb through the immunization and cellfusion techniques.The MAb 1F2 obtained was demonstrated to be very pure byMALDI/TOFMS.The subtype of MAb 1F2 is IgG2a, which has a relative molecular weightof 156,678.8 Da.No significant change in the intensity of absorption peaks in UV and CDspectra was observed over a pH range between 6 and 12.The high stability of the abzymeand the tight binding between Fe porphyrin and antibody were also demonstrated.Vmax, Km,κcat, κcat/Km for abzyme are 5.18 × 10-8 Ms-1, 1.50 × 10-8M , 0.518 s-1, 3.45 × 107 M-1s-1, respectively.The data obtained indicate that catalytic antibody has highcatalytic activity.The chloroperoxidase activity of MAb 1F2-Fe porphyrin complex is stablefrom 10 °C to 60 °C. Full article
(This article belongs to the Section Molecular Recognition)
Open AccessArticle Polarization of T Lymphocytes Is Regulated by Mesenchymal Stem Cells in NZBWF1 and BALB/c Mice
Int. J. Mol. Sci. 2007, 8(5), 455-469; doi:10.3390/i8050455
Received: 27 February 2007 / Revised: 17 April 2007 / Accepted: 9 May 2007 / Published: 30 May 2007
Cited by 2 | PDF Full-text (328 KB) | HTML Full-text | XML Full-text
Abstract
Mesenchymal stem cells (MSCs) have been shown to suppress proliferation andactivation of T lymphocytes in vivo and in vitro although the molecular mechanism of theimmunosuppressive effect is not completely understood. To investigate theimmunoregulatory effects of mice bone marrow mesenchymal stem cells on T
[...] Read more.
Mesenchymal stem cells (MSCs) have been shown to suppress proliferation andactivation of T lymphocytes in vivo and in vitro although the molecular mechanism of theimmunosuppressive effect is not completely understood. To investigate theimmunoregulatory effects of mice bone marrow mesenchymal stem cells on T lymphocyte,MSCs from NZBWF1 and BALB/c mice were isolated and expanded from bone marrow,and identified with cell morphology and the surface phenotypes. CD3+ T lymphocytesisolated by nylon wool columns were co-cultured with PMA with or without the two strainsof MSCs. Then T cell apoptosis and intercellular cytokines of T cell were assessed by flowcytometry. Quantification of transcription factors T-box (T-bet) and GATA-binding protein3 (GATA-3) expressed in T cells was detected by RT-PCR and western blot. Our resultsshowed that there was a decrease of CD3+ T cell apoptosis when NW MSCs or Bc MSCswere added, and an increase of Th2 subset by NW MSCs and Th1 subset by Bc MSCs wereobserved by co-culturing MSCs with T lymphocytes. It is suggested that, by favoring Th1-cell development and inhibitory Th2-cell development, normal MSCs might interfere withthe SLE development, and that marrow-derived NW MSCs had defectiveimmunoregulatory function when compared with MSCs from healthy mouse strains. Full article
(This article belongs to the Section Biochemistry, Molecular Biology and Biophysics)

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