Analysis of probe level patterns in Affymetrix microarray data

<p>Abstract</p> <p>Background</p> <p>Microarrays have been used extensively to analyze the expression profiles for thousands of genes in parallel. Most of the widely used methods for analyzing Affymetrix Genechip microarray data, including RMA, GCRMA and Model Based Expression Index (MBEI), summarize probe signal intensity data to generate a single measure of expression for each transcript on the array. In contrast, other methods are applied directly to probe intensities, negating the need for a summarization step.</p> <p>Results</p> <p>In this study, we used the Affymetrix rat genome Genechip to explore variability in probe response patterns within transcripts. We considered a number of possible sources of variability in probe sets including probe location within the transcript, middle base pair of the probe sequence, probe overlap, sequence homology and affinity. Although affinity, middle base pair and probe location effects may be seen at the gross array level, these factors only account for a small proportion of the variation observed at the gene level. A BLAST search and the presence of probe by treatment interactions for selected differentially expressed genes showed high sequence homology for many probes to non-target genes.</p> <p>Conclusion</p> <p>We suggest that examination and modeling of probe level intensities can be used to guide researchers in refining their conclusions regarding differentially expressed genes. We discuss implications for probe sequence selection for confirmatory analysis using real time PCR.</p

A scaling theory of 3D spinodal turbulence

A new scaling theory for spinodal decomposition in the inertial hydrodynamic regime is presented. The scaling involves three relevant length scales, the domain size, the Taylor microscale and the Kolmogorov dissipation scale. This allows for the presence of an inertial "energy cascade", familiar from theories of turbulence, and improves on earlier scaling treatments based on a single length: these, it is shown, cannot be reconciled with energy conservation. The new theory reconciles the t^{2/3} scaling of the domain size, predicted by simple scaling, with the physical expectation of a saturating Reynolds number at late times.Comment: 5 pages, no figures, revised version submitted to Phys Rev E Rapp Comm. Minor changes and clarification

The Egyptian wheat cultivar Gemmeiza-12 is a source of resistance against the fungus <i>Zymoseptoria tritici</i>

Background: Wheat is one of the world’s most important cereal crops. However, the fungal pathogen Zymoseptoria tritici can cause disease epidemics, leading to reduced yields. With climate change and development of new agricultural areas with suitable environments, Z. tritici may advance into geographical areas previously unaffected by this pathogen. It is currently unknown how Egyptian wheat will perform in the face of this incoming threat. This project aimed to assess the resistance of Egyptian wheat germplasm to Z. tritici, to identify cultivars with high levels of resistance and characterise the mechanism(s) of resistance present in these cultivars. Results: Eighteen Egyptian wheat cultivars were screened against two Z. tritici model isolates and exhibited a wide spectrum of responses. This ranged from resistance to complete susceptibility to one or both isolates tested. The most highly resistant cultivars from the initial screen were then tested under two environmental conditions against modern UK field isolates. Disease levels under UK-like conditions were higher, however, symptom development on the cultivar Gemmeiza-12 was noticeably slower than on other Egyptian wheats. The robustness of the resistance shown by Gemmeiza-12 was confirmed in experiments mimicking Egyptian environmental conditions, where degree of Z. tritici infection was lower. The Kompetitive allele-specific PCR (KASP) diagnostic assay suggested the presence of an Stb6 resistant allele in several Egyptian wheats including Gemmeiza-12. Infection assays using the IPO323 WT and IPO323ΔAvrStb6 mutant confirmed the presence of Stb6 in several Egyptian cultivars including Gemmeiza-12. Confocal fluorescence microscopy demonstrated that growth of the IPO323 strain is blocked at the point of stomatal penetration on Gemmeiza-12, consistent with previous reports of Stb gene mediated resistance. In addition to this R-gene mediated resistance, IPO323 spores showed lower adherence to leaves of Gemmeiza-12 compared to UK wheat varieties, suggesting other aspects of leaf physiology may also contribute to the resistance phenotype of this cultivar. Conclusion: These results indicate that Gemmeiza-12 will be useful in future breeding programs where improved resistance to Z. tritici is a priority

Signatures of two-dimensionalisation of 3D turbulence in presence of rotation

A reason has been given for the inverse energy cascade in the two-dimensionalised rapidly rotating 3D incompressible turbulence. For such system, literature shows a possibility of the exponent of wavenumber in the energy spectrum's relation to lie between -2 and -3. We argue the existence of a more strict range of -2 to -7/3 for the exponent in the case of rapidly rotating turbulence which is in accordance with the recent experiments. Also, a rigorous derivation for the two point third order structure function has been provided helping one to argue that even with slow rotation one gets, though dominated, a spectrum with the exponent -2.87, thereby hinting at the initiation of the two-dimensionalisation effect with rotation.Comment: An extended and typos-corrected version of the earlier submissio

Scaling and energy transfer in rotating turbulence

The inertial-range properties of quasi-stationary hydrodynamic turbulence under solid-body rotation are studied via high-resolution direct numerical simulations. For strong rotation the nonlinear energy cascade exhibits depletion and a pronounced anisotropy with the energy flux proceeding mainly perpendicularly to the rotation axis. This corresponds to a transition towards a quasi-two-dimensional flow similar to a linear Taylor-Proudman state. In contrast to the energy spectrum along the rotation axis which does not scale self-similarly, the perpendicular spectrum displays an inertial range with $k^{-2}_\perp$-behavior. A new phenomenology gives a rationale for the observations. The scaling exponents $\zeta_p$ of structure functions up to order $p=8$ measured perpendicular to the rotation axis indicate reduced intermittency with increasing rotation rate. The proposed phenomenology is consistent with the inferred asymptotic non-intermittent behavior $\zeta_p=p/2$.Comment: to be published in Europhysics Letters (www.epletters.net), minor changes to match version in prin

In-Situ Monitoring of a Bismuth-Tin Alloy Solidification Using MEPHISTO

Experiments were carried out to study the morphological stability of Bi- 1 atomic % Sn alloys using the MEPHISTO directional solidification apparatus aboard Space Shuttle Columbia (STS-87, launched Nov. 19, 1997) and in ground-based studies. The Seebeck signal and temperature measurements indicate that convection was significant for ground-based studies. In the space-based experiments, interface breakdown was observed at growth velocities of 6.7, 27, and 40 microns/sec, but not at 1.8 and 3.3 microns/sec

On two-dimensionalization of three-dimensional turbulence in shell models

Applying a modified version of the Gledzer-Ohkitani-Yamada (GOY) shell model, the signatures of so-called two-dimensionalization effect of three-dimensional incompressible, homogeneous, isotropic fully developed unforced turbulence have been studied and reproduced. Within the framework of shell models we have obtained the following results: (i) progressive steepening of the energy spectrum with increased strength of the rotation, and, (ii) depletion in the energy flux of the forward forward cascade, sometimes leading to an inverse cascade. The presence of extended self-similarity and self-similar PDFs for longitudinal velocity differences are also presented for the rotating 3D turbulence case