Short interfering RNA-mediated gene silencing in Globodera pallida and Meloidogyne incognita infective stage juveniles

The analysis of gene function through RNA interference (RNAi)-based reverse genetics in plant parasitic nematodes (PPNs) remains inexplicably reliant on the use of long double-stranded RNA (dsRNA) silencing triggers; a practice inherently disadvantageous due to the introduction of superfluous dsRNA sequence. increasing chances of aberrant or off-target gene silencing through interactions between nascent short interfering RNAs (siRNAs) and non-cognate mRNA targets. Recently, we have shown that non-nematode, long dsRNAs have a propensity to elicit profound impacts on the phenotype and migrational abilities of both root knot and cyst nematodes. This study presents, to our knowledge for the first time, gene-specific knockdown of FMRFamide-like peptide (flp) transcripts, using discrete 21 bp siRNAs in potato cyst nematode Globodera pallida, and root knot nematode Meloidogyne incognita infective (J2) stage juveniles. Both knockdown at the transcript level through quantitative (q)PCR analysis and functional data derived from migration assay, indicate that siRNAs targeting certain areas of the FMRFamide-like peptide (FLP) transcripts are potent and specific in the silencing of gene function. In addition, we present a method of manipulating siRNA activity through the management of strand thermodynamics. Initial evaluation of strand thermodynamics as a determinant of RNA-induced Silencing Complex (RISC) strand selection (inferred from knockdown efficacy) in the siRNAs presented here suggested that the purported influence of 5' stand stability on guide incorporation may be somewhat promiscuous. However, we have found that on strategically incorporating base mismatches in the sense strand of a G. pallida-specific siRNA we could specifically increase or decrease the knockdown of its target (specific to the antisense strand), presumably through creating more favourable thermodynamic profiles for incorporation of either the sense (non-target-specific) or antisense (target-specific) strand into a cleavage-competent RISC. Whilst the efficacy of similar approaches to siRNA modification has been demonstrated in the context of Drosophila whole-cell lysate preparations and in mammalian cell cultures, it remained to be seen how these sense strand mismatches may impact on gene silencing in vivo, in relation to different targets and in different sequence contexts. This work presents the first application of such an approach in a whole organism; initial results show promise. (C) 2009 Australian Society for Parasitology Inc. Published by Elsevier Ltd. All rights reserved.

Evaluation of Five Interleukin Genes for Association with End-Stage Renal Disease in White Europeans

Background: Genetic variation within interleukin genes has been reported to be associated with end-stage renal disease (ESRD). These findings have not been consistently replicated. No study has yet reported the comprehensive investigation of IL1A, IL1B, IL1RN, IL6 and IL10 genes. Methods: 664 kidney transplant recipients (cases) and 577 kidney donors (controls) were genotyped to establish if common variants in interleukin genes are associated with ESRD. Single nucleotide polymorphism (SNP) genotype data for each gene were downloaded for a northern and western European population from the International HapMap Project. Haploview was used to visualize linkage disequilibrium and select tag SNPs. Thirty SNPs were genotyped using MassARRAY (R) iPLEX Gold technology and data were analyzed using the chi(2) test for trend. Independent replication was conducted in 1,269 individuals with similar phenotypic characteristics. Results: Investigating all common variants in IL1A, IL1B, IL1RN, IL6 and IL10 genes revealed a statistically significant association (rs452204 p(empirical) = 0.02) with one IL1RN variant and ESRD. This IL1RN SNP tags three other variants, none of which have previously been reported to be associated with renal disease. Independent replication in a separate transplant population of comparable size did not confirm the original observation. Conclusions: Common variants in these five candidate interleukin genes are not major risk factors for ESRD in white Europeans. Copyright (C) 2010 S. Karger AG, Basel

Two-stage mixed discrete-continuous identification of radial basis function (RBF) neural models for nonlinear systems

The identification of nonlinear dynamic systems using radial basis function (RBF) neural models is studied in this paper. Given a model selection criterion, the main objective is to effectively and efficiently build a parsimonious compact neural model that generalizes well over unseen data. This is achieved by simultaneous model structure selection and optimization of the parameters over the continuous parameter space. It is a mixed-integer hard problem, and a unified analytic framework is proposed to enable an effective and efficient two-stage mixed discrete-continuous; identification procedure. This novel framework combines the advantages of an iterative discrete two-stage subset selection technique for model structure determination and the calculus-based continuous optimization of the model parameters. Computational complexity analysis and simulation studies confirm the efficacy of the proposed algorithm.

Spatial characterization of salt accumulation in early stage limestone weathering using probe permeametry

This research characterizes the weathering of natural building stone using an unsteady-state portable probe permeameter. Variations between the permeability properties of fresh rock and the same rocks after the early stages of a salt weathering simulation are used to examine the effects of salt accumulation on spatial variations in surface rock permeability properties in two limestones from Spain. The Fraga and Tudela limestones are from the Ebro basin and are of Miocene age. Both stone types figure largely in the architectural heritage of Spain and, in common with many other building limestones, they are prone to physical damage from salt crystallization in pore spaces. To examine feedbacks associated with salt accumulation during the early stages of this weathering process, samples of the two stone types were subjected to simulated salt weathering under laboratory conditions using magnesium sulphate and sodium chloride at concentrations of 5% and 15%. Permeability mapping and statistical analysis (aspatial statistics and spatial prediction) before and after salt accumulation are used to assess changes in the spatial variability of permeability and to correlate these changes with salt movement, porosity change, potential rock deterioration and textural characteristics. Statistical analyses of small-scale permeability measurements are used to evaluate the drivers for decay and hence aid the prediction of the weathering behaviour of the two limestones.

Screens, Closets, and Echo-Chambers of the Mind: The Struggle to Represent the Inner Life on Stage

Screens, Closets, and Echo-Chambers of the Mind: The Struggle to Represent the Inner Life on Stage

The early-stage risk capital market in Scotland since 2000: issues of scale, characteristics and market efficiency

In this paper we provide a detailed profile and analysis of the regional risk capital market in Scotland, using an innovative methodology and specially developed databases which cover risk capital investment in young companies in the periods 2000–04 and 2005–07. This identifies the investment activity of all actors in the market and provides estimates of the total flow of risk capital investment into early-stage Scottish companies over the period. The paper concludes by drawing out the implications for policy makers (providing a more robust evidence base for the development, implementation and monitoring of policy) and for academic researchers (on the methodologies for estimating market scale and efficiency).

Locally regularised two-stage learning algorithm for RBF network centre selection

Nonlinear models constructed from radial basis function (RBF) networks can easily be over-fitted due to the noise on the data. While information criteria, such as the final prediction error (FPE), can provide a trade-off between training error and network complexity, the tunable parameters that penalise a large size of network model are hard to determine and are usually network dependent. This article introduces a new locally regularised, two-stage stepwise construction algorithm for RBF networks. The main objective is to produce a parsomous network that generalises well over unseen data. This is achieved by utilising Bayesian learning within a two-stage stepwise construction procedure to penalise centres that are mainly interpreted by the noise.

Gene Expression Meta-Analysis Identifies VDAC1 as a Predictor of Poor Outcome in Early Stage Non-Small Cell Lung Cancer

Background: The bioenergetic status of non-small cell lung cancer correlates with tumour aggressiveness. The voltage dependent anion channel type 1 (VDAC1) is a component of the mitochondrial permeability transition pore, regulates mitochondrial ATP/ADP exchange suggesting that its over-expression could be associated with energy dependent processes including increased proliferation and invasiveness. To test this hypothesis, we conducted an in vivo gene-expression meta-analysis of surgically resected non-small cell lung cancer (NSCLC) using 602 individual expression profiles, to examine the impact of VDAC1 on survival.