Posterior Association Networks and Functional Modules Inferred from Rich Phenotypes of Gene Perturbations

Combinatorial gene perturbations provide rich information for a systematic exploration of genetic interactions. Despite successful applications to bacteria and yeast, the scalability of this approach remains a major challenge for higher organisms such as humans. Here, we report a novel experimental and computational framework to efficiently address this challenge by limiting the ‘search space’ for important genetic interactions. We propose to integrate rich phenotypes of multiple single gene perturbations to robustly predict functional modules, which can subsequently be subjected to further experimental investigations such as combinatorial gene silencing. We present posterior association networks (PANs) to predict functional interactions between genes estimated using a Bayesian mixture modelling approach. The major advantage of this approach over conventional hypothesis tests is that prior knowledge can be incorporated to enhance predictive power. We demonstrate in a simulation study and on biological data, that integrating complementary information greatly improves prediction accuracy. To search for significant modules, we perform hierarchical clustering with multiscale bootstrap resampling. We demonstrate the power of the proposed methodologies in applications to Ewing's sarcoma and human adult stem cells using publicly available and custom generated data, respectively. In the former application, we identify a gene module including many confirmed and highly promising therapeutic targets. Genes in the module are also significantly overrepresented in signalling pathways that are known to be critical for proliferation of Ewing's sarcoma cells. In the latter application, we predict a functional network of chromatin factors controlling epidermal stem cell fate. Further examinations using ChIP-seq, ChIP-qPCR and RT-qPCR reveal that the basis of their genetic interactions may arise from transcriptional cross regulation. A Bioconductor package implementing PAN is freely available online at http://bioconductor.org/packages/release/bioc/html/PANR.html

Organic nanofibers embedding stimuli-responsive threaded molecular components

While most of the studies on molecular machines have been performed in solution, interfacing these supramolecular systems with solid-state nanostructures and materials is very important in view of their utilization in sensing components working by chemical and photonic actuation. Host polymeric materials, and particularly polymer nanofibers, enable the manipulation of the functional molecules constituting molecular machines, and provide a way to induce and control the supramolecular organization. Here, we present electrospun nanocomposites embedding a self-assembling rotaxane-type system that is responsive to both optical (UV-visible light) and chemical (acid/base) stimuli. The system includes a molecular axle comprised of a dibenzylammonium recognition site and two azobenzene end groups, and a dibenzo[24]crown-8 molecular ring. The dethreading and rethreading of the molecular components in nanofibers induced by exposure to base and acid vapors, as well as the photoisomerization of the azobenzene end groups, occur in a similar manner to what observed in solution. Importantly, however, the nanoscale mechanical function following external chemical stimuli induces a measurable variation of the macroscopic mechanical properties of nanofibers aligned in arrays, whose Young's modulus is significantly enhanced upon dethreading of the axles from the rings. These composite nanosystems show therefore great potential for application in chemical sensors, photonic actuators and environmentally responsive materials.Comment: 39 pages, 16 figure

Detection and Characterization of Wolbachia Infections in Natural Populations of Aphids: Is the Hidden Diversity Fully Unraveled?

Aphids are a serious threat to agriculture, despite being a rather small group of insects. The about 4,000 species worldwide engage in highly interesting and complex relationships with their microbial fauna. One of the key symbionts in arthropods is Wolbachia, an α-Proteobacterium implicated in many important biological processes and believed to be a potential tool for biological control. Aphids were thought not to harbour Wolbachia; however, current data suggest that its presence in aphids has been missed, probably due to the low titre of the infection and/or to the high divergence of the Wolbachia strains of aphids. The goal of the present study is to map the Wolbachia infection status of natural aphids populations, along with the characterization of the detected Wolbachia strains. Out of 425 samples from Spain, Portugal, Greece, Israel and Iran, 37 were found to be infected. Our results, based mainly on 16S rRNA gene sequencing, indicate the presence of two new Wolbachia supergroups prevailing in aphids, along with some strains belonging either to supergroup B or to supergroup A

Continuous Membrane Emulsification with Pulsed (Oscillatory) Flow

This document is the Accepted Manuscript version of a Published Work that appeared in final form in Industrial and Engineering Chemistry Research, copyright © American Chemical Society after peer review and technical editing by the publisher. To access the final edited and published work see: http://dx.doi.org/10.1021/ie3020457Tubular micrometer pore sized sieve type membranes with internal diameter of 14 mm and length of 60 mm containing uniform pores of diameter 10 and 20 μm were used to generate emulsions of sunflower oil dispersed in water and stabilized by Tween 20 using oscillatory flow of the continuous phase. Drop diameters between 30 and 300 μm could be produced, in a controllable way and with span values of down to 0.4. By using pulsed flow it was possible to provide dispersed phase concentrations of up to 45% v/v in a single pass over the membrane, that is, without the need to recirculate the continuous phase through the membrane tube. It was possible to correlate the drop size produced with the shear conditions at the membrane surface using the wave shear stress equation. The oscillatory Reynolds number indicated flow varying from laminar to substantially turbulent, but the change in flow conditions did not show a notable influence on the drop diameters produced, over what is predicted by the varying wall shear stress applied to the wave equation. However, the 20 μm pore sized sieve type membrane appeared to allow the passage of the pressure pulse through the membrane pores, under certain operating conditions, which did lead to finer drop sizes produced than would be predicted. These through-membrane pulsations could be suppressed by changes in operating conditions: a higher dispersed phase injection rate or more viscous continuous phase, and they did not occur under similar operating conditions used with the 10 μm pore sized sieve type of membrane. Generating emulsions of this size using pulsed continuous phase flow provides opportunities for combining drop generation at high dispersed phase concentration, by membrane emulsification, with downstream processing such as reaction in plug flow reactors