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Cross-species hybridisation of pig RNA to human nylon microarrays
DE Moody, Z Zou, L McIntyre
BMC Genomics , 2002, DOI: 10.1186/1471-2164-3-27
Abstract: Reproducibility of microarray hybridisations of pig cDNA to human microarrays was high, as determined by Spearman and Pearson correlation coefficients and a Kappa statistic. Variability among replicate hybridisations was similar for human and pig data, indicating the reproducibility of results were not compromised in cross-species hybridisations. The concordance between data generated from hybridisations using pig and human skeletal muscle RNA was high, further supporting the use of human microarrays for the analysis of gene expression in the pig. No systematic effect of stripping and re-using nylon microarrays was found, and variability across microarrays was minimal.The majority of genes generated highly reproducible data in cross-species microarray hybridisations, although approximately 6% were identified as highly variable. Experimental designs that include at least three replicate hybridisations for each experimental treatment will enable the variability of individual genes to be considered appropriately. The use of cross-species microarray analysis looks promising. However, additional validation is needed to determine the specificity of cross-species hybridisations, and the validity of results.One approach for identifying novel genes associated with physiological pathways is to identify genes whose expression changes with differences in experimental treatment or phenotype. This approach has been implemented using several different techniques, including the use of cDNA microarrays to quantitate and evaluate the expression of thousands of genes simultaneously [1]. Various types of microarrays have been utilized to study a wide range of biological models (for example, [2-4]. To date, examples of experiments using microarrays to evaluate changes in gene expression in mammalian species other than humans and rodent species are lacking, primarily due to the limited availability of arrays. Although resources are being developed that will facilitate production of micro
Cross-species hybridisation of human and bovine orthologous genes on high density cDNA microarrays
James Adjaye, Ralf Herwig, Doris Herrmann, Wasco Wruck, Alia BenKahla, Thore C Brink, Monika Nowak, Joseph W Carnwath, Claus Hultschig, Heiner Niemann, Hans Lehrach
BMC Genomics , 2004, DOI: 10.1186/1471-2164-5-83
Abstract: As a proof of principle, total RNA derived from human and bovine fetal brains was used as a source of labelled targets for hybridisation onto a human cDNA microarray composed of 349 characterised genes. Each gene was spotted 20 times representing 6,980 data points thus enabling highly reproducible spot quantification. Employing high stringency hybridisation and washing conditions, followed by data analysis, revealed slight differences in the expression levels and reproducibility of the signals between the two species. We also assigned each of the genes into three expression level categories- i.e. high, medium and low. The correlation co-efficient of cross hybridisation between the orthologous genes was 0.94. Verification of the array data by semi-quantitative RT-PCR using common primer sequences enabled co-amplification of both human and bovine transcripts. Finally, we were able to assign gene names to previously uncharacterised bovine ESTs.Results of our study demonstrate the harnessing and utilisation power of comparative genomics and prove the feasibility of using human microarrays to facilitate the identification of co-expressed orthologous genes in common tissues derived from different species.Microarrays are routinely used for large scale transcriptome analyses and have been widely and successfully employed for simultaneously monitoring the expression of a potentially unlimited number of genes in parallel, thus providing the basis for identifying genes differentially expressed in distinct cell-types, developmental stages, disease states and cells subjected to exogenous reagents [1]. The rapid and significant improvements of cDNA-chip technologies and the availability of multi-species gene catalogues within the various data bases have made possible the comparison of gene expression levels within a single mammalian organism and across different organisms on a large-scale.The advantages of cross-species hybridisation are two-fold. First, cross-species gene-expres
In situ analysis of cross-hybridisation on microarrays and the inference of expression correlation
Tineke Casneuf, Yves Van de Peer, Wolfgang Huber
BMC Bioinformatics , 2007, DOI: 10.1186/1471-2105-8-461
Abstract: We demonstrate a positive relation between off-target reporter alignment strength and expression correlation in data from oligonucleotide genechips. Furthermore, we describe a method that allows the identification, from their expression data, of individual probe sets affected by off-target hybridization.The effects of off-target hybridization on expression correlation coefficients can be substantial, and can be alleviated by more accurate mapping between microarray reporters and the target transcriptome. We recommend attention to the mapping for any microarray analysis of gene expression patterns.Microarrays are a valuable tool in functional genomics research. The breadth of their applications is reflected by the myriad of computational methods that have been developed for their analysis in the last decade. One popular practice is to compare expression patterns of genes by calculating correlation coefficients on expression level estimates across a set of conditions. Many downstream analysis tools are based on the presence or absence of correlation in the expression profiles of genes, like the inference of co-expression [1-5], gene regulatory [6] and Bayesian networks [7-10] and the study of gene family evolution [11,12]. From a biological point of view, these approaches are useful and informative, but here we show that if care has not been taken as to how these correlations are calculated and how the reporters for each transcript are selected, incorrect conclusions can be drawn.A gene is represented on a microarray by one or more reporters, i. e. nucleotide sequences that are designed to uniquely match its transcript, or transcripts if different splice variants exist [13]. Affymetrix GeneChips are the most widely used microarray platform, and a wealth of data measured on these arrays is publicly available. Affymetrix reporters are 25-mer oligonucleotides whose sequence is complementary to the intended target. Each target is represented by a set of reporters, called
The Hybridisation of Higher Education in Canada  [cached]
Douglas Shale
International Review of Research in Open and Distance Learning , 2002,
Abstract: Canada's postsecondary institutions are becoming increasingly involved with technology enhanced learning, generally under the rubric of distance education. Growth and activity in distance education stems from rapid developments in communication and information technologies such as videoconferencing and the Internet. This case study focuses on the use of new technologies, primarily within the context of higher education institutions operating in Canada's English speaking provinces. Capitalising on the interactive capabilities of "new" learning technologies, some distance education providers are starting to behave more like conventional educational institutions in terms of forming study groups and student cohorts. Conversely, new telecommunications technologies are having a reverse impact on traditional classroom settings, and as a result conventional universities are beginning to establish administrative structures reflective of those used by distance education providers. When viewed in tandem, these trends reflect growing convergence between conventional and distance learning modes, leading to the hybridisation of higher education in Canada.
Adsorption models of hybridization and post-hybridisation behaviour on oligonucleotide microarrays  [PDF]
C. J. Burden,Y. Pittelkow,S. R. Wilson
Quantitative Biology , 2004, DOI: 10.1088/0953-8984/18/23/024
Abstract: Analysis of data from an Affymetrix Latin Square spike-in experiment indicates that measured fluorescence intensities of features on an oligonucleotide microarray are related to spike-in RNA target concentrations via a hyperbolic response function, generally identified as a Langmuir adsorption isotherm. Furthermore the asymptotic signal at high spike-in concentrations is almost invariably lower for a mismatch feature than for its partner perfect match feature. We survey a number of theoretical adsorption models of hybridization at the microarray surface and find that in general they are unable to explain the differing saturation responses of perfect and mismatch features. On the other hand, we find that a simple and consistent explanation can be found in a model in which equilibrium hybridization followed by partial dissociation of duplexes during the post-hybridization washing phase.
Understanding the physics of oligonucleotide microarrays: the Affymetrix spike-in data reanalysed  [PDF]
C. J. Burden
Quantitative Biology , 2007, DOI: 10.1088/1478-3975/5/1/016004
Abstract: The Affymetrix U95 and U133 Latin Square spike-in datasets are reanalysed, together with a dataset from a version of the U95 spike-in experiment without a complex non-specific background. The approach uses a physico-chemical model which includes the effects the specific and non-specific hybridisation and probe folding at the microarray surface, target folding and hybridisation in the bulk RNA target solution, and duplex dissociation during the post-hybridisatoin washing phase. The model predicts a three parameter hyperbolic response function that fits well with fluorescence intensity data from all three datasets. The importance of the various hybridisation and washing effects in determining each of the three parameters is examined, and some guidance is given as to how a practical algorithm for determining specific target concentrations might be developed.
Differential gene expression in recombinant Pichia pastoris analysed by heterologous DNA microarray hybridisation
Michael Sauer, Paola Branduardi, Brigitte Gasser, Minoska Valli, Michael Maurer, Danilo Porro, Diethard Mattanovich
Microbial Cell Factories , 2004, DOI: 10.1186/1475-2859-3-17
Abstract: We could show that it is possible to obtain new and valuable information about transcriptomic regulation in P. pastoris by probing S. cerevisiae DNA microarrays. The number of positive signals was about 66 % as compared to homologous S. cerevisiae hybridisation, and both the signal intensities and gene regulations correlated with high significance between data obtained from P. pastoris and S. cerevisiae samples. The differential gene expression patterns upon shift from glycerol to methanol as carbon source were investigated in more detail. Downregulation of TCA cycle genes and a decrease of genes related to ribonucleotide and ribosome synthesis were among the major effects identified.We could successfully demonstrate that heterologous microarray hybridisations allow deep insights into the transcriptomic regulation processes of P. pastoris. The observed downregulation of TCA cycle and ribosomal synthesis genes correlates to a significantly lower specific growth rate during the methanol feed phase.The methylotrophic yeast Pichia pastoris is well established as expression host for heterologous proteins (reviewed by [1] and [2]). However, despite the high technological impact of P. pastoris, the physiological and genetic information is still rather scarce. The genome sequence has not been published, and in fact less than 100 complete gene sequences have been deposited with GenBank by the time of writing. Consequently, as for most other non-model species, no DNA microarrays are being manufactured. Hence, one of the most powerful tools for the investigation of changes in expression patterns is not available for this yeast species.To circumvent this problem, heterologous hybridisation to commercially available DNA microarrays might be conceivable. In fact, the successful non-homologous probing to microarrays has been reported recently. These studies cover a wide variety of organisms, including bacteria [3], a yeast [4], but also plants [5] and metazoan organisms [6-9]. The
Acknowledgement to Reviewers of Microarrays in 2014  [PDF]
Microarrays Editorial Office
Microarrays , 2015, DOI: 10.3390/microarrays4010001
Abstract: The editors of Microarrays would like to express their sincere gratitude to the following reviewers for assessing manuscripts in 2014:[...]
Amyloid-Associated Nucleic Acid Hybridisation  [PDF]
Sebastian Braun,Christine Humphreys,Elizabeth Fraser,Andrea Brancale,Matthias Bochtler,Trevor C. Dale
PLOS ONE , 2012, DOI: 10.1371/journal.pone.0019125
Abstract: Nucleic acids promote amyloid formation in diseases including Alzheimer's and Creutzfeldt-Jakob disease. However, it remains unclear whether the close interactions between amyloid and nucleic acid allow nucleic acid secondary structure to play a role in modulating amyloid structure and function. Here we have used a simplified system of short basic peptides with alternating hydrophobic and hydrophilic amino acid residues to study nucleic acid - amyloid interactions. Employing biophysical techniques including X-ray fibre diffraction, circular dichroism spectroscopy and electron microscopy we show that the polymerized charges of nucleic acids concentrate and enhance the formation of amyloid from short basic peptides, many of which would not otherwise form fibres. In turn, the amyloid component binds nucleic acids and promotes their hybridisation at concentrations below their solution Kd, as shown by time-resolved FRET studies. The self-reinforcing interactions between peptides and nucleic acids lead to the formation of amyloid nucleic acid (ANA) fibres whose properties are distinct from their component polymers. In addition to their importance in disease and potential in engineering, ANA fibres formed from prebiotically-produced peptides and nucleic acids may have played a role in early evolution, constituting the first entities subject to Darwinian evolution.
Technological, mediatic and cultural hybridisation: Cultural mediations in the context of globalisation  [PDF]
Laan Mendes de Barros
Revista CIDOB d'Afers Internacionals , 2009,
Abstract: We live in a context of borders that are dissolving in many senses, of the convergence and hybridisation of technologies, mass media and cultures. The context is the resizing of practical time, of movements and links between the local and the global. In these times of interculturality, communication plays a very important role; not so much in its technological media dimension, but particularly in the dynamics of cultural mediations that are dividing off from mediatised relations. This article aims to reflect on the transformations in present-day communication processes, marked by strong movements of hybridisation, as well as examining how to consider interculturality in the context of cultural mediations, based on dialogue between Latin American and French authors. Also, using media material, the article presents illustrations of the Brazilian cultural scene, which is marked by a long history of hybridisation that is filled with intercultural dynamics.
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