Kinetic analysis of the coding properties of O6-methylguanine in DNA: the crucial role of the conformation of the phosphodiester bond

Production by N-nitroso compounds of O6-alkylguanine (O6-alkylG) in DNA directs the misincorporation of thymine during DNA replication, leading to G:C to A:T transition mutations, despite the fact that DNA containing O6-alkylG:T base pairs is less stable than that containing O6-alkylG:C pairs. We have examined the kinetics of incorporation by Klenow fragment (KF) of Escherichia coli DNA polymerase I of thymine (T) and of cytosine (C) opposite O6-MeG in the template DNA strand. Both T and C were incorporated opposite O6-MeG much slower than nucleotides forming regular A:T or G:C base pairs. Using various concentrations of dTTP, dCTP, or their phosphorothioate (Sp)-dNTP alpha S analogues, or a mixture of dTTP and dCTP, the progress of incorporation of a single nucleotide in a single catalytic cycle of a preformed KF-DNA complex was measured (pre-steady-state kinetics). The results were consistent with the kinetic scheme (Kuchta, R. D., Benkovic, P., & Benkovic, S. J. (1988) Biochemistry 27, 6716-6725): (1) binding of dNTP to polymerase-DNA; (2) conformational change in polymerase; (3) formation of phosphodiester between the dNTP and the 3'-OH of the primer; (4) conformational change of polymerase; (5) release of pyrophosphate. The results were analyzed mathematically to identify the steps at which the rate constants differ significantly between the incorporation of T and C. The only significant difference was the 5-fold difference in the rates of formation of the phosphodiester bond (for dTTP, kforward = 3.9 s-1 and kback = 1.9 s-1; for dCTP, kforward = 0.7 s-1 and kback = 0.9 s-1). These pre-steady-state progress curves were biphasic with a rapid initial burst followed by an apparently steady-state rise. Deconvolution of these curves gave direct evidence for the importance of the conformational change after polymerization by showing that the curves represented the sum of the rapid accumulation of the product of step 3 followed by the slow conversion of that to the product of step 5 (because of the rapidity of the release of pyrophosphate there was no significant accumulation of the product of step 4). The equilibrium constants for each step suggest that the greatest change in the Gibbs free energy occurs at the conformational change after polymerization and that while the formation of the phosphodiester bond to T is slightly exothermic, that to C is slightly endothermic.(ABSTRACT TRUNCATED AT 400 WORDS)     

Differentiating anxiety and depression in older adults with generalized anxiety disorder.

To examine affect and cognition in differentiating anxiety and depression, 83 older participants with generalized anxiety disorder completed the Cognitive Checklist (CCL) and the Positive and Negative Affect Schedule (PANAS). A 3-factor solution was found for the PANAS: positive affect (PA), anxiety and anger (Negative Affect 1 [NA-1]), and guilt and shame (Negative Affect 2 [NA-2]). A 2-factor structure was noted for the CCL. Correlations with anxiety and depression measures suggested that the CCL Depression (CCL-D) subscale showed stronger correlations with depression, whereas the CCL Anxiety subscale did not uniquely correlate with anxiety. The NA-1 subscale correlated positively with measures of depression and anxiety, whereas the PA subscale showed negative correlations. Hierarchical regression suggested that the CCL-D subscale was a significant predictor of self-reported depression. (PsycINFO Database Record (c) 2010 APA, all rights reserved)     

The Estimation of Restrainers

A quantitative method is described for the chromatographic separation and subsequent polarographic estimation of adenine in gelatin. The method, which has been applied to about 200 gelatins, has two important features. It is specific for adenine and enables a visual assessment of other purines and pyrimidines to be mode in the course of the procedure.

Hide gelatins have adenine contents from 10 200 ppm., but the large majority are from SO 50 ppm., ossein gelatin contains from 4–6 ppm., and pigskin between 30 and 50 ppm.     

l-Cystathionine Inhibits the Mitochondria-Mediated Macrophage Apoptosis Induced by Oxidized Low Density Lipoprotein

This study was designed to investigate the regulatory role of l-cystathionine in human macrophage apoptosis induced by oxidized low density lipoprotein (ox-LDL) and its possible mechanisms. THP-1 cells were induced with phorbol 12-myristate 13-acetate (PMA) and differentiated into macrophages. Macrophages were incubated with ox-LDL after pretreatment with l-cystathionine. Superoxide anion, apoptosis, mitochondrial membrane potential, and mitochondrial permeability transition pore (MPTP) opening were examined. Caspase-9 activities and expression of cleaved caspase-3 were measured. The results showed that compared with control group, ox-LDL treatment significantly promoted superoxide anion generation, release of cytochrome c (cytc) from mitochondrion into cytoplasm, caspase-9 activities, cleavage of caspase-3, and cell apoptosis, in addition to reduced mitochondrial membrane potential as well as increased MPTP opening. However, 0.3 and 1.0 mmol/L l-cystathionine significantly reduced superoxide anion generation, increased mitochondrial membrane potential, and markedly decreased MPTP opening in ox-LDL + l-cystathionine macrophages. Moreover, compared to ox-LDL treated-cells, release of cytc from mitochondrion into cytoplasm, caspase-9 activities, cleavage of caspase-3, and apoptosis levels in l-cystathionine pretreated cells were profoundly attenuated. Taken together, our results suggested that l-cystathionine could antagonize mitochondria-mediated human macrophage apoptosis induced by ox-LDL via inhibition of cytc release and caspase activation.     

The impact of family and community violence on children’s depression trajectories: Examining the interactions of violence exposure, family social support, and gender.

This longitudinal study used multilevel modeling to examine the relationships between witnessing intimate partner violence (IPV), community and school violence exposure (CSVE), family social support, gender, and depression over 2 years within a sample of 100 school-aged children. We found significant between-child differences in both the initial levels of depression and the trajectories of depression; depression over time was positively associated with change in witnessing IPV and CSVE and negatively associated with change in support. Two significant 3-way interactions were found: Gender and initial support, as well as gender and initial witnessing IPV, both significantly moderated the effect of change in witnessing IPV on the children’s depression over time. (PsycINFO Database Record (c) 2010 APA, all rights reserved)     

Sperm phospholipase Czeta from humans and cynomolgus monkeys triggers Ca2+ oscillations,activation and development of mouse oocytes

Fusion with a fertilizing spermatozoon induces the mammalian oocyte to undergo a remarkable series of oscillations in cytosolic Ca(2+), leading to oocyte activation and development of the embryo. The exact molecular mechanism for generating Ca(2+) oscillations has not been established. A sperm-specific zeta isoform of phospholipase C (PLCzeta) has been identified in mice. Mouse PLCzeta triggers Ca(2+) oscillations in mouse oocytes and exhibits properties synonymous with the 'sperm factor' that has been proposed to diffuse into the oocyte after gamete fusion. The present study isolated the PLCzeta homologue from human and cynomolgus monkey testes. Comparison with mouse and monkey PLCzeta protein sequences indicates a shorter X-Y linker region in human PLCzeta and predicts a distinctly different isoelectric point. Microinjection of complementary RNA for both human and cynomolgus monkey PLCzeta elicits Ca(2+) oscillations in mouse oocytes equivalent to those seen during fertilization in mice. Moreover, human PLCzeta elicits mouse egg activation and early embryonic development up to the blastocyst stage, and exhibits greater potency than PLCzeta from monkeys and mice. These results are consistent with the proposal that sperm PLCzeta is the molecular trigger for egg activation during fertilization and that the role and activity of PLCzeta is highly conserved across mammalian species.     

Maximum Likelihood Estimation Using Parallel Computing: An Introduction to MPI

The computational difficulty of econometric problems has increased dramatically in recent years as econometricians examine more complicated models and utilize more sophisticated estimation techniques. Many problems in econometrics are `embarrassingly parallel' and can take advantage of parallel computing to reduce the wall clock time it takes to solve a problem. In this paper I demonstrate a method that can be used to solve a maximum likelihood problem using the MPI message passing library. The econometric problem is a simple multinomial logit model that does not require parallel computing but illustrates many of the problems one would confront when estimating more complicated models.     

Sedimentary records of sewage pollution using faecal markers in contrasting peri-urban shallow lakes

Sewage contamination in shallow lake sediments is of concern because the pathogens, organic matter and nutrients contribute to the deterioration of the water-bodies' health and ecology. Sediment cores from three shallow lakes (Coneries, Church and Clifton Ponds) within Attenborough nature reserve located downstream of sewage treatment works were analysed for TOC, C/N, δ¹³C, δ¹⁵N, bacterial coliforms and faecal sterols. ²¹⁰Pb and ¹³⁷Cs activities were used to date the sediments. Elemental analysis suggests that the source of organic matter was algal and down profile changes in δ¹³C indicate a possible decrease in productivity with time which could be due to improvements in sewage treatment. δ¹⁵N for Coneries Pond are slightly higher than those observed in Church or Clifton and are consistent with a sewage-derived nitrate source which has been diluted by non-sewage sources of N. The similarity in δ¹⁵N values (+ 12‰ to + 10‰) indicates that the three ponds were not entirely hydrologically isolated. Analysis by gas chromatography/mass spectrometry (GC/MS) reveals that Coneries Pond had sterol concentrations in the range 20 to 30 μg/g (dry wt.), whereas, those from Clifton and Church Ponds were lower. The highest concentrations of the human-sourced sewage marker 5β-coprostanol were observed in the top 40 cm of Coneries Pond with values up to 2.2 μg/g. In contrast, Church and Clifton Pond sediments contain only trace amounts throughout. Down-profile comparison of 5β-coprostanol/cholesterol, 5β-coprostanol/(5β-coprostanol + 5α-cholestanol) and 5β-epicoprostanol/coprostanol as well as 5α-cholestanol/cholesterol suggests that Coneries Pond has received appreciable amounts of faecal contamination. Examination of 5β-stigmastanol (marker for herbivorous/ruminant animals) down core concentrations suggests a recent decrease in manure slurry input to Coneries Pond. The greater concentration of β-sitosterol in sediments from Church and Clifton Ponds as compared to Coneries is attributed in part to their greater diversity and extent of aquatic plants and avian faeces.     

Contributions of sibling relations to the adaptation of youths with insulin-dependent diabetes mellitus.

Associations among sibling relations and the psychosocial and illness-specific adaptation of youths (N?=?66) with insulin-dependent diabetes mellitus (IDDM) were examined. The findings suggest that sibling relations, especially sibling conflict, contribute an independent source of variance above and beyond that contributed by demographic characteristics, sibling constellation variables, and important dimensions of family relations in predicting the youths' adaptation. High family-life stress and high sibling status/power contributed unique variance in predicting internalizing behaviors, and male gender and sibling conflict contributed independently to externalizing problems. Sibling conflict also contributed unique variance to the youths' general self-esteem, along with social class and family cohesion, and to their adjustment to IDDM. Data suggest that parent–child dyads and sibling dyads represent interrelated and independent subsystems within the family, and that both subsystems may influence the psychosocial functioning of youths with IDDM. (PsycINFO Database Record (c) 2010 APA, all rights reserved)