Synthesis and characterization of binuclear mercury(II) complexes of phosphorus ylides, X-ray analysis and multinuclear NMR measurements

The reactions of phosphorus ylide (p-tolyl)₃PCHC(O)CH₃ (Y₁) with HgX₂ (X = Cl and Br) and (p-tolyl)₃PCHC(O)C₆H₄NO₂ (Y₂) with HgX₂ (X = Cl, Br and I) in equimolar ratios using methanol as a solvent are reported. These reactions led to binuclear complexes. C-Coordination of ylides and trans-like structure of complexes [(Y₁) · HgBr₂]₂ and [(Y₂) · HgBr₂]₂ · 2DMSO are demonstrated by single crystal X-ray analyses. The IR, ¹H, ¹³C and ³¹P NMR data for the other synthesized compounds are similar to the latter complexes, indicating similar structures. Elemental analyses indicate a 1:1 stoichiometry between the ylide and Hg(II) halide in all the products. The ab initio studies indicated that for all dimeric compounds, the observed trans-like structures are 7-10 kcal/mol more stable than the alternative possible cis-like isomers. Although the calculated bond lengths are slightly longer than the measured ones, the similarity of calculated and measured bond angles reflects the similar geometrical structures for these compounds in both the solid state and the gas phase.     

National Center for Biomedical Ontology: advancing biomedicine through structured organization of scientific knowledge

The National Center for Biomedical Ontology is a consortium that comprises leading informaticians, biologists, clinicians, and ontologists, funded by the National Institutes of Health (NIH) Roadmap, to develop innovative technology and methods that allow scientists to record, manage, and disseminate biomedical information and knowledge in machine-processable form. The goals of the Center are (1) to help unify the divergent and isolated efforts in ontology development by promoting high quality open-source, standards-based tools to create, manage, and use ontologies, (2) to create new software tools so that scientists can use ontologies to annotate and analyze biomedical data, (3) to provide a national resource for the ongoing evaluation, integration, and evolution of biomedical ontologies and associated tools and theories in the context of driving biomedical projects (DBPs), and (4) to disseminate the tools and resources of the Center and to identify, evaluate, and communicate best practices of ontology development to the biomedical community. Through the research activities within the Center, collaborations with the DBPs, and interactions with the biomedical community, our goal is to help scientists to work more effectively in the e-science paradigm, enhancing experiment design, experiment execution, data analysis, information synthesis, hypothesis generation and testing, and understand human disease.     

Extremely rapid turnover of S-adenosylmethionine decarboxylase in Crithidia fasciculata

The activity of S-adenosylmethionine decarboxylase (AdoMetDC) in Crithidia fasciculata was shown to be correlated to the growth of the parasite. An increase in activity was observed during exponential growth. Inhibition of protein synthesis induced an extremely rapid decay of AdoMetDC activity. The half-life of the enzyme was estimated to be about 3 min, which is the shortest half-life ever recorded for an eukaryotic AdoMetDC. The reduction in AdoMetDC activity was correlated with a decrease in AdoMetDC protein content, demonstrating a rapid turnover of the enzyme. No polyamine-mediated feedback regulation of AdoMetDC was observed in the parasite.     

Activity of dermaseptin K4-S4 against foodborne pathogens

Dermaseptin S4 and its substituted derivative K(4)-S4 were investigated against various food-related pathogenic bacteria in culture media. K(4)-S4, but not the native peptide displayed significant growth inhibitory activity against all bacteria tested. Next, activity of K(4)-S4 against Escherichia coli O157:H7 was defined in terms of milieu dependencies. Salt-dependent kinetic studies in growth medium indicated that the peptide's antibacterial activity is maintained at fairly high (up to 600mM) NaCl concentrations but inhibited at higher concentrations. Similarly, antibacterial activity was reduced at high but not low pH conditions. Importantly, antibacterial activity was significantly maintained at temperatures lower than 37 degrees C and significantly enhanced at 42 degrees C. With respect to bactericidal kinetics, negative cultures were obtained in LB as well as in commercial apple juice, respectively, within 1 and 2h treatment, at twice the minimal inhibitory concentration (MIC) value. Overall, the data collected is indicative of a certain interest for dermaseptin derivatives as potential food preservatives.     

Non-linear heteroscedastic regression model for determination of methotrexate in human plasma by high-performance liquid chromatography

Generalized least squares regression with variance function estimation was used to derive the calibration function for measurement of methotrexate plasma concentration and its results were compared with weighted least squares regression by usual weight factors and also with that of ordinary least squares method. In the calibration curve range of 0.05 to 100 microM, both heteroscedasticity and non-linearity were present therefore ordinary least squares linear regression methods could result in large errors in the calculation of methotrexate concentration. Generalized least squares regression with variance function estimation worked better than both the weighted regression with the usual weight factors and ordinary least squares regression and gave better estimates for methotrexate concentration.     

Role of PTPα in the Destruction of Periodontal Connective Tissues

IL-1β contributes to connective tissue destruction in part by up-regulating stromelysin-1 (MMP-3), which in fibroblasts is a focal adhesion-dependent process. Protein tyrosine phosphatase-α (PTPα) is enriched in and regulates the formation of focal adhesions, but the role of PTPα in connective tissue destruction is not defined. We first examined destruction of periodontal connective tissues in adult PTPα^+/+ and PTPα^−/− mice subjected to ligature-induced periodontitis, which increases the levels of multiple cytokines, including IL-1β. Three weeks after ligation, maxillae were processed for morphometry, micro-computed tomography and histomorphometry. Compared with unligated controls, there was ∼1.5–3 times greater bone loss as well as 3-fold reduction of the thickness of the gingival lamina propria and 20-fold reduction of the amount of collagen fibers in WT than PTPα^−/− mice. Immunohistochemical staining of periodontal tissue showed elevated expression of MMP-3 at ligated sites. Second, to examine mechanisms by which PTPα may regulate matrix degradation, human MMP arrays were used to screen conditioned media from human gingival fibroblasts treated with vehicle, IL-1β or TNFα. Although MMP-3 was upregulated by both cytokines, only IL-1β stimulated ERK activation in human gingival fibroblasts plated on fibronectin. TIRF microscopy and immunoblotting analyses of cells depleted of PTPα activity with the use of various mutated constructs or with siRNA or PTPα^KO and matched wild type fibroblasts were plated on fibronectin to enable focal adhesion formation and stimulated with IL-1β. These data showed that the catalytic and adaptor functions of PTPα were required for IL-1β-induced focal adhesion formation, ERK activation and MMP-3 release. We conclude that inflammation-induced connective tissue degradation involving fibroblasts requires functionally active PTPα and in part is mediated by IL-1β signaling through focal adhesions.     

The effect of C-terminal fragment of JNK2 on the stability of p53 and cell proliferation

The basal activity of JNK is low in normal growing cells and inactivated JNK targets p53 for ubiquitination. To elucidate if the C-terminal part of JNK is responsible for its binding to p53, the low background tet-off inducible NIH3T3 cell line was selected by luciferase reporter gene and a double stable C-JNK Aa (203-424) cell line was established. After withdrawing tetracycline, the C-JNK fragment expression was induced and cell growth was dramatically inhibited 24 h later. However, the expresion of p53 was found to be increased after the induction of C-JNK fragment, evaluated by transfecting p21^waf-luciferase reporter genes. Our further studies showed that C-JNK fragment could form complex with p53 both in vivo and in vitro. Induction of C-JNK fragment in vivo can increase p53 stability by inhibiting p53 ubiquitination.     

Superior feature-set ranking for small samples using bolstered error estimation

MOTIVATION: Ranking feature sets is a key issue for classification, for instance, phenotype classification based on gene expression. Since ranking is often based on error estimation, and error estimators suffer to differing degrees of imprecision in small-sample settings, it is important to choose a computationally feasible error estimator that yields good feature-set ranking. RESULTS: This paper examines the feature-ranking performance of several kinds of error estimators: resubstitution, cross-validation, bootstrap and bolstered error estimation. It does so for three classification rules: linear discriminant analysis, three-nearest-neighbor classification and classification trees. Two measures of performance are considered. One counts the number of the truly best feature sets appearing among the best feature sets discovered by the error estimator and the other computes the mean absolute error between the top ranks of the truly best feature sets and their ranks as given by the error estimator. Our results indicate that bolstering is superior to bootstrap, and bootstrap is better than cross-validation, for discovering top-performing feature sets for classification when using small samples. A key issue is that bolstered error estimation is tens of times faster than bootstrap, and faster than cross-validation, and is therefore feasible for feature-set ranking when the number of feature sets is extremely large.