Role of Direct Interactions between the Histone H4 Tail and the H2A Core in Long Range Nucleosome Contacts

In eukaryotic nuclei the majority of genomic DNA is believed to exist in higher order chromatin structures. Nonetheless, the nature of direct, long range nucleosome interactions that contribute to these structures is poorly understood. To determine whether these interactions are directly mediated by contacts between the histone H4 amino-terminal tail and the acidic patch of the H2A/H2B interface, as previously demonstrated for short range nucleosomal interactions, we have characterized the extent and effect of disulfide cross-linking between residues in histones contained in different strands of nucleosomal arrays. We show that in 208-12 5 S rDNA and 601-177-12 nucleosomal array systems, direct interactions between histones H4-V21C and H2A-E64C can be captured. This interaction depends on the extent of initial cross-strand association but does not require these specific residues, because interactions with residues flanking H4-V21C can also be captured. Additionally, we find that trapping H2A-H4 intra-array interactions antagonizes the ability of these arrays to undergo intermolecular self-association.     

Semiparametric Bayesian Survival Analysis using Models with Log‐linear Median

Summary We present a novel semiparametric survival model with a log‐linear median regression function. As a useful alternative to existing semiparametric models, our large model class has many important practical advantages, including interpretation of the regression parameters via the median and the ability to address heteroscedasticity. We demonstrate that our modeling technique facilitates the ease of prior elicitation and computation for both parametric and semiparametric Bayesian analysis of survival data. We illustrate the advantages of our modeling, as well as model diagnostics, via a reanalysis of a small‐cell lung cancer study. Results of our simulation study provide further support for our model in practice.     

Oxygen uptake capacity of gills and skin in relation to body weight of the air-breathing siluroid fish, Clarias batrachus (Linn.).

Oxygen consumption through gills and skin in relation to body weight was estimated in the air-breathing catfish, Clarias batrachus, under two experimental conditions, viz., (i) when access to air was allowed and (ii) when air-breathing was prevented. There was a positive correlation between VO2 (ml/hr) and body weight in both experimental conditions. Oxygen consumption (ml/hr) increased by a power of 0.869 when access to air was allowed whereas the power was slightly less (b = 0.841) when air-breathing was prevented. As the values for exponent (b) were less than 1.0, the weight specific VO2 (ml/kg/hr) decreased with increasing body weight. The decrease was more marked (b = - 0.180) in fishes which were not allowed air than in those where access to air was allowed (b = - 0.148). Under normal conditions of water and air-breathing the rate of VO2 (ml/kg/hr) via gills and skin from water ranged from 39.7 +/- 3.21 to 76.7 +/- 9.01 and this increased to 42.17 +/- 6.2 to 105.9 +/- 8.33 when air-breathing was prevented. The increase in the rate of VO2 was perhaps associated with the increase in the volume of water irrigating the gills per unit time.     

Systematic revision and sexual dimorphism in Choffatia (Ammonoidea: Perisphinctoidea) from the Callovian of Kutch,India

The genus Choffatia (Siemiradzki) is an important Callovian ammonite in Kutch biostratigraphy. Several species of the genus were described by the early workers who did not recognize intraspecific variability and sexual dimorphism in terms of the modern concepts. We have described here three dimorphic species based on material reposited in the Geological Survey of India, Kolkata as well as systematically collected additional specimens with precise stratigraphic information. These species are: Choffatia recuperoi (Gemmellaro, 1873), Choffatia cobra (Waagen, 1875), and Choffatia perdagata (Waagen, 1875). The microconchs of the three species, described here for the first time, are lappeted whereas the macroconchs have a simple aperture. However, these species have similar shell morphologies and they intergrade in shell shape and sculpture; thus it is difficult to distinguish them qualitatively. Statistical analyses (both bivariate and multivariate) support that they are distinct species and there is a good correlation among the degree of involution, the degree of inflation, and the strength of ornamentation. C. cobra is the most evolute, depressed, and strongly ribbed whereas C. perdagata is the most involute, compressed, and weakly ribbed. C. recuperoi occupies the intermediate position. This interspecific diversity of Choffatia thus supports Buckman's Law of Covariation.     

Inhibition of factor Xa by a peptidyl-alpha-ketothiazole involves two steps. Evidence for a stabilizing conformational change.

Recently, peptidylketothiazoles have been shown to be potent inhibitors of proteases, but the details of the interaction have not yet been studied. In the work presented here, the interaction of factor Xa, a coagulation protease, with the transition state inhibitor BnSO(2)-D-Arg-Gly-Arg-ketothiazole (C921-78) is characterized. C921-78 is a tight and selective inhibitor of the coagulation protease factor Xa (K(d) = 14 pM). The hydrolytic activity of factor Xa was inhibited by C921-78 in a time-dependent manner. The rate-limiting step of the bimolecular combination of inhibitor and enzyme was competitive with the substrate. Conversely, the inhibitor could be displaced from the active site of the enzyme after exposure of the preformed complex to an excess of substrate or to the active site inhibitor dansyl-Glu-Gly-Arg-chloromethyl ketone (DEGR-CMK) in a slow reaction. The formation of the C921-78-factor Xa complex resulted in a 60% increase in the magnitude of the fluorescence emission spectrum. Rapid mixing of the enzyme and inhibitor produces a monophasic fluorescence increase, compatible with spectral transition in a single step. The rate constant for this reaction increased hyperbolically with the concentration of C921-78, but the amplitude remained constant. These results are consistent with the initial formation of an enzyme-inhibitor complex (EI), followed by a unimolecular conversion of EI to EI linked to a spectral transition. The rate constants of the isomerization provide an estimate of 300000-fold stabilization. Thus, the inhibition of factor Xa by C921-78 follows a mechanism similar to that described classically for slow tight binding inhibitors. However, the two steps of the reaction cannot be kinetically separated by the rapid equilibrium assumption, and therefore, the formation of EI is partially rate-limiting, too. The driving energy for the unusually fast isomerization step may result from the highly favorable interactions of the inhibitor in the primary binding site.     

Molecular Basis for the Selective Inhibition of Respiratory Syncytial Virus RNA Polymerase by 2'-Fluoro-4'-Chloromethyl-Cytidine Triphosphate

Respiratory syncytial virus (RSV) causes severe lower respiratory tract infections, yet no vaccines or effective therapeutics are available. ALS-8176 is a first-in-class nucleoside analog prodrug effective in RSV-infected adult volunteers, and currently under evaluation in hospitalized infants. Here, we report the mechanism of inhibition and selectivity of ALS-8176 and its parent ALS-8112. ALS-8176 inhibited RSV replication in non-human primates, while ALS-8112 inhibited all strains of RSV in vitro and was specific for paramyxoviruses and rhabdoviruses. The antiviral effect of ALS-8112 was mediated by the intracellular formation of its 5''-triphosphate metabolite (ALS-8112-TP) inhibiting the viral RNA polymerase. ALS-8112 selected for resistance-associated mutations within the region of the L gene of RSV encoding the RNA polymerase. In biochemical assays, ALS-8112-TP was efficiently recognized by the recombinant RSV polymerase complex, causing chain termination of RNA synthesis. ALS-8112-TP did not inhibit polymerases from host or viruses unrelated to RSV such as hepatitis C virus (HCV), whereas structurally related molecules displayed dual RSV/HCV inhibition. The combination of molecular modeling and enzymatic analysis showed that both the 2''F and the 4''ClCH₂ groups contributed to the selectivity of ALS-8112-TP. The lack of antiviral effect of ALS-8112-TP against HCV polymerase was caused by Asn291 that is well-conserved within positive-strand RNA viruses. This represents the first comparative study employing recombinant RSV and HCV polymerases to define the selectivity of clinically relevant nucleotide analogs. Understanding nucleotide selectivity towards distant viral RNA polymerases could not only be used to repurpose existing drugs against new viral infections, but also to design novel molecules.     

Optical Properties Simulation of Magneto-Plasmonic Alloys Nanostructures

Plasmonics - The optical properties of magneto-plasmonic nanostructures are a current subject of research with fast-growing experimental and theoretical activities. The coexistence of iron (Fe) and...     

Lidocaine patch (5%) is no more potent than placebo in treating chronic back pain when tested in a randomised double blind placebo controlled brain imaging study

ABSTRACT: The 5% Lidocaine patch is used for treating chronic neuropathic pain conditions such as chronic back pain (CBP), diabetic neuropathy and complex regional pain syndrome, but is effective in a variable proportion of patients. Our lab has reported that this treatment reduces CBP intensity and associated brain activations when tested in an open labelled preliminary study. Notably, effectiveness of the 5% Lidocaine patch has not been tested against placebo for treating CBP. In this study, effectiveness of the 5% Lidocaine patch was compared with placebo in 30 CBP patients in a randomised double-blind study where 15 patients received 5% Lidocaine patches and the remaining patients received placebo patches. Functional MRI was used to identify brain activity for fluctuations of spontaneous pain, at baseline and at two time points after start of treatment (6 hours and 2 weeks). There was no significant difference between the treatment groups in either pain intensity, sensory and affective qualities of pain or in pain related brain activation at any time point. However, 50% patients in both the Lidocaine and placebo arms reported a greater than 50% decrease in pain suggesting a marked placebo effect. When tested against an untreated CBP group at similar time points, the patch treated subjects showed significantly greater decrease in pain compared to the untreated group (n=15). These findings suggest that although the 5% Lidocaine is not better than placebo in its effectiveness for treating pain, the patch itself induces a potent placebo effect in a significant proportion of CBP patients.     

Replication of Drosophila chromosomes. IX. Stimulation of initiation of polytene replication cycles in vitro by juvenile hormone

A greater proportion of polytene nuclei show [3H]thymidine incorporation when third instar larval salivary glands of Drosophila nasuta are pulse-labelled after in vitro culture (3-24 h) in the presence of a juvenile hormone mimic, ZR 515. In glands chronically labelled with [3H]thymidine in the presence of ZR 515, more nuclei are seen to have entered new polytene replication cycles. Similarly, when salivary glands from larvae fed on 5-fluorodeoxyuridine to block polytene replication cycles at intersynthetic periods were cultured in vitro, new polytene replication cycles were initiated more quickly in the presence of ZR 515. These results suggest a stimulatory effect of juvenile hormone on new polytene replication cycles.