Heterologous oligonucleotide microarrays for transcriptomics in a non-model species; a proof-of-concept study of drought stress in Musa

<p>Abstract</p> <p>Background</p> <p>'Systems-wide' approaches such as microarray RNA-profiling are ideally suited to the study of the complex overlapping responses of plants to biotic and abiotic stresses. However, commercial microarrays are only available for a limited number of plant species and development costs are so substantial as to be prohibitive for most research groups. Here we evaluate the use of cross-hybridisation to Affymetrix oligonucleotide GeneChip^®microarrays to profile the response of the banana (<it>Musa </it>spp.) leaf transcriptome to drought stress using a genomic DNA (gDNA)-based probe-selection strategy to improve the efficiency of detection of differentially expressed <it>Musa </it>transcripts.</p> <p>Results</p> <p>Following cross-hybridisation of <it>Musa </it>gDNA to the Rice GeneChip^®Genome Array, ~33,700 gene-specific probe-sets had a sufficiently high degree of homology to be retained for transcriptomic analyses. In a proof-of-concept approach, pooled RNA representing a single biological replicate of control and drought stressed leaves of the <it>Musa </it>cultivar 'Cachaco' were hybridised to the Affymetrix Rice Genome Array. A total of 2,910 <it>Musa </it>gene homologues with a >2-fold difference in expression levels were subsequently identified. These drought-responsive transcripts included many functional classes associated with plant biotic and abiotic stress responses, as well as a range of regulatory genes known to be involved in coordinating abiotic stress responses. This latter group included members of the ERF, DREB, MYB, bZIP and bHLH transcription factor families. Fifty-two of these drought-sensitive <it>Musa </it>transcripts were homologous to genes underlying QTLs for drought and cold tolerance in rice, including in 2 instances QTLs associated with a single underlying gene. The list of drought-responsive transcripts also included genes identified in publicly-available comparative transcriptomics experiments.</p> <p>Conclusion</p> <p>Our results demonstrate that despite the general paucity of nucleotide sequence data in <it>Musa </it>and only distant phylogenetic relations to rice, gDNA probe-based cross-hybridisation to the Rice GeneChip^®is a highly promising strategy to study complex biological responses and illustrates the potential of such strategies for gene discovery in non-model species.</p

Transhiatal vs extended transthoracic resection in oesophageal carcinoma: patients' utilities and treatment preferences

To assess patients' utilities for health state outcomes after transhiatal or transthoracic oesophagectomy for oesophageal cancer and to investigate the patients' treatment preferences for either procedure. The study group consisted of 48 patients who had undergone either transhiatal or transthoracic oesophagectomy. In an interview they were presented with eight possible health states following oesophagectomy. Visual Analogue Scale and standard gamble techniques were used to measure utilities. Treatment preference for either transhiatal or transthoracic oesophagectomy was assessed. Highest scores were found for the patients' own current health state (Visual Analogue Scale: 0.77; standard gamble: 0.97). Lowest scores were elicited for the health state ‘irresectable tumour’ (Visual Analogue Scale: 0.13; standard gamble: 0.34). The Visual Analogue Scale method produced lower estimates (P<0.001) than the standard gamble method for all health states. Most patient characteristics and clinical factors did not correlate with the utilities. Ninety-five per cent of patients who underwent a transthoracic procedure and 52% of patients who underwent a transhiatal resection would prefer the transthoracic treatment. No significant associations between any patient characteristics or clinical characteristics and treatment preference were found. Utilities after transhiatal or transthoracic oesophagectomy were robust because they generally did not vary by patient or clinical characteristics. Overall, most patients preferred the transthoracic procedure

Accurate SNP-calling with the Illumina Infinium 8K apple SNP-chip

Introduction: Recently an Illumina Infinium 8K apple SNP-chip was developed by the International RosBREED SNP Consortium for high-throughput genotyping and association studies (Chagne et al, 2012). We have used this SNP-chip to genotype 144 individuals of a Malus x domestica germplasm collection consisting of old Belgian and commercial cultivars, as well as 128 individual progeny of a mapping population. Aims: The genotype data generated was used i) to evaluate the overall performance of the chip and the robustness of the SNP calling both within a group of related individuals, as well as across a wider germplasm and ii) to develop a set of filter parameters to allow accurate automatic calling of the correct SNP genotype. Results: Overall only 9% of the SNPs failed completely. However, when comparing the genotypes of cultivars common to two different datasets, it was clear that differences in population structure between the datasets strongly influences SNP-calling, due to difficulties in clustering fluorescent intensities into the different genotype classes. This in turn is due to the presence of homologous sequences that also hybridize to the chip probes used for the SNP genotyping. This leads to shifts in the observed fluorescence used for genotype calling (AA, AB, BB) and shifts in the allele frequencies depending on the number of homologous loci and the degree of sequence identity. In order to remove those SNPs that show differences between datasets, a bootstrap analysis was done and cut-off values for a range of quality parameters commonly used for filtering SNP-chip data, were established using the variability of the callings over the bootstrap populations. Secondly a visual inspection of the intensity clustering used to genotype each SNP was carried out. This showed that even after automatic filtering, some SNPs showed deviations from the expected distributions due to the presence of the paralogous sequences. The fluorescence plot of these SNPs showed shifted clusters, the presence of additional genotype groups in the plot or a combination of both making it often hard to determine the true genotypes for the different individuals. In order to remove SNPs for which the genotype calling was influenced by the presence of paralogous sequences in the genome, two additional parameters were introduced: one for the cluster position and one for the cluster width since the additional groups were combined into the existing clusters leading to wider clusters. Depending on the stringency of the applied cut-off values for the filter parameters, the number of SNPs that are retained varies between 2,000and 3,500 SNPs. With manual inspection, the proportion of SNPs that were considered to be accurately called rose from 45% without filtering to 85-90.6% depending on the stringency of the filter parameter

Street-level Bureaucrats’ Attitude toward Clients: A Study of Work Group Influence in the Dutch and Belgian Tax Administration.

Contains fulltext : 230145.pdf (publisher's version ) (Open Access

Tax officials’ image of taxpayers and rule-bending behaviours

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Cost-effectiveness, domestic favouritism and sustainability in public procurement: A comparative study of public preferences

Purpose – The purpose of this paper is to explore and explain public preferences for different public procurement practices. The paper looks into public support for cost-effectiveness, discriminatory procurement in favour of domestic suppliers, and sustainable procurement. Design/methodology/approach – This study uses Eurobarometer public opinion data on 26.836 EU citizens from 27 EU countries. Findings – This paper shows that EU citizens want public authorities to evaluate multiple aspects of any procurement offer in their public procurement decisions. It also found that, although cost-effectiveness and domestic favouritism are still important to EU citizens, citizens are most supportive of the objectives of sustainable procurement. Some associations between citizens’ procurement preferences and their social characteristics and political attitudes were found. Country of residence has the strongest association with citizens’ acceptance of the objectives of sustainable procurement. Research limitations/implications – The explanatory power of the models tested in this study is rather low, meaning that the predictors explain citizen procurement preferences only to a limited extent. Also, even though the data contain information on the procurement preferences of a large number of EU citizens, it is a topic of inquiry that is sensitive to social desirability bias. Originality/value – This paper contributes to the empirical understanding of public attitudes toward public procurement. It is one of few studies on citizen attitudes toward different public procurement practices.status: publishe

Cost-effectiveness, domestic favouritism and sustainability in public procurement: A comparative study of public preferences.

Item does not contain fulltex

Understanding street-level bureaucrats’ attitude towards clients: Towards a measurement instrument

Contains fulltext : 208317.pdf (publisher's version ) (Closed access) Contains fulltext : 208317pre.pdf (Author’s version preprint ) (Open Access)2 augustus 201830 p