Natural variation in abiotic stress responsive gene expression and local adaptation to climate in Arabidopsis thaliana.

Gene expression varies widely in natural populations, yet the proximate and ultimate causes of this variation are poorly known. Understanding how variation in gene expression affects abiotic stress tolerance, fitness, and adaptation is central to the field of evolutionary genetics. We tested the hypothesis that genes with natural genetic variation in their expression responses to abiotic stress are likely to be involved in local adaptation to climate in Arabidopsis thaliana. Specifically, we compared genes with consistent expression responses to environmental stress (expression stress responsive, "eSR") to genes with genetically variable responses to abiotic stress (expression genotype-by-environment interaction, "eGEI"). We found that on average genes that exhibited eGEI in response to drought or cold had greater polymorphism in promoter regions and stronger associations with climate than those of eSR genes or genomic controls. We also found that transcription factor binding sites known to respond to environmental stressors, especially abscisic acid responsive elements, showed significantly higher polymorphism in drought eGEI genes in comparison to eSR genes. By contrast, eSR genes tended to exhibit relatively greater pairwise haplotype sharing, lower promoter diversity, and fewer nonsynonymous polymorphisms, suggesting purifying selection or selective sweeps. Our results indicate that cis-regulatory evolution and genetic variation in stress responsive gene expression may be important mechanisms of local adaptation to climatic selective gradients

Ascorbic acid causes spuriously low blood glucose measurements

CITATION: Strijdom, J.G., Marais, B.J. & Koeslag, J.H. 1993. Ascorbic acid causes spuriously low blood glucose measurements. S Afr Med J, 83(1):64-65.The original publication is available at http://www.samj.org.za[No abstract available]Publisher’s versio

Homogeneous Open Quantum Random Walks on a lattice

We study Open Quantum Random Walks for which the underlying graph is a lattice, and the generators of the walk are translation-invariant. We consider the quantum trajectory associated with the OQRW, which is described by a position process and a state process. We obtain a central limit theorem and a large deviation principle for the position process, and an ergodic result for the state process. We study in detail the case of homogeneous OQRWs on a lattice, with internal space $h={\mathbb C}^2$

Sensitivity to grid resolution in the ability of a chemical transport model to simulate observed oxidant chemistry under high-isoprene conditions

Formation of ozone and organic aerosol in continental atmospheres depends on whether isoprene emitted by vegetation is oxidized by the high-NOx pathway (where peroxy radicals react with NO) or by low-NOx pathways (where peroxy radicals react by alternate channels, mostly with HO2). We used mixed layer observations from the SEAC4RS aircraft campaign over the Southeast US to test the ability of the GEOS-Chem chemical transport model at different grid resolutions (0.25°  ×  0.3125°, 2°  ×  2.5°, 4°  ×  5°) to simulate this chemistry under high-isoprene, variable-NOx conditions. Observations of isoprene and NOx over the Southeast US show a negative correlation, reflecting the spatial segregation of emissions; this negative correlation is captured in the model at 0.25°  ×  0.3125° resolution but not at coarser resolutions. As a result, less isoprene oxidation takes place by the high-NOx pathway in the model at 0.25°  ×  0.3125° resolution (54 %) than at coarser resolution (59 %). The cumulative probability distribution functions (CDFs) of NOx, isoprene, and ozone concentrations show little difference across model resolutions and good agreement with observations, while formaldehyde is overestimated at coarse resolution because excessive isoprene oxidation takes place by the high-NOx pathway with high formaldehyde yield. The good agreement of simulated and observed concentration variances implies that smaller-scale non-linearities (urban and power plant plumes) are not important on the regional scale. Correlations of simulated vs. observed concentrations do not improve with grid resolution because finer modes of variability are intrinsically more difficult to capture. Higher model resolution leads to decreased conversion of NOx to organic nitrates and increased conversion to nitric acid, with total reactive nitrogen oxides (NOy) changing little across model resolutions. Model concentrations in the lower free troposphere are also insensitive to grid resolution. The overall low sensitivity of modeled concentrations to grid resolution implies that coarse resolution is adequate when modeling continental boundary layer chemistry for global applications

Earthshine observation of vegetation and implication for life detection on other planets - A review of 2001 - 2006 works

The detection of exolife is one of the goals of very ambitious future space missions that aim to take direct images of Earth-like planets. While associations of simple molecules present in the planet's atmosphere ($O_2$, $O_3$, $CO_2$ etc.) have been identified as possible global biomarkers, we review here the detectability of a signature of life from the planet's surface, i.e. the green vegetation. The vegetation reflectance has indeed a specific spectrum, with a sharp edge around 700 nm, known as the "Vegetation Red Edge" (VRE). Moreover vegetation covers a large surface of emerged lands, from tropical evergreen forest to shrub tundra. Thus considering it as a potential global biomarker is relevant. Earthshine allows to observe the Earth as a distant planet, i.e. without spatial resolution. Since 2001, Earthshine observations have been used by several authors to test and quantify the detectability of the VRE in the Earth spectrum. The egetation spectral signature is detected as a small 'positive shift' of a few percents above the continuum, starting at 700 nm. This signature appears in most spectra, and its strength is correlated with the Earth's phase (visible land versus visible ocean). The observations show that detecting the VRE on Earth requires a photometric relative accuracy of 1% or better. Detecting something equivalent on an Earth-like planet will therefore remain challenging, moreover considering the possibility of mineral artifacts and the question of 'red edge' universality in the Universe.Comment: Invited talk in "Strategies for Life Detection" (ISSI Bern, 24-28 April 2006) to appear in a hardcopy volume of the ISSI Space Science Series, Eds, J. Bada et al., and also in an issue of Space Science Reviews. 13 pages, 8 figures, 1 tabl

Critical Values for Yen’s Q3: Identification of Local Dependence in the Rasch model using Residual Correlations

The assumption of local independence is central to all IRT models. Violations can lead to inflated estimates of reliability and problems with construct validity. For the most widely used fit statistic Q3 there are currently no well-documented suggestions of the critical values which should be used to indicate local dependence, and for this reason a variety of arbitrary rules of thumb are used. In this study, we used an empirical data example and Monte Carlo simulation to investigate the different factors that can influence the null distribution of residual correlations, with the objective of proposing guidelines that researchers and practitioners can follow when making decisions about local dependence during scale development and validation. We propose that a parametric bootstrapping procedure should be implemented in each separate situation in order to obtain the critical value of local dependence applicable to the data set, and provide example critical values for a number of data structure situations. The results show that for the Q3 fit statistic no single critical value is appropriate for all situations, as the percentiles in the empirical null distribution are influenced by the number of items, the sample size, and the number of response categories. Furthermore, our results show that local dependence should be considered relative to the average observed residual correlation, rather than to a uniform value, as this results in more stable percentiles for the null distribution of an adjusted fit statistic

Clustered bottlenecks in mRNA translation and protein synthesis

We construct an algorithm that generates large, band-diagonal transition matrices for a totally asymmetric exclusion process (TASEP) with local hopping rate inhomogeneities. The matrices are diagonalized numerically to find steady-state currents of TASEPs with local variations in hopping rate. The results are then used to investigate clustering of slow codons along mRNA. Ribosome density profiles near neighboring clusters of slow codons interact, enhancing suppression of ribosome throughput when such bottlenecks are closely spaced. Increasing the slow codon cluster size, beyond $\approx 3-4$, does not significantly reduce ribosome current. Our results are verified by extensive Monte-Carlo simulations and provide a biologically-motivated explanation for the experimentally-observed clustering of low-usage codons