Escherichia coli genome-wide promoter analysis: Identification of additional AtoC binding target elements

<p>Abstract</p> <p>Background</p> <p>Studies on bacterial signal transduction systems have revealed complex networks of functional interactions, where the response regulators play a pivotal role. The AtoSC system of <it>E. coli </it>activates the expression of <it>atoDAEB </it>operon genes, and the subsequent catabolism of short-chain fatty acids, upon acetoacetate induction. Transcriptome and phenotypic analyses suggested that <it>atoSC </it>is also involved in several other cellular activities, although we have recently reported a palindromic repeat within the <it>atoDAEB </it>promoter as the single, <it>cis</it>-regulatory binding site of the AtoC response regulator. In this work, we used a computational approach to explore the presence of yet unidentified AtoC binding sites within other parts of the <it>E. coli </it>genome.</p> <p>Results</p> <p>Through the implementation of a computational <it>de novo </it>motif detection workflow, a set of candidate motifs was generated, representing putative AtoC binding targets within the <it>E. coli </it>genome. In order to assess the biological relevance of the motifs and to select for experimental validation of those sequences related robustly with distinct cellular functions, we implemented a novel approach that applies Gene Ontology Term Analysis to the motif hits and selected those that were qualified through this procedure. The computational results were validated using Chromatin Immunoprecipitation assays to assess the <it>in vivo </it>binding of AtoC to the predicted sites. This process verified twenty-two additional AtoC binding sites, located not only within intergenic regions, but also within gene-encoding sequences.</p> <p>Conclusions</p> <p>This study, by tracing a number of putative AtoC binding sites, has indicated an AtoC-related cross-regulatory function. This highlights the significance of computational genome-wide approaches in elucidating complex patterns of bacterial cell regulation.</p

Photocatalytic splitting of water.

The use of photocatalysis for the photosplitting of water to generate hydrogen and oxygen has gained interest as a method for the conversion and storage of solar energy. The application of photocatalysis through catalyst engineering, mechanistic studies and photoreactor development has highlighted the potential of this technology, with the number of publications significantly increasing in the past few decades. In 1972 Fujishima and Honda described a photoelectrochemical system capable of generating H2 and O2 using thin-film TiO2. Since this publication, a diverse range of catalysts and platforms have been deployed, along with a varying range of photoreactors coupled with photoelectrochemical and photovoltaic technology. This chapter aims to provide a comprehensive overview of photocatalytic technology applied to overall H2O splitting. An insight into the electronic and geometric structure of catalysts is given based upon the one- and two-step photocatalyst systems. One-step photocatalysts are discussed based upon their d0 and d10 electron configuration and core metal ion including transition metal oxides, typical metal oxides and metal nitrides. The two-step approach, referred to as the Z-scheme, is discussed as an alternative approach to the traditional one-step mechanism, and the potential of the system to utilise visible and solar irradiation. In addition to this the mechanistic procedure of H2O splitting is reviewed to provide the reader with a detailed understanding of the process. Finally, the development of photoreactors and reactor properties are discussed with a view towards the photoelectrochemical splitting of H2O

Hydrogen storage and thermal transport properties of pelletized porous Mg-2 wt.% multiwall carbon nanotubes and Mg-2 wt.% graphite composites

We synthesized pelletized porous composites of Mg admixed with 2 wt.% of either multiwall carbon nanotubes or graphite. The composites were prepared by high energy ball-milling of Mg powder with carbonaceous additives, followed by uniaxial compression and sintering in hydrogen environment under mechanical constraint. The correlations between ball-milling conditions, composite microstructure, hydrogenation kinetics, and thermal conductivity of the pellets were established. The presence and condition of carbon additives controls the morphology of Mg particles and, consequently, the mechanical stability of the pellet upon hydrogenation cycling. The best combination of hydrogen desorption kinetics, thermal conductivity, and mechanical stability was obtained for the pellets synthesized from the mixture of Mg with 2 wt.% of carbon nanotubes processed by 4 h of co-milling. The milling transformed carbon nanotubes into carbon nano-particles/nano-onions. These carbonaceous species promote metal nucleation from the hydride phase and allow formation of Mg-Mg bonds between the Mg particles contributing to mechanical stability of the pellet

libFastMesh: An optimized finite-volume framework for computational aeroacoustics

This paper presents an optimized framework for simulating aeroacoustic flow on unstructured meshes. The libFastMesh (LFM) framework is based on a low-dissipation finite–volume discretization, together with high-order explicit time integration, for direct computation of aeroacoustic fields. These methods were previously implemented in caafoam, an OpenFOAM-based solver developed by D'Alessandro et al. [1] to resolve aeroacoustic flows. The new framework is specifically developed from scratch to alleviate two of the main bottlenecks currently limiting the performance of OpenFOAM-based solvers at large scale: memory bandwidth and inter-node communication. Compact data structures and compute kernel fusion are employed to enhance cache utilization and re-use, respectively. Separate treatment of inter-process boundary cells, together with non-blocking MPI communication enable effective overlap between communication and flux computations. The accuracy and robustness of libFastMesh are established via simulations of well-established aeroacoustic flow benchmarks. Comparison to previous simulation results obtained with caafoam, and to DNS data serve to validate the code. Finally, the effectiveness of the aforementioned optimizations is demonstrated through rigorous analysis of the proposed solver performance in single-node and multi-node operation modes. The obtained results show that libFastMesh offers a speed-up of up to 20x with respect to the previously developed OpenFOAM-based solver, caafoam, in large-scale computations. Moreover, LFM is shown to scale extremely for cell-per-core ratios of less than 500. These results are particularly appealing given the highly resource-demanding nature of direct computational aeroacoustics (CAA). Consequently, LFM could be an extremely attractive tool for scientists who wish to conduct large-scale CAA simulations on modern, exascale architectures. Program summary: Program Title: libFastMesh CPC Library link to program files: https://doi.org/10.17632/7w9fy2xtcf.1 Developer's repository link: https://github.com/TRC-HPC/LFM_Public Licensing provisions: GPLv3 Programming language: C++ Nature of problem: This software solves compressible Navier–Stokes equations. The adopted numerics and flow models allow to capture with high accuracy aerodinamically generated sound. The solver is also designed to take advantage of the massively parallel computing systems which are strictly required for facing real–life aeroacoustic problems. Solution method: The libFastMesh (LFM) framework is based on a low-dissipation finite–volume discretization, together with high-order explicit time integration, for direct computation of aeroacoustic fields on unstructured meshes. Convective terms can be approximated using either the Kurganov–Noelle–Petrova (KNP) scheme or Pirozzoli's energy conserving approach. Time integration is fully–explicit and relies on a low-storage, 4th order Runge–Kutta scheme. The solver is specifically developed to run efficiently on modern many-core CPUs, and at large-scale where it exhibits excellent strong scaling features. This is made possible thanks to several optimizations that alleviate memory bandwidth and inter-node communication bottlenecks. Additional comments: OpenFOAM-v2112+ is an installation prerequisite. Standard OpenFOAM pre-processing and post-processing tools, as well as mesh decomposition and reordering methods may be used with the solver