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

Affymetrix probes containing runs of contiguous guanines are not gene-specific

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 the designated probe set will provide a consistent message signifying the gene&#x27;s presence. However, we demonstrate by data mining thousands of CEL files from NCBI&#x27;s GEO database that 4G-probes (defined as probes containing sequences of four or more consecutive guanine (G) bases) do not react in the intended way. Rather, possibly due to the formation of G-quadruplexes, most 4G-probes are correlated, irrespective of the expression of the thousands of genes for which they were separately intended. It follows that 4G-probes should be ignored when calculating gene expression levels. Furthermore, future microarray designs should make no use of 4G-probes

Pyrimido[1,2-a]-purin-10(3H)-one, M(1)G, is less prone to artifact than base oxidation

Pyrimido[1,2-a]-purin-10(3H)-one (M(1)G) is a secondary DNA damage product arising from primary reactive oxygen species (ROS) damage to membrane lipids or deoxyribose. The present study investigated conditions that might lead to artifactual formation or loss of M(1)G during DNA isolation. The addition of antioxidants, DNA isolation at low temperature or non-phenol extraction methods had no statistically significant effect on the number of M(1)G adducts measured in either control or positive control tissue samples. The number of M(1)G adducts in nuclear DNA isolated from brain, liver, kidney, pancreas, lung and heart of control male rats were 0.8, 1.1, 1.1, 1.1, 1.8 and 4.2 M(1)G/10(8) nt, respectively. In rat liver tissue, the mitochondrial DNA contained a 2-fold greater number of M(1)G adducts compared with nuclear DNA. Overall, the results from this study demonstrated that measuring M(1)G is a reliable way to assess oxidative DNA damage because the number of M(1)G adducts is significantly affected by the amount of ROS production, but not by DNA isolation procedures. In addition, this study confirmed that the background number of M(1)G adducts reported in genomic DNA could have been overestimated by one to three orders of magnitude in previous reports

Evidence of hybrid institutional logics in the U.S. public research university

While the ascendancy of market behaviours in public research universities is well documented, the extent to which universities have transformed themselves into industry-like organisations has been called into question. So to what extent are universities displaying transformation in their core values? The concept of institutional logics, with its focus on the relationship between organisational design and underlying beliefs and values, shows potential to address this question. Yet study of institutional logics at the campus level has to date been limited. This paper presents an empirical analysis of three U.S. research universities’ organising principles as expressed in key mission and planning documents over a fifteen-year period. Of the multiple strategies at play in the universities’ responses to potentially competing values, the creation of new, hybrid logics is of particular interest. The concept of hybrid logics suggests a promising framework for understanding how universities can and do manage tensions in their mission

Large emergency-response exercises: qualitative characteristics - a survey

Exercises, drills, or simulations are widely used, by governments, agencies and commercial organizations, to simulate serious incidents and train staff how to respond to them. International cooperation has led to increasingly large-scale exercises, often involving hundreds or even thousands of participants in many locations. The difference between ‘large’ and ‘small’ exercises is more than one of size: (a) Large exercises are more ‘experiential’ and more likely to undermine any model of reality that single organizations may create; (b) they create a ‘play space’ in which organizations and individuals act out their own needs and identifications, and a ritual with strong social implications; (c) group-analytic psychotherapy suggests that the emotions aroused in a large group may be stronger and more difficult to control. Feelings are an unacknowledged major factor in the success or failure of exercises; (d) successful large exercises help improve the nature of trust between individuals and the organizations they represent, changing it from a situational trust to a personal trust; (e) it is more difficult to learn from large exercises or to apply the lessons identified; (f) however, large exercises can help develop organizations and individuals. Exercises (and simulation in general) need to be approached from a broader multidisciplinary direction if their full potential is to be realized

Giant Magnon Gap in Bilayer Iridate Sr3Ir2O7: Enhanced Pseudo-dipolar Interactions Near the Mott Transition

Using resonant inelastic x-ray scattering, we observe in the bilayer iridate Sr3Ir2O7, a spin-orbit coupling driven magnetic insulator with a small charge gap, a magnon gap of ~92 meV for both acoustic and optical branches. This exceptionally large magnon gap exceeds the total magnon bandwidth of ~70 meV and implies a marked departure from the Heisenberg model, in stark contrast to the case of the single-layer iridate Sr2IrO4. Analyzing the origin of these observations, we find that the giant magnon gap results from bond-directional pseudo-dipolar interactions that are strongly enhanced near the metal-insulator transition boundary. This suggests that novel magnetism, such as that inspired by the Kitaev model built on the pseudo-dipolar interactions, may emerge in small charge-gap iridates

Isospin Dynamics in Sr2IrO4 : Forging Links to Cuprate Superconductivity

We used resonant inelastic x-ray scattering to reveal the nature of magnetic interactions in Sr2IrO4, a 5d transition-metal oxide with a spin-orbit entangled ground state and Jeff=1/2 magnetic momemts, referred to as 'isospins'. The magnon dispersion in Sr2IrO4 is well described by an antiferromagnetic Heisenberg model with isospin one-half moments on a square lattice, which renders the low-energy effective physics of Sr2IrO4 much akin to that in superconducting cuprates. This is further supported by the observation of exciton modes in Sr2IrO4 whose dispersion is strongly renormalized by magnons, which can be understood by analogy to the hole propagation in the background of antiferromagnetically ordered spins in the cuprates