CompMoby: Comparative MobyDick for detection of cis-regulatory motifs

<p>Abstract</p> <p>Background</p> <p>The regulation of gene expression is complex and occurs at many levels, including transcriptional and post-transcriptional, in metazoans. Transcriptional regulation is mainly determined by sequence elements within the promoter regions of genes while sequence elements within the 3' untranslated regions of mRNAs play important roles in post-transcriptional regulation such as mRNA stability and translation efficiency. Identifying cis-regulatory elements, or motifs, in multicellular eukaryotes is more difficult compared to unicellular eukaryotes due to the larger intergenic sequence space and the increased complexity in regulation. Experimental techniques for discovering functional elements are often time consuming and not easily applied on a genome level. Consequently, computational methods are advantageous for genome-wide cis-regulatory motif detection. To decrease the search space in metazoans, many algorithms use cross-species alignment, although studies have demonstrated that a large portion of the binding sites for the same trans-acting factor do not reside in alignable regions. Therefore, a computational algorithm should account for both conserved and nonconserved cis-regulatory elements in metazoans.</p> <p>Results</p> <p>We present CompMoby (Comparative MobyDick), software developed to identify cis-regulatory binding sites at both the transcriptional and post-transcriptional levels in metazoans without prior knowledge of the trans-acting factors. The CompMoby algorithm was previously shown to identify cis-regulatory binding sites in upstream regions of genes co-regulated in embryonic stem cells. In this paper, we extend the software to identify putative cis-regulatory motifs in 3' UTR sequences and verify our results using experimentally validated data sets in mouse and human. We also detail the implementation of CompMoby into a user-friendly tool that includes a web interface to a streamlined analysis. Our software allows detection of motifs in the following three categories: one, those that are alignable and conserved; two, those that are conserved but not alignable; three, those that are species specific. One of the output files from CompMoby gives the user the option to decide what category of cis-regulatory element to experimentally pursue based on their biological problem. Using experimentally validated biological datasets, we demonstrate that CompMoby is successful in detecting cis-regulatory target sites of known and novel trans-acting factors at the transcriptional and post-transcriptional levels.</p> <p>Conclusion</p> <p>CompMoby is a powerful software tool for systematic <it>de novo </it>discovery of evolutionarily conserved and nonconserved cis-regulatory sequences involved in transcriptional or post-transcriptional regulation in metazoans. This software is freely available to users at <url>http://genome.ucsf.edu/compmoby/</url>.</p

Structural and magnetic properties of Fe1+dTe single crystals

We have grown single crystals of Fe1+dTe by a conventional self-flux method. We obtained plate-like single crystals with dnom \geq 0.1. The value of the magnetization increased with increasing excess Fe concentration, and a broadening of the antiferromagnetic transition was observed for dnom >1.15. Further, we noted that the antiferromagnetic transition of Fe1.134Te (dnom = 0.15) was clearly suppressed to a lower temperature, which would indicate a possibility of controllability of magnetism by excess Fe concentration.Comment: 6 pages, 4 figures. Submitted to ISS 2011 proceedin

Investigation of Novel Noncontacting Measurement Method by the Design of Loop-Type Probe and Reconstruction of Radiation Modeling

Because the ICs’ application frequency and speed become higher and trends of system packaging and device under test request higher reliability, a novel technology combining noncontacting measurement method and reconstructing radiation model was proposed to solve signal deliveries in system packages or PCBs. In this study, a novel noncontacting method for the ICs’ measurements was investigated by the design of loop-type near-field probe and reconstructed the radiation model to substitute the traditional measurement methods, such as using probes and SMA connectors. A near-field probe was used to receive the coupling signal. The assessing circuit modeling could be completed by some synthesized theorems. According to the study’s results, frequency responses of reconstruction model developed by theorems, radiation measurements, and simulated by EM methods were highly curve fitting

Microstructural analysis of phase separation in iron chalcogenide superconductors

The interplay between superconductivity, magnetism and crystal structure in iron-based superconductors is a topic of great interest amongst the condensed matter physics community as it is thought to be the key to understanding the mechanisms responsible for high temperature superconductivity. Alkali metal doped iron chalcogenide superconductors exhibit several unique characteristics which are not found in other iron-based superconducting materials such as antiferromagnetic ordering at room temperature, the presence of ordered iron vacancies and high resistivity normal state properties. Detailed microstructural analysis is essential in order to understand the origin of these unusual properties. Here we have used a range of complementary scanning electron microscope based techniques, including high-resolution electron backscatter di raction mapping, to assess local variations in composition and lattice parameter with high precision and sub-micron spatial resolution. Phase separation is observed in the Csx Fe2-ySe2 crystals, with the minor phase distributed in a plate-like morphology throughout the crystal. Our results are consistent with superconductivity occurring only in the minority phase.Comment: Accepted for publication in a special edition of Supercond. Sci. Techno

Imperatorin ameliorates pulmonary fibrosis via GDF15 expression

Background: Pulmonary fibrosis features in damaged pulmonary structure or over-produced extracellular matrix and impaired lung function, leading to respiratory failure and eventually death. Fibrotic lungs are characterized by the secretion of pro-fibrotic factors, transformation of fibroblasts to myofibroblasts, and accumulation of matrix proteins.Hypothesis/purpose: Imperatorin shows anti-inflammatory effects on alveolar macrophages against acute lung injury. We attempt to evaluate the properties of imperatorin on the basis of fibroblasts.Methods: In in vitro, zymosan was introduced to provoke pro-fibrotic responses in NIH/3T3 or MRC-5 pulmonary fibroblasts. Imperatorin was given for examining its effects against fibrosis. The mice were stimulated by bleomycin, and imperatorin was administered to evaluate the prophylactic potential in vivo.Results: The upregulated expression of connective tissue growth factor (CTGF), α-smooth muscle actin (α-SMA), and collagen protein due to zymosan introduction was decreased by imperatorin in fibroblasts. Zymosan induced the activity of transglutaminase 2 (TGase2) and lysyl oxidase (LOX), which was also inhibited by the administration of imperatorin. Imperatorin alone enhanced sirtuin 1 (SIRT1) activity and growth differentiation factor 15 (GDF15) secretion in fibroblasts via LKB1/AMPK/CREB pathways. In addition, GDF15 exerted a beneficial effect by reducing the protein expression of CTGF, α-SMA, and collagen and the activities of TGase and LOX. Moreover, orally administered imperatorin showed prophylactic effects on bleomycin-induced pulmonary fibrosis in mice.Conclusion: Imperatorin reduces fibrotic marker expression in fibroblasts and also increases GDF15 secretion via the LKB1/AMPK/CREB pathway, attenuating pro-fibrotic responses in vitro. Imperatorin also alleviates pulmonary fibrosis induced by bleomycin in vivo

An earthquake slip zone is a magnetic recorder

International audienceDuring an earthquake, the physical and the chemical transformations along a slip zone lead to an intense deformation within the gouge layer of a mature fault zone. Because the gouge contains ferromagnetic minerals, it has the capacity to behave as a magnetic recorder during an earthquake. This constitutes a conceivable way to identify earthquakes slip zones. In this paper, we investigate the magnetic record of the Chelungpu fault gouge that hosts the principal slip zone of the Chi-Chi earthquake (Mw 7.6, 1999, Taiwan) using Taiwan Chelungpu-fault Drilling Project core samples. Rock magnetic investigation pinpoints the location of the Chi-Chi mm-thick principal slip zone within the 16-cm thick gouge at ~1 km depth. A modern magnetic dipole of Earth magnetic field is recovered throughout this gouge but not in the wall rocks nor in the two other adjacent fault zones. This magnetic record resides essentially in two magnetic minerals; magnetite in the principal slip zone, and neoformed goethite elsewhere in the gouge. We propose a model where magnetic record: 1) is preserved during inter-seismic time, 2) is erased during co-seismic time and 3) is imprinted during post-seismic time when fluids cooled down. We suggest that the identification of a stable magnetic record carried by neoformed goethite may be a signature of friction-heating process in seismic slip zone

Growth conditions, structure, and superconductivity of pure and metal-doped FeTe1-xSex single crystals

Superconducting single crystals of pure FeTe1 xSex and FeTe0.65Se0.35 doped with Co, Ni, Cu, Mn, Zn, Mo, Cd, In, Pb, Hg, V, Ga, Mg, Al, Ti, Cr, Sr or Nd into Fe ions site have been grown applying Bridgman's method. It has been found that the sharpness of transition to the superconducting state in FeTe1 xSex is evidently inversely correlated with crystallographic quality of the crystals. Among all of the studied dopants only Co, Ni and Cu substitute Fe ions in FeTe0.65Se0.35 crystals. The remaining examined ions do not incorporate into the crystal structure. Nevertheless, they form inclusions together with selenium, tellurium and/or iron, what changes the chemical composition of host matrix and therefore influences Tc value. Small disorder introduced into magnetic sublattice, by partial replacement of Fe ions by slight amount of nonmagnetic ions of Cu (~ 1.5 at%) or by magnetic ions of Ni (~ 2 at%) and Co (~5 at%) with spin value different than that of Fe ion, completely suppresses superconductivity in FeTe1 xSex system. This indicates that even if superconductivity is observed in the system containing magnetic ions it can not survive when the disorder in magnetic ions sublattice is introduced, most likely because of magnetic scattering of Cooper pairs.Comment: 18 pages, 12 figures, 3 table