Gene regulatory mechanisms underpinning prostate cancer susceptibility

Molecular characterization of genome-wide association study (GWAS) loci can uncover key genes and biological mechanisms underpinning complex traits and diseases. Here we present deep, high-throughput characterization of gene regulatory mechanisms underlying prostate cancer risk loci. Our methodology integrates data from 295 prostate cancer chromatin immunoprecipitation and sequencing experiments with genotype and gene expression data from 602 prostate tumor samples. The analysis identifies new gene regulatory mechanisms affected by risk locus SNPs, including widespread disruption of ternary androgen receptor (AR)-FOXA1 and AR-HOXB13 complexes and competitive binding mechanisms. We identify 57 expression quantitative trait loci at 35 risk loci, which we validate through analysis of allele-specific expression. We further validate predicted regulatory SNPs and target genes in prostate cancer cell line models. Finally, our integrated analysis can be accessed through an interactive visualization tool. This analysis elucidates how genome sequence variation affects disease predisposition via gene regulatory mechanisms and identifies relevant genes for downstream biomarker and drug development.

An Ultrasonic Relaxation Study of 1-Alkyl-3-Methylmidazolium-Based Room Temperature Ionic Liquids: Probing the Role of Alkyl Chain Length in the Cation

Ultrasound absorption spectra of four 1-alkyl-3-methylimidazolium bis(trifluoromethylsulfonyl)imide were determined as a function of the alkyl chain length on the cation from 1-propyl- to 1-hexyl- from 293.15 to 323.15 K at ambient pressure. Herein, the ultrasound absorption measurements were carried out using a standard pulse technique within a frequency range from 10 to 300 MHz. Additionally the speed of sound, density and viscosity have been measured. The presence of strong dissipative processes during the ultrasound wave propagation was found experimentally, i.e. relaxation processes in the megahertz range were observed for all compounds over the whole temperature range. The relaxation spectra (both relaxation amplitude and relaxation frequency) were shown to be dependent on the alkyl side chain length of the 1-alkyl-3-methylimidazolium ring. In most cases, a single Debye model described the absorption spectra very well. However, a comparison of the determined spectra with the spectra of a few other imidazolium-based ionic liquids reported in the literature (in part recalculated in this work) shows that the complexity of the spectra increases rapidly with the elongation of the alkyl chain length on the cation. This complexity indicates that both the volume viscosity and the shear viscosity are involved in relaxation processes even in relatively low frequency ranges. As a consequence, the sound velocity dispersion is present at relatively low megahertz frequencies.

Effect of cation structure on the oxygen solubility and diffusivity in a range of bis{(trifluoromethyl)sulfonyl}imide anion based ionic liquids for lithium-air battery electrolytes

This paper reports on the solubility and diffusivity of dissolved oxygen in a series of ionic liquids (ILs) based on the bis{(trifluoromethyl)sulfonyl}imide anion with a range of related alkyl and ether functionalised cyclic alkylammonium cations. Cyclic voltammetry has been used to observe the reduction of oxygen in ILs at a microdisk electrode and chronoamperometric measurements have then been applied to simultaneously determine both the concentration and the diffusion coefficient of oxygen in the different ILs. The viscosity of the ILs and the calculated molar volume and free volume is also reported. It is found that, within this class of ILs, the oxygen diffusivity generally increases with decreasing viscosity of the neat IL. An inverse relationship between oxygen solubility and IL free volume is reported for the two IL families implying oxygen is not simply occupying the available empty space. In addition, it is reported that the introduction of ether-group into the IL cation structure promotes the diffusivity of dissolved oxygen but reduces the solubility of the gas.

The Influence of Cation Structure on the Chemical-Physical Properties of Protic Ionic Liquids

In this study we investigated the influence of five different cations on the physical-chemical properties of protic ionic liquids (PILs) based on bis(trifluoromethanesulfonyl)imide (TFSI-). We showed that the viscosities, ionic conductivities, densities and thermal properties of these PIL are strongly affected by the structure of the protic cation. Furthermore, the influence of the cation structure on the lithium coordination was investigated by Raman spectroscopy for all investigated PIL-based electrolytes for lithium-ion batteries (LIBs). This investigation clearly demonstrates, that the lithium average coordination number in PIL-based electrolytes is strongly affected by (ring) size and the number of protons on the cations structure and, more importantly, it might be significantly lower (more than 60 of that of electrolytes containing aprotic ionic liquids (AILs). Electrochemical performances of these PILs-based electrolytes were then also investigated to dress some conclusion on their applicability for LIB.

Temperature and Pressure Induced Structural Changes of Cobalt (II) in a Phosphonium Based Ionic Liquid

In this paper the temperature and pressure induced paramagnetic switching of cobalt (II) complex in binary mixture of phosphonium based ionic liquid [P6,6,6,14]SCN and [Co(NCS)2], is reported. This arises from a structural change in the coordination of the cobalt (II) center from tetrahedral [Co(NCS)4]2- to octahedral [Co(NCS)6]4- when mobile thiocyanate ions are added. These properties are reflected in the abrupt change of conductivity behavior of the magnetic ionic liquid. Therefore, as demonstrated herein the reversible switching in coordination of cobalt from tetrahedral to octahedral can be easily monitored at ambient as well as elevated pressure by tracking the dc-conductivity changes.

Techno-Economic Feasibility of Selective CO2 Capture Processes from Biogas Streams using Ionic Liquids as Physical Absorbents

Biogas from anaerobic digestion of sewage sludge is a renewable resource with high energy content, which is formed mainly of CH4 (40-75 vol.%) and CO2 (15-60 vol.%) Other components such as water (H2O, 5-10 vol.%) and trace amounts of hydrogen sulfide and siloxanes can also be present. A CH4-rich stream can be produced by removing the CO2 and other impurities so that the upgraded bio-methane can be injected into the natural gas grid or used as a vehicle fuel. The main objective of this paper is to develop a new modeling methodology to assess the technical and economic performance of biogas upgrading processes using ionic liquids which physically absorb CO2. Three different ionic liquids, namely the 1-ethyl-3-methylimidazolium bis[(trifluoromethyl)sulfonyl]imide, 1-hexyl-3-methylimidazoliumbis[(trifluoromethyl)sulfonyl]imide and trihexyl(tetradecyl)phosphonium bis[(trifluoromethyl)sulfonyl]imide, are considered for CO2 capture in a pressure-swing regenerative absorption process. The simulation software Aspen Plus and Aspen Process Economic Analyzer is used to account for mass and energy balances as well as equipment cost. In all cases, the biogas upgrading plant consists of a multistage compressor for biogas compression, a packed absorption column for CO2 absorption, a flash evaporator for solvent regeneration, a centrifugal pump for solvent recirculation, a pre-absorber solvent cooler and a gas turbine for electricity recovery. The evaluated processes are compared in terms of energy efficiency, capital investment and bio-methane production costs. The overall plant efficiency ranges from 71-86 % whereas the bio-methane production cost ranges from £6.26-7.76 per GJ (LHV). A sensitivity analysis is also performed to determine how several technical and economic parameters affect the bio-methane production costs. The results of this study show that the simulation methodology developed can predict plant efficiencies and production costs of large scale CO2 capture processes using ionic liquids without having to rely on gas solubility experimental data.