G-spots cause incorrect expression measurement in Affymetrix microarrays

Abstract Background High Density Oligonucleotide arrays (HDONAs), such as the Affymetrix HG-U133A GeneChip, use sets of probes chosen to match specified genes, with the expectation that if a particular gene is highly expressed then all the probes in that gene's probe set will provide a consistent message signifying the gene's presence. However, probes that contain a G-spot (a sequence of four or more guanines) behave abnormally and it has been suggested that these probes are responding to some biochemical effect such as the formation of G-quadruplexes. Results We have tested this expectation by examining the correlation coefficients between pairs of probes using the data on thousands of arrays that are available in the NCBI Gene Expression Omnibus (GEO) repository. We confirm the finding that G-spot probes are poorly correlated with others in their probesets and reveal that, by contrast, they are highly correlated with one another. We demonstrate that the correlation is most marked when the G-spot is at the 5' end of the probe. Conclusion Since these G-spot probes generally show little correlation with the other members of their probesets they are not fit for purpose and their values should be excluded when calculating gene expression values. This has serious implications, since more than 40% of the probesets in the HG-U133A GeneChip contain at least one such probe. Future array designs should avoid these untrustworthy probes. </jats:sec

A Comparative Study of the Impact of G-Stack Probes on Various Affymetrix GeneChips of Mammalia

We have previously discovered that probes containing runs of four or more contiguous guanines are not reliable for measuring gene expression in the Human HG_U133A Affymetrix GeneChip data. These probes are not correlated with other members of their probe set, but they are correlated with each other. We now extend our analysis to different3′GeneChip designs of mouse, rat, and human. We find that, in all these chip designs, the G-stack probes (probes with a run of exactly four consecutive guanines) are correlated highly with each other, indicating that such probes are not reliable measures of gene expression in mammalian studies. Furthermore, there is no specific position of G-stack where the correlation is highest in all the chips. We also find that the latest designs of rat and mouse chips have significantly fewer G-stack probes compared to their predecessors, whereas there has not been a similar reduction in G-stack density across the changes in human chips. Moreover, we find significant changes in RMA values (after removing G-stack probes) as the number of G-stack probes increases.</jats:p

Projected expansion of Trichodesmium’s geographical distribution and increase of growth potential in response to climate change

Estimates of marine N₂ fixation range from 52 to 73 Tg N yr‾¹, of which we calculate up to 84% is from Trichodesmium based on previous measurements of nifH gene abundance and our new model of Trichodesmium growth. Here we assess the likely effects of four major climate change‐related abiotic factors on the spatiotemporal distribution and growth potential of Trichodesmium for the last glacial maximum (LGM), the present (2006‐2015) and the end of this century (2100) by mapping our model of Trichodesmium growth onto inferred global surface ocean fields of pCO₂, temperature, light and Fe. We conclude that growth rate was severely limited by low pCO₂ at the LGM, that current pCO₂ levels do not significantly limit Trichodesmium growth and thus, the potential for enhanced growth from future increases of CO₂ is small. We also found that the area of the ocean where sea surface temperatures (SST) are within Trichodesmium’s thermal niche increased by 32% from the LGM to present, but further increases in SST due to continued global warming will reduce this area by 9%. However, the range reduction at the equator is likely to be offset by enhanced growth associated with expansion of regions with optimal or near optimal Fe and light availability. Between now and 2100, the ocean area of optimal SST and irradiance is projected to increase by 7%, and the ocean area of optimal SST, irradiance and iron is projected to increase by 173%. Given the major contribution of this keystone species to annual N₂ fixation and thus pelagic ecology, biogeochemistry and CO₂ sequestration, the projected increase in the geographical range for optimal growth could provide a negative feedback to increasing atmospheric CO₂ concentrations

Profile of subjective quality of life and its correlates in a nation-wide sample of high school students in an Arab setting using the WHOQOL-Bref

<p>Abstract</p> <p>Background</p> <p>The upsurge of interest in the quality of life (QOL) of children is in line with the 1989 Convention on the Rights of the Child, which stressed the child's right to adequate circumstances for physical, mental, and social development. The study's objectives were to: (i) highlight how satisfied Kuwaiti high school students were with life circumstances as in the WHOQOL-Bref; (ii) assess the prevalence of at risk status for impaired QOL and establish the QOL domain normative values; and (iii) examine the relationship of QOL with personal, parental, and socio-environmental factors.</p> <p>Method</p> <p>A nation-wide sample of students in senior classes in government high schools (N = 4467, 48.6% boys; aged 14-23 years) completed questionnaires that included the WHOQOL-Bref.</p> <p>Results</p> <p>Using Cummins' norm of 70% - 80%, we found that, as a group, they barely achieved the well-being threshold score for physical health (70%), social relations (72.8%), environment (70.8%) and general facet (70.2%), but not for psychological health (61.9%). These scores were lower than those reported from other countries. Using the recommended cut-off of <1<it>SD </it>of population mean, the prevalence of at risk status for impaired QOL was 12.9% - 18.8% (population age-adjusted: 15.9% - 21.1%). In all domains, boys had significantly higher QOL than girls, mediated by anxiety/depression; while the younger ones had significantly higher QOL (<it>p </it>< 0.001), mediated by difficulty with studies and social relations. Although poorer QOL was significantly associated with parental divorce and father's low socio-economic status, the most important predictors of poorer QOL were perception of poor emotional relationship between the parents, poor self-esteem and difficulty with studies.</p> <p>Conclusion</p> <p>Poorer QOL seemed to reflect a circumstance of social disadvantage and poor psychosocial well-being in which girls fared worse than boys. The findings indicate that programs that address parental harmony and school programs that promote study-friendly atmospheres could help to improve psychosocial well-being. The application of QOL as a school population health measure may facilitate risk assessment and the tracking of health status.</p

The Detection of Blur in Affymetrix GeneChips

High correlations were obtained between probes in seemingly unrelated probe sets, following an examination of the data from thousands of Affymetrix GeneChips. Investigation revealed that these unexpected correlations were between probes that were adjacent to high-valued probes. Using carefully selected probes, together with simple linear models, the extent of blur has been measured for each CEL file. The cause is shown to be attributable to poorly performing scanners. Blur can result in the doubling of the values of thousands of probes. This in turn can lead to the doubling of the expression level for hundreds of probe sets. Copyright © 2010 Berkeley Electronic Press

Reducing Spatial Flaws in Oligonucleotide Arrays by Using Neighborhood Information

We address the problem of detection and correction of spatial flaws in oligonucleotide microarrays. We present two similar procedures, of which one is intended solely for use with replicates and the other has wider applicability. By constructing a set of replicates, with one realistically flawed, we are able to examine the extent to which our procedures are capable of repairing the flaw. We find that, for this purpose, our procedures are superior to the existing 'Harshlight' procedure. Copyright ©2008 The Berkeley Electronic Press. All rights reserved

One motif to bind them: A small-XXX-small motif affects transmembrane domain 1 oligomerization, function, localization, and cross-talk between two yeast GPCRs

G protein-coupled receptors (GPCRs) are the largest family of cell-surface receptors in mammals and facilitate a range of physiological responses triggered by a variety of ligands. GPCRs were thought to function as monomers, however it is now accepted that GPCR homo- and hetero-oligomers also exist and influence receptor properties. The Schizosaccharomyces pombe GPCR Mam2 is a pheromone-sensing receptor involved in mating and has previously been shown to form oligomers in vivo. The first transmembrane domain (TMD) of Mam2 contains a small-XXX-small motif, overrepresented in membrane proteins andwell-known for promoting helix-helix interactions. An ortholog of Mam2 in Saccharomyces cerevisiae, Ste2, contains an analogous small-XXX-small motif which has been shown to contribute to receptor homo-oligomerization, localization and function. Here we have used experimental and computational techniques to characterize the role of the small-XXX-small motif in function and assembly of Mam2 for the first time. We find that disruption of the motif via mutagenesis leads to reduction of Mam2 TMD1 homo-oligomerization and pheromone-responsive cellular signaling of the fulllength protein. It also impairs correct targeting to the plasma membrane. Mutation of the analogous motif in Ste2 yielded similar results, suggesting a conservedmechanismfor assembly. Using co-expression of the two fungal receptors in conjunction with computational models, we demonstrate a functional change in G protein specificity and propose that this is brought about through hetero-dimeric interactions of Mam2 with Ste2 via the complementary small-XXX-small motifs. This highlights the potential of these motifs to affect a range of properties that can be investigated in other GPCRs

Identifying the impact of G-Quadruplexes on Affymetrix exon arrays using cloud computing

Memon FN, Sanchez Graillet O, Upton GJG, Owen AM, Harrison AP. Identifying the impact of G-Quadruplexes on Affymetrix exon arrays using cloud computing. In: CIB'2009. Proceedings. 2009: 50-60

Identifying the impact of G-Quadruplexes on Affymetrix exon arrays using cloud computing

Memon FN, Sanchez Graillet O, Upton GJG, Owen AM, Harrison AP. Identifying the impact of G-Quadruplexes on Affymetrix exon arrays using cloud computing. In: CIB'2009. Proceedings. 2009: 50-60