Additional file 2: of DIVAN: accurate identification of non-coding disease-specific risk variants using multi-omics profiles

Supplementary Figures S1–S11. Supplementary figures with legends in the pages (1–4). (PDF 2596 kb

Design and fabrication of a micro reciprocating engine

This papa-presents an ongoing project of developing a micro reciprocating internal combustion engine. The engine is designed on the basis of a hvo stroke piston engine, but heavy modifications have been made to suit the 2D MEMS fabrication. All the engine parts are located in two layers. Piston seals are not used and leakage is prevented by the introduction ofmicrogrooves on the piston, tight tolerance control and an extended contact area hehveen the piston and the cylinder. With the assistance of a film of lubrication oil, these measures prove effective in preventing leakage. A new approach has been developed to fabricate high temperature resistant engine components at low cost. The approach relies on the UltraThick SU-8 Process (UTSP) to make micromoulds: then ceramic and metallic engine components can be produced based on the moulds. The UTSP is a UV lithography process for producing up to 1000 ?m thick SU-8 layers and the quality of the fabrication results can be compared with those made by using X ray exposure process in the same Ihichiess. A complete microengine has been fabricated in SU-8 using the UTSP for test drive. High quality ceramic and metallic components have been produced based on the SU-8 moulds, proving the new approach is feasible for {wilding durable micro hot engines at a low cost

The Drosophila Helicase MLE Targets Hairpin Structures in Genomic Transcripts

<div><p>RNA hairpins are a common type of secondary structures that play a role in every aspect of RNA biochemistry including RNA editing, mRNA stability, localization and translation of transcripts, and in the activation of the RNA interference (RNAi) and microRNA (miRNA) pathways. Participation in these functions often requires restructuring the RNA molecules by the association of single-strand (ss) RNA-binding proteins or by the action of helicases. The Drosophila MLE helicase has long been identified as a member of the MSL complex responsible for dosage compensation. The complex includes one of two long non-coding RNAs and MLE was shown to remodel the roX RNA hairpin structures in order to initiate assembly of the complex. Here we report that this function of MLE may apply to the hairpins present in the primary RNA transcripts that generate the small molecules responsible for RNA interference. Using stocks from the Transgenic RNAi Project and the Vienna Drosophila Research Center, we show that MLE specifically targets hairpin RNAs at their site of transcription. The association of MLE at these sites is independent of sequence and chromosome location. We use two functional assays to test the biological relevance of this association and determine that MLE participates in the RNAi pathway.</p></div

MLE is enriched at the plasmid integration site when transcription of the transgene is active.

<p>Left panel, Polytene chromosomes from male larvae expressing a dsRNA targeting <i>Hrb87F</i> (<i>Hrb87F</i> RNAi) under the induction of <i>Actin5C-GAL4</i> or larvae in which the production of the dsRNA is not activated (ctrl). MLE paints the X chromosome in both samples and is enriched at the integration site of the plasmid only in <i>Hrb87F</i> RNAi larvae. The white arrows indicate the plasmid integration site. In the right panel is a detail of the region marked by the arrows.</p

Identification of Pur α-interacting proteins.

<p>A. Silver-staining gel with distinct bands for recombinant proteins and affinity-purified proteins. The captured proteins were further analyzed by mass spectrometry, and distinct classes of proteins were identified. B. <i>Rm62</i> and <i>Hts</i> mutants enhance rCGG-mediated neurodegeneration in fly. Column 1: wild-type fly; Column 2: fly expressing (CGG)₉₀-EGFP only; Column 3: fly expressing (CGG)₉₀-EGFP in the heterozygous background of <i>Hts</i>⁰¹¹⁰³ Loss-of-Function (LOF) mutation; Column 4: fly expressing CGG₉₀-EGFP in the heterozygous background of <i>Rm62</i>⁰¹⁰⁸⁴ Loss-of-Function (LOF) mutation; Column 5: fly expressing CGG₉₀-EGFP in the heterozygous background of <i>Rm62</i>^(3)3607 overexpression (Gain-of-Function (GOF). SEM eye images are shown.</p

Distributional similarity for Chinese: exploiting characters and radicals

Distributional Similarity has attracted considerable attention in the field of natural language processing as an automatic means of countering the ubiquitous problem of sparse data. As a logographic language, Chinese words consist of characters and each of them is composed of one or more radicals. The meanings of characters are usually highly related to the words which contain them. Likewise, radicals often make a predictable contribution to the meaning of a character: characters that have the same components tend to have similar or related meanings. In this paper, we utilize these properties of the Chinese language to improve Chinese word similarity computation. Given a content word, we first extract similar words based on a large corpus and a similarity score for ranking. This rank is then adjusted according to the characters and components shared between the similar word and the target word. Experiments on two gold standard datasets show that the adjusted rank is superior and closer to human judgments than the original rank. In addition to quantitative evaluation, we examine the reasons behind errors drawing on linguistic phenomena for our explanations

Fragile X premutation rCGG repeats cause the nuclear accumulation of Hsp70 mRNA.

<p>A. Quantitative analysis of <i>Hsp70</i> mRNA levels by real-time PCR from the adult heads of genotypes: <i>+/+</i> (wild-type (WT)); <i>elav; rCGG₆₀</i> (rCGG-expressing homozygous flies); <i>elav/+; rCGG₆₀/+</i> (rCGG-heterozygous flies); <i>Rm62^LOF/+</i> (Rm62 mutation heterozygous flies); and <i>rCGG₆₀/+; Rm62^LOF/+</i> (interaction). Housekeeping ribosomal protein 32 (<i>Rpl32</i>) mRNA was used as an internal control. *: p<0.05 B. Western blot with anti-histone 3 antibody, and α tubulin. C. Quantitative analysis of <i>Hsp70</i> mRNA levels by real-time PCR on cytoplasmic and nuclear RNA fractions obtained from adult heads of wild-type (WT) and rCGG-expressing flies. <i>Rpl32</i> mRNA was used as control. D. Quantitative analysis of <i>Hsp70</i> mRNA levels in total RNA fractions upon heat shock. Both wild-type (WT) and rCGG-expressing flies were heat shocked for 30 min. No heat shock (NHS) represents non-heat shocked controls. Flies were decapitated at the indicated time after heat shock. Heads were collected and total RNA isolated from them. Both WT and rCGG-expressing flies displayed robust expression of <i>Hsp70</i> in response to heat shock. After the removal of heat shock, <i>Hsp70</i> transcripts declined radically in the WT, whereas in rCGG-expressing flies, <i>Hsp70</i> transcripts show prolonged accumulation. Control samples do not display any overt differences in the timing or expression levels of <i>Hsp70</i> during the initial response to a short heat shock. Real time against <i>Fmr1</i> serves as a control on fractionated samples. The data represent mean ± SEM, n = 3.</p

MLE targets shRNA at their site of transcription.

<p>MLE staining of polytene chromosomes from female larvae expressing short hairpin RNAs after induction with <i>Actin5C-GAL4</i>.</p

MLE localization at the integration site of the plasmid does not require the MSL complex.

<p><b>(A)</b> Left panel, Polytene chromosomes from male larvae expressing a dsRNA targeting <i>Hrb87F</i> (<i>Hrb87F</i> RNAi) under the induction of <i>Actin5C-GAL4</i>. MSL1, MSL3 and MOF paint the X chromosome but are absent at the integration site of the plasmid indicated by the white arrows. In the right panel is a detail of the region marked by the arrows. <b>(B)</b> Polytene chromosomes from female larvae expressing a dsRNA targeting <i>Hrb87F</i> (<i>Hrb87F</i> RNAi) following induction with <i>Actin5C-GAL4</i> and larvae in which the production of the dsRNA is not induced (ctrl).</p

MLE mutation affects RNAi efficiency.

<p><b>(A)</b> Wing phenotypes from female flies in which Notch dsRNA expression is induced by <i>C96-GAL4</i>. Class1: wild type; class 2: missing margin bristles and absent notching; class 3: moderate notching; class 4: extensive notching; class 5: missing most of the wing margins; class 6: complete lack of margins and reduced wing blade. The chart on the right side of the figure represents the <i>Notch</i> RNAi wing phenotypes distribution in <i>wild type</i>, <i>mle</i> homozygous mutant and <i>mle</i> heterozygous mutant background. The results are the sum of three to six independent crosses per genotype. <b>(B)</b> Wing phenotypes from female flies in which Egfr dsRNA expression is induced by <i>ms1096-GAL4</i>. Class1: wild type; class 2: all the veins present; class 3: absent anterior cross vein (acv) or presence of a partial longitudinal vein; class 4: absent acv plus one partial longitudinal vein; class 5: absent acv plus two partial longitudinal veins; class 6: acv vein absent plus one longitudinal vein absent plus one partial longitudinal vein; class 7: most of the veins absent. The chart on the right side of the figure represents the <i>Egfr</i> RNAi wing phenotypes distribution respectively in <i>wild type</i> and <i>mle</i> homozygous mutant background. The results are the sum of four to five independent crosses per genotype.</p