Epigenomic Modifications Predict Active Promoters and Gene Structure in Toxoplasma gondii

Mechanisms of gene regulation are poorly understood in Apicomplexa, a phylum that encompasses deadly human pathogens like Plasmodium and Toxoplasma. Initial studies suggest that epigenetic phenomena, including histone modifications and chromatin remodeling, have a profound effect upon gene expression and expression of virulence traits. Using the model organism Toxoplasma gondii, we characterized the epigenetic organization and transcription patterns of a contiguous 1% of the T. gondii genome using custom oligonucleotide microarrays. We show that methylation and acetylation of histones H3 and H4 are landmarks of active promoters in T. gondii that allow us to deduce the position and directionality of gene promoters with >95% accuracy. These histone methylation and acetylation “activation” marks are strongly associated with gene expression. We also demonstrate that the pattern of histone H3 arginine methylation distinguishes certain promoters, illustrating the complexity of the histone modification machinery in Toxoplasma. By integrating epigenetic data, gene prediction analysis, and gene expression data from the tachyzoite stage, we illustrate feasibility of creating an epigenomic map of T. gondii tachyzoite gene expression. Further, we illustrate the utility of the epigenomic map to empirically and biologically annotate the genome and show that this approach enables identification of previously unknown genes. Thus, our epigenomics approach provides novel insights into regulation of gene expression in the Apicomplexa. In addition, with its compact genome, genetic tractability, and discrete life cycle stages, T. gondii provides an important new model to study the evolutionarily conserved components of the histone code

Geometry-Dependent Electronic Properties of Highly Fluorescent Conjugated Molecules

URL:http://link.aps.org/doi/10.1103/PhysRevLett.85.2388 DOI:10.1103/PhysRevLett.85.2388We present a combined experimental/theoretical study of the electronic properties of conjugated para- phenylene type molecules under high pressure up to 80 kbar. Pressure is used as a tool to vary the molecular geometry and intermolecular interaction. The influence of the latter two on singlet and triplet excitons as well as polarons is monitored via optical spectroscopy. We have performed band structure calculations for the planar poly(para-phenylene) and calculated the dielectric function. By varying the intermolecular distances and the length of the polymer repeat unit the observed pressure effects can be explained.Supported by the University of Missouri Research Board, OeNB Project No. 6608, the vector-computer facilities at the University of Graz

Excited States of Ladder-type Poly-p-phenylene Oligomers

Ground state properties and excited states of ladder-type paraphenylene oligomers are calculated applying semiempirical methods for up to eleven phenylene rings. The results are in qualitative agreement with experimental data. A new scheme to interpret the excited states is developed which reveals the excitonic nature of the excited states. The electron-hole pair of the S1-state has a mean distance of approximately 4 Angstroem.Comment: 24 pages, 21 figure

Subpicosecond exciton dynamics in polyfluorene films from experiment and microscopic theory

The authors acknowledge financial support from the UK EPSRC (Grants EP/E065066/1, EP/E062636/1, EP/J009318/1 and EP/J009019/1), from the EPSRC Scottish Centre for Doctoral training in Condensed Matter Physics and from the European Union Seventh Framework Programme under Grant Agreement 321305.Electronic energy transfer (EET) in organic materials is a key mechanism that controls the efficiency of many processes, including light harvesting antennas in natural and artificial photosynthesis, organic solar cells, and biological systems. In this paper we have examined EET in solid-state thin-films of polyfluorene, a prototypical conjugated polymer, with ultrafast photoluminescence experiments and theoretical modeling. We observe EET occurring on a 680 ± 300 fs time scale by looking at the depolarisation of photoluminescence. An independent, predictive microscopic theoretical model is built by defining 125 000 chromophores containing both spatial and energetic disorder appropriate for a spin-coated thin film. The model predicts time-dependent exciton dynamics, without any fitting parameters, using the incoherent Förster-type hopping model. Electronic coupling between the chromophores is calculated by an improved version of the usual line-dipole model for resonant energy transfer. Without the need for higher level interactions, we find that the model is in general agreement with the experimentally observed 680 ± 300 fs depolarisation caused by EET. This leads us to conclude that femtosecond EET in polyfluorene can be described well by conventional resonant energy transfer, as long as the relevant microscopic parameters are well captured. The implications of this finding are that dipole-dipole resonant energy transfer can in some circumstances be fully adequate to describe ultrafast EET without needing to invoke strong or intermediate coupling mechanisms.PostprintPeer reviewe

Chemical interaction at the buried silicon/zinc oxide thin-film solar cell interface as revealed by hard x-ray photoelectron spectroscopy

Hard X-ray photoelectron spectroscopy (HAXPES) is used to identify chemical interactions (such as elemental redistribution) at the buried silicon /aluminum-doped zinc oxide thin-film solar cell interface. Expanding our study of the interfacial oxidation of silicon upon its solid-phase crystallization (SPC), in which we found zinc oxide to be the source of oxygen, in this investigation we address chemical interaction processes involving zinc and aluminum. In particular, we observe an increase of zinc- and aluminum-related HAXPES signals after SPC of the deposited amorphous silicon thin films. Quantitative analysis suggests an elemental redistribution in the proximity of the silicon/aluminum-doped zinc oxide interface – more pronounced for aluminum than for zinc – as explanation. Based on these insights the complex chemical interface structure is discussed

X-ray Raman scattering study of aligned polyfluorene

We present a non-resonant inelastic x-ray scattering study at the carbon K-edge on aligned poly[9,9-bis(2-ethylhexyl)-fluorene-2,7-diyl] and show that the x-ray Raman scattering technique can be used as a practical alternative to x-ray absorption measurements. We demonstrate that this novel method can be applied to studies on aligned $\pi$-conjugated polymers complementing diffraction and optical studies. Combining the experimental data and a very recently proposed theoretical scheme we demonstrate a unique property of x-ray Raman scattering by performing the symmetry decomposition on the density of unoccupied electronic states into $s$- and $p$-type symmetry contributions.Comment: 19 pages, 8 figure

Side-chain influence on the mass density and refractive index of polyfluorenes and star-shaped oligofluorene truxenes

The density of organic semiconductor films is an important quantity because it is related to intermolecular spacing which in turn determines the electronic and photophysical properties. We report thin film density and refractive index measurements of polyfluorenes and star-shaped oligofluorene truxene molecules. An ellipsometer and a procedure using a spectrophotometer were used to determine film thickness and mass of spin-coated films, respectively. We present a study of the effect of alkyl side-chain length on the volumetric mass density and refractive index of the materials studied. The density measured for poly(9,9-di-n-octylfluorene) (PF8) was 0.88 ± 0.04 g/cm3 and decreased with longer alkyl side chains. For the truxene molecule with butyl side chains (T3 butyl), we measured a density of 0.90 ± 0.04 g/cm3, which also decreased with increasing side-chain length