Integrating transcriptomic and proteomic data for accurate assembly and annotation of genomes

© 2017 Wong et al.; Published by Cold Spring Harbor Laboratory Press. Complementing genome sequence with deep transcriptome and proteome data could enable more accurate assembly and annotation of newly sequenced genomes. Here, we provide a proof-of-concept of an integrated approach for analysis of the genome and proteome of Anopheles stephensi, which is one of the most important vectors of the malaria parasite. To achieve broad coverage of genes, we carried out transcriptome sequencing and deep proteome profiling of multiple anatomically distinct sites. Based on transcriptomic data alone, we identified and corrected 535 events of incomplete genome assembly involving 1196 scaffolds and 868 protein-coding gene models. This proteogenomic approach enabled us to add 365 genes that were missed during genome annotation and identify 917 gene correction events through discovery of 151 novel exons, 297 protein extensions, 231 exon extensions, 192 novel protein start sites, 19 novel translational frames, 28 events of joining of exons, and 76 events of joining of adjacent genes as a single gene. Incorporation of proteomic evidence allowed us to change the designation of more than 87 predicted noncoding RNAs to conventional mRNAs coded by protein-coding genes. Importantly, extension of the newly corrected genome assemblies and gene models to 15 other newly assembled Anopheline genomes led to the discovery of a large number of apparent discrepancies in assembly and annotation of these genomes. Our data provide a framework for how future genome sequencing efforts should incorporate transcriptomic and proteomic analysis in combination with simultaneous manual curation to achieve near complete assembly and accurate annotation of genomes

Improved functionalization of oleic acid-coated iron oxide nanoparticles for biomedical applications

Superparamagnetic iron oxide nanoparticles can providemultiple benefits for biomedical applications in aqueous environments such asmagnetic separation or magnetic resonance imaging. To increase the colloidal stability and allow subsequent reactions, the introduction of hydrophilic functional groups onto the particles’ surface is essential. During this process, the original coating is exchanged by preferably covalently bonded ligands such as trialkoxysilanes. The duration of the silane exchange reaction, which commonly takes more than 24 h, is an important drawback for this approach. In this paper, we present a novel method, which introduces ultrasonication as an energy source to dramatically accelerate this process, resulting in high-quality waterdispersible nanoparticles around 10 nmin size. To prove the generic character, different functional groups were introduced on the surface including polyethylene glycol chains, carboxylic acid, amine, and thiol groups. Their colloidal stability in various aqueous buffer solutions as well as human plasma and serum was investigated to allow implementation in biomedical and sensing applications.status: publishe

A parametric study of vibration of rotating pre-twisted and tapered low aspect ratio cantilever plates

A finite element technique has been used to determine the natural frequencies of a pre-twisted and tapered plate mounted on the periphery of a rotating disc. The pre-twisted plate has been idealized as an assemblage of three noded triangular shell elements with six degrees of freedom at each node. In the analysis the initial stress effect (geometric stiffness) and other rotational effects except the Coriolis acceleration effect have been included. The eigenvalues have been extracted by using a simultaneous iteration technique. Computation of frequencies has been carried out for plates of aspect ratios 1 and 2. Other parameters considered are pre-twist, taper, skew angle and disc radius. From the results of computations an extension to the existing empirical formulae derived by Dokainiah and Rawtani [1] has been suggested for computing natural frequencies of rotating pre-twisted and tapered cantilever plates

DYNAMIC STRESS-ANALYSIS OF ROTATING TWISTED AND TAPERED BLADES

In this paper the finite element method has been used to determine the stresses and deformations of pre-twisted and tapered blades. Three-dimensional, twenty-noded isoparametric elements have been used for the analysis. Extensive analysis has been done for various pre-twist angles, skew angles, breadth to length ratios, and breadth to thickness ratios of the blades. Experiments were carried out to determine the stresses for the verification of the numerical results and they were found to be in good agreement

Vibration analysis of pre-twisted low aspect ratio cantilever plates

The trends of variation of first five frequencies of low aspect ratio cantilever plates with pre-twist angle have been studied using three dimensional elements as well as shell elements. Both the analyses agree as far as the trend of variation is considered. However the frequencies obtained using three-dimensional approach are slightly higher in the case of fundamental mode and in the other cases they are lower compared with the analysis using shell elements. First flap-wise bending, frequency and the first edgewise bending frequency have a decreasing trend while the other higher mode frequencies have an increasing trend. Except for the first mode frequency all the higher mode frequencies are sensitive to thickness variation particularly the torsional mode frequencies, when the plate is twisted

Effect of a tip mass on the natural frequencies of a rotating pre-twisted cantilever plate

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Prediction of micro-spun yarn lea CSP using artificial neural networks

372-377<span style="font-size: 14.0pt;mso-bidi-font-size:8.0pt;font-family:" times="" new="" roman","serif""="">A back-propagation artificial neural network has been used to develop a model relating to cotton fibre properties and micro-spun yarn lea CSP. Fibre properties such as span length , bundle strength, fineness, breaking elongation, uniformity ratio and percentage of mature fibres have been studied. It is observed that a neural network architecture having five hidden neurons in one hidden layer and an epoch size of 12 gives better prediction. The predictions are more accurate than those obtained from regression models. The mean absolute error of neural network model is found to be 60% lower than those of the regression models. </span

Amide linkage in novel three-ring bent-core molecular assemblies: polar mesophases and importance of H-bonding

<p>Here, we report the first examples of achiral unsymmetrical three-ring bent-shaped liquid crystals comprising amide and imine linkages with transverse substituents of methyl and chloro moieties on the central phenyl ring in the core, exhibiting polar banana phases. The extensive intra and inter molecular H-bonding induced novel banana mesomorphic phases. One-dimensional stacking in the mesomorphic phase as well as ferroelectric polar order promoted by intermolecular H-bonding of amide linkage is demonstrated. The compounds exhibit multifunctional properties viz., the enantiotropic liquid crystalline (LC) phase at ambient temperatures, electro-optical response, spontaneous polarisation, emission characteristics with large Stokes shift, and even charge distribution with large voltage holding ratio (VHR) values. The smectic type phase was confirmed by XRD studies and polar order was established by switching current and dielectric investigations. DFT studies revealed the importance of their suitability for display applications.</p