Discovery of cis-elements between sorghum and rice using co-expression and evolutionary conservation

<p>Abstract</p> <p>Background</p> <p>The spatiotemporal regulation of gene expression largely depends on the presence and absence of <it>cis</it>-regulatory sites in the promoter. In the economically highly important grass family, our knowledge of transcription factor binding sites and transcriptional networks is still very limited. With the completion of the sorghum genome and the available rice genome sequence, comparative promoter analyses now allow genome-scale detection of conserved <it>cis</it>-elements.</p> <p>Results</p> <p>In this study, we identified thousands of phylogenetic footprints conserved between orthologous rice and sorghum upstream regions that are supported by co-expression information derived from three different rice expression data sets. In a complementary approach, <it>cis</it>-motifs were discovered by their highly conserved co-occurrence in syntenic promoter pairs. Sequence conservation and matches to known plant motifs support our findings. Expression similarities of gene pairs positively correlate with the number of motifs that are shared by gene pairs and corroborate the importance of similar promoter architectures for concerted regulation. This strongly suggests that these motifs function in the regulation of transcript levels in rice and, presumably also in sorghum.</p> <p>Conclusion</p> <p>Our work provides the first large-scale collection of <it>cis</it>-elements for rice and sorghum and can serve as a paradigm for <it>cis</it>-element analysis through comparative genomics in grasses in general.</p

In situ loading and delivery of short single- And double-stranded dna by supramolecular organic frameworks

Short DNA represents an important class of biomacromolecules that are widely applied in gene therapy, editing, and modulation. However, the development of simple and reliable methods for their intracellular delivery remains a challenge. Herein, we describe that seven water-soluble, homogeneous supramolecular organic frameworks (SOFs) with a well-defined pore size and high stability in water that can accomplish in situ inclusion of single-stranded (ss) and double-stranded (ds) DNA (21, 23, and 58 nt) and effective intracellular delivery (including two noncancerous and six cancerous cell lines). Fluorescence quenching experiments for single and double endlabeled ss- and ds-DNA support that the DNA sequences can be completely enveloped by the SOFs. Confocal laser scanning microscopy and flow cytometry reveal that five of the SOFs exhibit excellent delivery efficiencies that, in most of the studied cases, outperform the commercial standard Lipo2000, even at low SOF-nucleic acid ratios. In addition to high delivery efficiencies, the watersoluble, self-assembled SOF carriers have a variety of advantages, including convenient preparation, high stability, and in situ DNA inclusion, which are all critical for practical applications in nucleic acid delivery

Fast Predictive Image Registration

We present a method to predict image deformations based on patch-wise image appearance. Specifically, we design a patch-based deep encoder-decoder network which learns the pixel/voxel-wise mapping between image appearance and registration parameters. Our approach can predict general deformation parameterizations, however, we focus on the large deformation diffeomorphic metric mapping (LDDMM) registration model. By predicting the LDDMM momentum-parameterization we retain the desirable theoretical properties of LDDMM, while reducing computation time by orders of magnitude: combined with patch pruning, we achieve a 1500x/66x speed up compared to GPU-based optimization for 2D/3D image registration. Our approach has better prediction accuracy than predicting deformation or velocity fields and results in diffeomorphic transformations. Additionally, we create a Bayesian probabilistic version of our network, which allows evaluation of deformation field uncertainty through Monte Carlo sampling using dropout at test time. We show that deformation uncertainty highlights areas of ambiguous deformations. We test our method on the OASIS brain image dataset in 2D and 3D

Improving the efficiency of polymer solar cells by incorporating gold nanoparticles into all polymer layers

We demonstrate efficiency improvement in polymer solar cells (PSCs) by ∼22 through incorporating Au nanoparticles (NPs) into all polymer layers. Au NPs are found to have distinct mechanisms in improving device performance when incorporated in different polymer layers. Au NPs in poly-(3,4- ethylenedioxythiophene):poly(styrenesulfonate) mainly contribute to better hole collection while Au NPs in active layer contributes to the enhanced optical absorption and more balanced charge-transport. Our theoretical result shows that the absorption enhancement at the active layer is attributed to plasmon resonances with strong near-field distributions penetrated into absorption polymers. These findings can be applied to design high-efficiency metallic NPs-incorporated PSCs. © 2011 American Institute of Physics.published_or_final_versio

Distribution and Excretion of TEGDMA in Guinea Pigs and Mice

The monomer triethyleneglycoldimethacrylate (TEGDMA) is used as a diluent in many resin-based dental materials. It was previously shown in vitro that TEGDMA was released into the adjacent biophase from such materials during the first days after placement. In this study, the uptake, distribution, and excretion of 14C-TEGDMA applied via gastric, intradermal, and intravenous administration at dose levels well above those encountered in dental care were examined in vivo in guinea pigs and mice as a test of the hypothesis that TEGDMA reaches cytotoxic levels in mammalian tissues. 14C-TEGDMA was taken up rapidly from the stomach and small intestine after gastric administration in both species and was widely distributed in the body following administration by each route. Most 14C was excreted within one day as 14 CO2. The peak equivalent TEGDMA levels in all mouse and guinea pig tissues examined were at least 1000-fold less than known toxic levels. The study therefore did not support the hypothesis

Optical and electrical effects of gold nanoparticles in the active layer of polymer solar cells

The effects of Au nanoparticles (NPs) incorporated into the active layer of polymer solar cells (PSCs) with a newly synthesized donor polymer are investigated in detail. Our work shows that localized surface plasmon resonance (LSPR) introduced by the metallic NPs can experimentally and theoretically enhance the light absorption in the active layer of PSCs because the strong LSPR near field mainly distributes laterally along the active layer. The understanding can be applied to other metallic NP incorporated organic solar cells. Meanwhile, our results show that electrical properties can counter-diminish the optical enhancement from LSPR and thus reduce the overall performance improvement. It is important that both optical and electrical properties need to be studied and optimized simultaneously for achieving improved power conversion efficiency. The study contributes to better understanding the uses of Au NPs for enhancing PSC performances. © The Royal Society of Chemistry 2011.postprin

Structural evolution of GeMn/Ge superlattices grown by molecular beam epitaxy under different growth conditions

GeMn/Ge epitaxial 'superlattices' grown by molecular beam epitaxy with different growth conditions have been systematically investigated by transmission electron microscopy. It is revealed that periodic arrays of GeMn nanodots can be formed on Ge and GaAs substrates at low temperature (approximately 70°C) due to the matched lattice constants of Ge (5.656 Å) and GaAs (5.653 Å), while a periodic Ge/GeMn superlattice grown on Si showed disordered GeMn nanodots with a large amount of stacking faults, which can be explained by the fact that Ge and Si have a large lattice mismatch. Moreover, by varying growth conditions, the GeMn/Ge superlattices can be manipulated from having disordered GeMn nanodots to ordered coherent nanodots and then to ordered nanocolumns

Thickness dependence of microstructures in La0.8Ca0.2MnO3 thin films

The thickness dependence of microstructures of La0.8Ca0.2MnO3 (LCMO)/SrTiO3 (STO) thin films was investigated by high-resolution x-ray diffraction, small angle x-ray reflection, grazing incidence x-ray diffraction, scanning electron microscopy, and atomic force microscopy. The results show that all the LCMO films are well oriented in (00l) direction perpendicular to the substrate surface. Self-organized crystalline grains with a tetragonal shape are uniformly distributed on the film surface, indicating the deposition condition being of benefit to the formation of the crystalline grains. With increasing the film thickness, the crystalline quality of the LCMO film is improved, while the surface becomes rougher. There exists a nondesigned cap layer on the upper surface of the LCMO layer for all the samples. The mechanism is discussed briefly.published_or_final_versio

Coherent magnetic semiconductor nanodot arrays

In searching appropriate candidates of magnetic semiconductors compatible with mainstream Si technology for future spintronic devices, extensive attention has been focused on Mn-doped Ge magnetic semiconductors. Up to now, lack of reliable methods to obtain high-quality MnGe nanostructures with a desired shape and a good controllability has been a barrier to make these materials practically applicable for spintronic devices. Here, we report, for the first time, an innovative growth approach to produce self-assembled and coherent magnetic MnGe nanodot arrays with an excellent reproducibility. Magnetotransport experiments reveal that the nanodot arrays possess giant magneto-resistance associated with geometrical effects. The discovery of the MnGe nanodot arrays paves the way towards next-generation high-density magnetic memories and spintronic devices with low-power dissipation

Pseudo-static tests of terminal stirrup-confined concrete-filled rectangular steel tubular columns

© 2017 Elsevier Ltd This paper mainly presents a pseudo-static test program on 12 terminal stirrup-confined square concrete-filled steel tube (SCFT) columns and 14 rectangular SCFT columns under constant axial pressure. The effects of various factors on the hysteretic behavior of specimens are investigated. These factors include with or without stirrups, height of terminal stirrup region, equivalent stirrup ratio, stirrup form, loading direction, height-length ratio (L/B), length-width ratio (B/D), axial compression ratio (n) and sliding support. The failure mode, strain ratio, hysteretic curve, skeleton curve, ultimate bearing capacity, ductility, stiffness degradation, energy dissipation, as well as the residual deformation of the specimens are analyzed. The results indicate that: (1) When n is relatively larger, the bidirectional stirrups can effectively delay the local buckling of steel tube and greatly increase the ultimate bearing capacity, stiffness, equivalent damping viscosity index, residual deformation rate and ductility index, and further significantly improve the seismic behavior of the rectangular SCFT columns; (2) Axial pressure can improve the confinement effect from the steel tube to the core concrete, also bidirectional stirrups can directly confine the core concrete to decrease strain ratio of the steel tube; (3) With the same value of n, increasing the height of terminal stirrup region or increasing the equivalent stirrup ratio can effectively improve the seismic behavior of the rectangular SCFT columns; (4) The influence of loading direction, L/B and B/D on the ductility of rectangular SCFT columns are not obvious