Calculation of binding isotherms for heterogenous polymers

The matrix method of statistical mechanics is used to calculate equilibria for the binding of small molecules to polymers. When there is only one kind of binding site the problem is simple; some examples are given for illustrative purposes. If, however, the binding sites are not all equivalent and the bound molecules interact or interfere with each other, the problem is no longer trivial, being formally analogous with calculation of the helix–coil transition equilibrium in a heterogeneous polypeptide. Particular difficulties arise when the sequence of binding sites is aperiodic; most naturally occurring materials fall in this class. The purpose of this paper is to point out that problems of this type are readily solved with good accuracy by use of random-number methods on a high-speed digital computer. One such calculation is presented for illustration. The methods developed are applicable to such systems as the binding of actinomycin, Hg^–, and acridine dyes to DNA.     

Interacting selection diversifies warning signals in a polytypic frog: an examination with the strawberry poison frog

Aposematic signals represent one of the most accessible traits to evaluate the interaction of natural and sexual selection on signal evolution. Here we investigate the contributions of these two selective forces on the aposematic signal evolution of the highly polytypic strawberry poison frog, Oophaga pumilio, of Bocas del Toro, Panama. Previous research has shown that the brightness of O. pumilio warning coloration can inform predators of the toxicity levels associated with different populations of the archipelago. Other studies suggest that sexual selection may be influencing warning signal brightness within populations via female mate choice (Isla Solarte, Isla Bastimentos, and Aquacate Peninsula populations) and male–male competition (Isla Solarte). Here we present two non-exclusive scenarios for how natural and sexual selection interact to drive phenotypic variation across this archipelago: (1) predators impose a selective regime whereby populations above a toxicity-brightness threshold are at liberty to diversify via sexual selection and below which populations are constrained to maintain a stricter resemblance to a more cryptic population mean, and (2) synergistic/additive effects of inter- and intrasexual selection drive the evolution of brighter males within populations above this toxicity threshold. We investigate whether aposematic patterns of divergence across the archipelago relative to the common mainland phenotype meet these predictions using existing data on O. pumilio morph toxicity measures and overall conspicuousness estimates to an avian predator. Using standardized z-scores to evaluate the range of trait values, we find that indeed the population representative of the common mainland phenotype (Almirante) represents an intermediate level of both toxicity and conspicuousness, and that derived Bocas del Toro populations vary in each of those components in directions predicted by the proposed scenarios. Furthermore, we find greater divergence towards conspicuousness than crypsis, a pattern suggestive of sexual and natural selection acting synergistically in morphs with high toxicity.     

Light Absorption and Recycling in Hybrid Metal Halide Perovskite Photovoltaic Devices

The production of highly efficient single‐ and multijunction metal halide perovskite (MHP) solar cells requires careful optimization of the optical and electrical properties of these devices. Here, precise control of CH₃NH₃PbI₃ perovskite layers is demonstrated in solar cell devices through the use of dual source coevaporation. Light absorption and device performance are tracked for incorporated MHP films ranging from ≈67 nm to ≈1.4 µm thickness and transfer‐matrix optical modeling is utilized to quantify optical losses that arise from interference effects. Based on these results, a device with 19.2% steady‐state power conversion efficiency is achieved through incorporation of a perovskite film with near‐optimum predicted thickness (≈709 nm). Significantly, a clear signature of photon reabsorption is observed in perovskite films that have the same thickness (≈709 nm) as in the optimized device. Despite the positive effect of photon recycling associated with photon reabsorption, devices with thicker (>750 nm) MHP layers exhibit poor performance owing to competing nonradiative charge recombination in a “dead‐volume” of MHP. Overall, these findings demonstrate the need for fine control over MHP thickness to achieve the highest efficiency cells, and accurate consideration of photon reabsorption, optical interference, and charge transport properties.     

tigaR: integrative significance analysis of temporal differential gene expression induced by genomic abnormalities

Background

To determine which changes in the host cell genome are crucial for cervical carcinogenesis, a longitudinal in vitro model system of HPV-transformed keratinocytes was profiled in a genome-wide manner. Four cell lines affected with either HPV16 or HPV18 were assayed at 8 sequential time points for gene expression (mRNA) and gene copy number (DNA) using high-resolution microarrays. Available methods for temporal differential expression analysis are not designed for integrative genomic studies.

Results

Here, we present a method that allows for the identification of differential gene expression associated with DNA copy number changes over time. The temporal variation in gene expression is described by a generalized linear mixed model employing low-rank thin-plate splines. Model parameters are estimated with an empirical Bayes procedure, which exploits integrated nested Laplace approximation for fast computation. Iteratively, posteriors of hyperparameters and model parameters are estimated. The empirical Bayes procedure shrinks multiple dispersion-related parameters. Shrinkage leads to more stable estimates of the model parameters, better control of false positives and improvement of reproducibility. In addition, to make estimates of the DNA copy number more stable, model parameters are also estimated in a multivariate way using triplets of features, imposing a spatial prior for the copy number effect.

Conclusion

With the proposed method for analysis of time-course multilevel molecular data, more profound insight may be gained through the identification of temporal differential expression induced by DNA copy number abnormalities. In particular, in the analysis of an integrative oncogenomics study with a time-course set-up our method finds genes previously reported to be involved in cervical carcinogenesis. Furthermore, the proposed method yields improvements in sensitivity, specificity and reproducibility compared to existing methods. Finally, the proposed method is able to handle count (RNAseq) data from time course experiments as is shown on a real data set.

Electronic supplementary material

The online version of this article (doi:10.1186/1471-2105-15-327) contains supplementary material, which is available to authorized users.