The first potassium channel toxin from the venom of the Iranian scorpion Odonthobuthus doriae

The very first member of K(+) channels toxins from the venom of the Iranian scorpion Odonthobuthus doriae (OdK1) was purified, sequenced and characterized physiologically. OdK1 has 29 amino acids, six conserved cysteines and a pI value of 4.95. Based on multiple sequence alignments, OdK1 was classified as alpha-KTx 8.5. The pharmacological effects of OdK1 were studied on six different cloned K(+) channels (vertebrate Kv1.1-Kv1.5 and Shaker IR) expressed in Xenopus laevis oocytes. Interestingly, OdK1 selectively inhibited the currents through Kv1.2 channels with an IC50 value of 183+/-3 nM but did not affect any of the other channels.     

The two-sample problem with induced dependent censorship

Induced dependent censorship is a general phenomenon in health service evaluation studies in which a measure such as quality-adjusted survival time or lifetime medical cost is of interest. We investigate the two-sample problem and propose two classes of nonparametric tests. Based on consistent estimation of the survival function for each sample, the two classes of test statistics examine the cumulative weighted difference in hazard functions and in survival functions. We derive a unified asymptotic null distribution theory and inference procedure. The tests are applied to trial V of the International Breast Cancer Study Group and show that long duration chemotherapy significantly improves time without symptoms of disease and toxicity of treatment as compared with the short duration treatment. Simulation studies demonstrate that the proposed tests, with a wide range of weight choices, perform well under moderate sample sizes.     

Synthesis of novel steroidal agonists,partial agonists,and antagonists for the glucocorticoid receptor

Adverse effects of glucocorticoids could be limited by developing new compounds that selectively modulate anti-inflammatory activity of the glucocorticoid receptor (GR). We have synthesized a novel series of steroidal GR ligands, including potent agonists, partial agonists and antagonists with a wide range of effects on inhibiting secretion of interleukin-6. Some of these new ligands were designed to directly impact conformational stability of helix-12, in the GR ligand-binding domain (LBD). These compounds modulated GR activity and glucocorticoid-induced gene expression in a manner that was inversely correlated to the degree of inflammatory response. In contrast, compounds designed to directly modulate LBD epitopes outside helix-12, led to dissociated levels of GR-mediated gene expression and inflammatory response. Therefore, these new series of compounds and their derivatives will be useful to dissect the ligand-dependent features of GR signaling specificity.     

Survival analysis in clinical trials: past developments and future directions

The field of survival analysis emerged in the 20th century and experienced tremendous growth during the latter half of the century. The developments in this field that have had the most profound impact on clinical trials are the Kaplan-Meier (1958, Journal of the American Statistical Association 53, 457-481) method for estimating the survival function, the log-rank statistic (Mantel, 1966, Cancer Chemotherapy Report 50, 163-170) for comparing two survival distributions, and the Cox (1972, Journal of the Royal Statistical Society, Series B 34, 187-220) proportional hazards model for quantifying the effects of covariates on the survival time. The counting-process martingale theory pioneered by Aalen (1975, Statistical inference for a family of counting processes, Ph.D. dissertation, University of California, Berkeley) provides a unified framework for studying the small- and large-sample properties of survival analysis statistics. Significant progress has been achieved and further developments are expected in many other areas, including the accelerated failure time model, multivariate failure time data, interval-censored data, dependent censoring, dynamic treatment regimes and causal inference, joint modeling of failure time and longitudinal data, and Baysian methods.     

Contributions of water transfer energy to protein‐ligand association and dissociation barriers: Watermap analysis of a series of p38α MAP kinase inhibitors

In our previous work, we proposed that desolvation and resolvation of the binding sites of proteins can serve as the slowest steps during ligand association and dissociation, respectively, and tested this hypothesis on two protein‐ligand systems with known binding kinetics behavior. In the present work, we test this hypothesis on another kinetically‐determined protein‐ligand system—that of p38α and eight Type II BIRB 796 inhibitor analogs. The k_on values among the inhibitor analogs are narrowly distributed (10⁴ ≤ k_on ≤ 10⁵ M^?1 s^?1), suggesting a common rate‐determining step, whereas the k_off values are widely distributed (10^?1 ≤ k_off ≤ 10^?6 s^?1), suggesting a spectrum of rate‐determining steps. We calculated the solvation properties of the DFG‐out protein conformation using an explicit solvent molecular dynamics simulation and thermodynamic analysis method implemented in WaterMap to predict the enthalpic and entropic costs of water transfer to and from bulk solvent incurred upon association and dissociation of each inhibitor. The results suggest that the rate‐determining step for association consists of the transfer of a common set of enthalpically favorable solvating water molecules from the binding site to bulk solvent. The rate‐determining step for inhibitor dissociation consists of the transfer of water from bulk solvent to specific binding site positions that are unfavorably solvated in the apo protein, and evacuated during ligand association. Different sets of unfavorable solvation are evacuated by each ligand, and the observed dissociation barriers are qualitatively consistent with the calculated solvation free energies of those sets.     

The Role of the N-Terminus of the Myosin Essential Light Chain in Cardiac Muscle Contraction

To study the regulation of cardiac muscle contraction by the myosin essential light chain (ELC) and the physiological significance of its N-terminal extension, we generated transgenic (Tg) mice by partially replacing the endogenous mouse ventricular ELC with either the human ventricular ELC wild type (Tg-WT) or its 43-amino-acid N-terminal truncation mutant (Tg-Δ43) in the murine hearts. The mutant protein is similar in sequence to the short ELC variant present in skeletal muscle, and the ELC protein distribution in Tg-Δ43 ventricles resembles that of fast skeletal muscle. Cardiac muscle preparations from Tg-Δ43 mice demonstrate reduced force per cross-sectional area of muscle, which is likely caused by a reduced number of force-generating myosin cross-bridges and/or by decreased force per cross-bridge. As the mice grow older, the contractile force per cross-sectional area further decreases in Tg-Δ43 mice and the mutant hearts develop a phenotype of nonpathologic hypertrophy while still maintaining normal cardiac performance. The myocardium of older Tg-Δ43 mice also exhibits reduced myosin content. Our results suggest that the role of the N-terminal ELC extension is to maintain the integrity of myosin and to modulate force generation by decreasing myosin neck region compliance and promoting strong cross-bridge formation and/or by enhancing myosin attachment to actin.     

Estimating regression parameters and degree of dependence for multivariate failure time data

Multivariate failure time data are frequently encountered in longitudinal studies when subjects may experience several events or when there is a grouping of individuals into a cluster. To take into account the dependence of the failure times within the unit (the individual or the cluster) as well as censoring, two multivariate generalizations of the Cox proportional hazards model are commonly used. The marginal hazard model is used when the purpose is to estimate mean regression parameters, while the frailty model is retained when the purpose is to assess the degree of dependence within the unit. We propose a new approach based on the combination of the two aforementioned models to estimate both these quantities. This two-step estimation procedure is quicker and more simple to implement than the EM algorithm used in frailty models estimation. Simulation results are provided to illustrate robustness, consistency, and large-sample properties of estimators. Finally, this method is exemplified on a diabetic retinopathy study in order to assess the effect of photocoagulation in delaying the onset of blindness as well as the dependence between the two eyes blindness times of a patient.     

Trypanosoma vivax: Courses of infection with three stabilates in inbred mouse strains

The courses of infection in inbred mouse strains were compared following infection with three Stabilates of high, intermediate, and low virulence of Trypanosoma vivax stock Zaria Y486. Mouse strains could only be shown to differ in their resistance to T. vivax infections as judged by the height of the initial parasitemia and survival times when a trypanosome population of low or intermediate virulence was used. A T. vivax population of high virulence was uniformly lethal. Comparison of lytic antibody titers between groups of resistant ($\text{C}\text{57}\text{B}\text{1}\text{6}$) and susceptible ($\text{Balb}\text{c}$) mice did not show any significant differences in titers of the surviving mice but the mice in either group which did not control the initial parasitemia had lower lytic antibody titers than those which did. A significantly larger number of $\text{Balb}\text{c}$ mice failed to control the initial infection as compared to the $\text{C}\text{57}\text{B}\text{1}\text{6}$. Treatment with cyclophosphamide did not ablate differences in susceptibility between the two strains. The use of congenic mice showed that these differences in susceptibility were not related to differences in the major histocompatibility complex between these strains.     

Trace metal bioavailability in municipal solid waste and sewage sludge composts

A sequential extraction procedure was employed to determine the soil fractions, and assess plant availability of Cr, Cu, Ni, Pb and Zn in a Glynwood silt loam amended with five rates (0, 30, 60, 120 and 240 metric tons/ha) of composted municipal solid waste (CMSW) or composted sewage sludge (CSS) cropped to oats (Avena sativa). The application of the composts tended to shift the solid phase forms of the metals away from those extractable with HNO₃ to those extractable with NaOH and EDTA. The more labile fractions (KNO₃ and H₂O extracts) of the metals typically decreased with application of CMSW and CSS. Crop dry matter increased at the 30 and 60 MT/ha CMSW rates by 142 and 152%, respectively, after which yields declined to below control values. Yields at all rates of CSS declined. The CMSW and CSS had an insignificant effect on concentrations of Cr and Pb in oat tissue, but tissue levels of Cu, Ni and Zn increased with increased rate of compost application.     

Phylogeny and speciation of the eastern Asian cyprinid genus Sarcocheilichthys

The genus Sarcocheilichthys is a group of small cyprinid fishes comprising 10 species/sub‐species widely distributed in East Asia, which represents a valuable model for understanding the speciation of freshwater fishes in East Asia. In the present study, the molecular phylogenetic relationship of the genus Sarcocheilichthys was investigated using a 1140 bp section of the mitochondrial cytochrome b gene. Two different tree‐building methods, maximum parsimony (MP) and Bayesian methods, yielded trees with almost the same topology, yielding high bootstrap values or posterior probabilities. The results showed that the genus Sarcocheilichthys consists of two large clades, clades I and II. Clade I contains Sarcocheilichthys lacustris, Sarcocheilichthys sinensis and Sarcocheilichthys parvus, with S. parvus at a basal position. In clade II, Sarcocheilichthys variegatus microoculus is at a basal position; samples of the widespread species, Sarcocheilichthys nigripinnis, form a large subclade containing another valid species Sarcocheilichthys czerskii. Sarcocheilichthys kiangsiensis is retained at an intermediate position. Since S. czerskii is a valid species in the S. nigripinnis clade, remaining samples of S. nigripinnis form a paraphyly. This speciation process is attributed to geographical isolation and special environmental conditions experienced by S. czerskii and stable environments experienced by the other S. nigripinnis populations. This type of speciation process was suggested to be very common. Samples of Sarcocheilichthys sinensis sinensis and Sarcocheilichthys sinensis fukiensis that did not form their own monophyletic groups suggest an early stage of speciation and support their sub‐species status. Molecular clock analysis indicates that the two major lineages of the genus Sarcocheilichthys, clades I and II diverged c. 8·89 million years ago (mya). Sarcocheilichthys v. microoculus from Japan probably diverged 4·78 mya from the Chinese group. The northern–southern clades of S. nigripinnis began to diverge c. 2·12 mya, while one lineage of S. nigripinnis evolved into a new species, S. czerski, c. 0·34 mya.