Transposon variants and their effects on gene expression in arabidopsis

Transposable elements (TEs) make up the majority of many plant genomes. Their transcription and transposition is controlled through siRNAs and epigenetic marks including DNA methylation. To dissect the interplay of siRNA–mediated regulation and TE evolution, and to examine how TE differences affect nearby gene expression, we investigated genome-wide differences in TEs, siRNAs, and gene expression among three Arabidopsis thaliana accessions. Both TE sequence polymorphisms and presence of linked TEs are positively correlated with intraspecific variation in gene expression. The expression of genes within 2 kb of conserved TEs is more stable than that of genes next to variant TEs harboring sequence polymorphisms. Polymorphism levels of TEs and closely linked adjacent genes are positively correlated as well. We also investigated the distribution of 24-nt-long siRNAs, which mediate TE repression. TEs targeted by uniquely mapping siRNAs are on average farther from coding genes, apparently because they more strongly suppress expression of adjacent genes. Furthermore, siRNAs, and especially uniquely mapping siRNAs, are enriched in TE regions missing in other accessions. Thus, targeting by uniquely mapping siRNAs appears to promote sequence deletions in TEs. Overall, our work indicates that siRNA–targeting of TEs may influence removal of sequences from the genome and hence evolution of gene expression in plants

Measurement of the Proton and Deuteron Spin Structure Functions g2 and Asymmetry A2

We have measured the spin structure functions g2p and g2d and the virtual photon asymmetries A2p and A2d over the kinematic range 0.02 < x < 0.8 and 1.0 < Q^2 < 30(GeV/c)^2 by scattering 38.8 GeV longitudinally polarized electrons from transversely polarized NH3 and 6LiD targets.The absolute value of A2 is significantly smaller than the sqrt{R} positivity limit over the measured range, while g2 is consistent with the twist-2 Wandzura-Wilczek calculation. We obtain results for the twist-3 reduced matrix elements d2p, d2d and d2n. The Burkhardt-Cottingham sum rule integral - int(g2(x)dx) is reported for the range 0.02 < x < 0.8.Comment: 12 pages, 4 figures, 1 tabl

Neutral weak currents in pion electroproduction on the nucleon

Parity violating asymmetry in inclusive scattering of longitudinally polarized electrons by unpolarized protons with $\pi^0$ or $\pi^+$ meson production, is calculated as a function of the momentum transfer squared $Q^2$ and the total energy $W$ of the $\pi N$-system. This asymmetry, which is induced by the interference of the one-photon exchange amplitude with the parity-odd part of the $Z^0$-exchange amplitude, is calculated for the $\gamma^*(Z^*)+p\to N+\pi$ processes ($\gamma^*$ is a virtual photon and $Z^*$ a virtual Z-boson) considering the $\Delta$-contribution in the $s-$channel, the standard Born contributions and vector meson ($\rho$ and $\omega$) exchanges in the $t-$channel. Taking into account the known isotopic properties of the hadron electromagnetic and neutral currents, we show that the P-odd term is the sum of two contributions. The main term is model independent and it can be calculated exactly in terms of fundamental constants. It is found to be linear in $Q^2$. The second term is a relatively small correction which is determined by the isoscalar component of the electromagnetic current. Near threshold and in the $\Delta$-region, this isoscalar part is much smaller (in absolute value) than the isovector one: its contribution to the asymmetry depend on the polarization state (longitudinal or transverse) of the virtual photon.Comment: 30 pages 9 figure

The mutational dynamics of the Arabidopsis centromeres

Centromeres are specialized chromosome regions essential for sister chromatid cohesion and spindle attachment during mitosis. Many centromeres comprise highly variable, megabase-scale satellite DNA arrays, yet the mutation spectrum driving this variability remains poorly understood. Using replicated genome assemblies of six Arabidopsis mutation accumulation lines, we identified centromeric mutations consisting almost exclusively of point mutations and structure-preserving, in-frame indels spanning a few kilobases. Centromeric point mutations occurred at a ninefold higher rate (6.1×10-8/bp/gen) than in chromosome arms, frequently introduced by non-allelic gene conversions from closely linked repeat units. Forward-in-time simulations based on the observed mutation spectrum recapitulated the emergence of megabase-scale higher-order repeat (HOR) structures, including long-range sequence similarities, without requiring large-scale rearrangements, closely mirroring centromeric divergence among natural genomes. Our results show that centromere evolution is driven by a unique mutational spectrum, providing a quantitative framework to understand how small-scale mutations shape and maintain the large-scale architecture of centromeric DNA

Macroinvertebrate-based index of biotic integrity for protection of streams in west-central Mexico

The water and habitat quality of many streams in west-central Mexico are influenced by municipal and industrial effluent, as well as water diversion for irrigation, livestock, and deforestation. Restoration efforts have been hampered by a lack of clear standards against which to judge the degree and trend in environmental degradation. We describe the development and characteristics of a macroinvertebrate-based index of biotic integrity (IBI) designed to provide such standards. Eight metrics chosen a priori comprised the IBI: catch per unit effort, generic richness, % Ephemeroptera-Plecoptera-Trichoptera genera, % Chironomidae individuais, Hilsenhoff Biotic Index, % depositional individuais, % predator individuais, and % gatherer genera. Each metric distinguished sites with minimum or moderate human influence from sites with severe influence. The IBI was developed with data from 27 sites and validated with 6 others. Values from the development data set correlated well with the measures of human influence based on qualitative assessment of habitat and water quality (Pearson's r = 0.86). IBI values for 7 sites on Río Ayuquila corresponded with a documented longitudinal pattern of human influence and the existing fish-based IBI (Pearson's r = 0.87). This macroinvertebrate IBI shows promise for developing biological standards, facilitating long-term monitoring, and improving ecological integrity of streams in west-central Mexico

Macroinvertebrate-based index of biotic integrity for protection of streams in west-central Mexico

The water and habitat quality of many streams in west-central Mexico are influenced by municipal and industrial effluent, as well as water diversion for irrigation, livestock, and deforestation. Restoration efforts have been hampered by a lack of clear standards against which to judge the degree and trend in environmental degradation. We describe the development and characteristics of a macroinvertebrate-based index of biotic integrity (IBI) designed to provide such standards. Eight metrics chosen a priori comprised the IBI: catch per unit effort, generic richness, % Ephemeroptera-Plecoptera-Trichoptera genera, % Chironomidae individuais, Hilsenhoff Biotic Index, % depositional individuais, % predator individuais, and % gatherer genera. Each metric distinguished sites with minimum or moderate human influence from sites with severe influence. The IBI was developed with data from 27 sites and validated with 6 others. Values from the development data set correlated well with the measures of human influence based on qualitative assessment of habitat and water quality (Pearson's r = 0.86). IBI values for 7 sites on Río Ayuquila corresponded with a documented longitudinal pattern of human influence and the existing fish-based IBI (Pearson's r = 0.87). This macroinvertebrate IBI shows promise for developing biological standards, facilitating long-term monitoring, and improving ecological integrity of streams in west-central Mexico

A role for the F-box protein HAWAIIAN SKIRT in plant miRNA function

AbstractAs regulators of gene expression in multicellular organisms, microRNAs (miRNAs) are crucial for growth and development. While a plethora of factors involved in their biogenesis and action in Arabidopsis thaliana have been described, these processes and their fine-tuning are not fully understood in plants. Here, we used plants expressing an artificial miRNA target mimic (MIM) to screen for negative regulators of miR156 activity. We identified a new mutant allele of the F-box protein HAWAIIAN SKIRT (HWS; At3G61590), hws-5, as a suppressor of the MIM156-induced developmental and molecular phenotypes. In hws plants, levels of endogenous miRNAs are increased and their mRNA targets decreased. Plants constitutively expressing full-length HWS - but not a truncated version lacking the F-box domain - display morphological and molecular phenotypes resembling those of mutants defective in miRNA biogenesis and activity. In combination with such mutants, hws loses its delayed floral organ abscission (‘skirt’) phenotype, suggesting epistasis. Also, the overall hws transcriptome profile partially resembles well-known miRNA mutants hyl1-2 and se-3, indicating action in a common pathway. We thus propose HWS as a novel, F-box dependent regulator of miRNA biogenesis.Summary statementHAWAIIAN SKIRT is a regulator of Arabidopsis thaliana microRNA biogenesis and acts in an F-box-dependent manner.</jats:sec

Regulation of pri-miRNA processing by the hnRNP-like protein AtGRP7 in Arabidopsis

The hnRNP-like glycine-rich RNA-binding protein AtGRP7 regulates pre-mRNA splicing in Arabidopsis. Here we used small RNA-seq to show that AtGRP7 also affects the miRNA inventory. AtGRP7 overexpression caused a significant reduction in the level of 30 miRNAs and an increase for 14 miRNAs with a minimum log2 fold change of ±0.5. Overaccumulation of several pri-miRNAs including pri-miR398b, pri-miR398c, pri-miR172b, pri-miR159a and pri-miR390 at the expense of the mature miRNAs suggested that AtGRP7 affects pri-miRNA processing. Indeed, RNA immunoprecipitation revealed that AtGRP7 interacts with these pri-miRNAs in vivo. Mutation of an arginine in the RNA recognition motif abrogated in vivo binding and the effect on miRNA and pri-miRNA levels, indicating that AtGRP7 inhibits processing of these pri-miRNAs by direct binding. In contrast, pri-miRNAs of selected miRNAs that were elevated or not changed in response to high AtGRP7 levels were not bound in vivo. Reduced accumulation of miR390, an initiator of trans-acting small interfering RNA (ta-siRNA) formation, also led to lower TAS3 ta-siRNA levels and increased mRNA expression of the target AUXIN RESPONSE FACTOR4. Furthermore, AtGRP7 affected splicing of pri-miR172b and pri-miR162a. Thus, AtGRP7 is an hnRNP-like protein with a role in processing of pri-miRNAs in addition to its role in pre-mRNA splicing