Protein interactions in Xenopus germ plasm RNP particles

Hermes is an RNA-binding protein that we have previously reported to be found in the ribonucleoprotein (RNP) particles of Xenopus germ plasm, where it is associated with various RNAs, including that encoding the germ line determinant Nanos1. To further define the composition of these RNPs, we performed a screen for Hermes-binding partners using the yeast two-hybrid system. We have identified and validated four proteins that interact with Hermes in germ plasm: two isoforms of Xvelo1 (a homologue of zebrafish Bucky ball) and Rbm24b and Rbm42b, both RNA-binding proteins containing the RRM motif. GFP-Xvelo fusion proteins and their endogenous counterparts, identified with antisera, were found to localize with Hermes in the germ plasm particles of large oocytes and eggs. Only the larger Xvelo isoform was naturally found in the Balbiani body of previtellogenic oocytes. Bimolecular fluorescence complementation (BiFC) experiments confirmed that Hermes and the Xvelo variants interact in germ plasm, as do Rbm24b and 42b. Depletion of the shorter Xvelo variant with antisense oligonucleotides caused a decrease in the size of germ plasm aggregates and loosening of associated mitochondria from these structures. This suggests that the short Xvelo variant, or less likely its RNA, has a role in organizing and maintaining the integrity of germ plasm in Xenopus oocytes. While GFP fusion proteins for Rbm24b and 42b did not localize into germ plasm as specifically as Hermes or Xvelo, BiFC analysis indicated that both interact with Hermes in germ plasm RNPs. They are very stable in the face of RNA depletion, but additive effects of combinations of antisense oligos suggest they may have a role in germ plasm structure and may influence the ability of Hermes protein to effectively enter RNP particles

Bubbles and jackets: new scaling bounds in topological group field theories

We use a reformulation of topological group field theories in 3 and 4 dimensions in terms of variables associated to vertices, in 3d, and edges, in 4d, to obtain new scaling bounds for their Feynman amplitudes. In both 3 and 4 dimensions, we obtain a bubble bound proving the suppression of singular topologies with respect to the first terms in the perturbative expansion (in the cut-off). We also prove a new, stronger jacket bound than the one currently available in the literature. We expect these results to be relevant for other tensorial field theories of this type, as well as for group field theory models for 4d quantum gravity.Comment: v2: Minor modifications to match published versio

Computational identification of condition-specific miRNA targets based on gene expression profiles and sequence information

<p>Abstract</p> <p>Background</p> <p>MicroRNAs (miRNAs) are small and noncoding RNAs that play important roles in various biological processes. They regulate target mRNAs post-transcriptionally through complementary base pairing. Since the changes of miRNAs affect the expression of target genes, the expression levels of target genes in specific biological processes could be different from those of non-target genes. Here we demonstrate that gene expression profiles contain useful information in separating miRNA targets from non-targets.</p> <p>Results</p> <p>The gene expression profiles related to various developmental processes and stresses, as well as the sequences of miRNAs and mRNAs in <it>Arabidopsis</it>, were used to determine whether a given gene is a miRNA target. It is based on the model combining the support vector machine (SVM) classifier and the scoring method based on complementary base pairing between miRNAs and mRNAs. The proposed model yielded low false positive rate and retrieved condition-specific candidate targets through a genome-wide screening.</p> <p>Conclusion</p> <p>Our approach provides a novel framework into screening target genes by considering the gene regulation of miRNAs. It can be broadly applied to identify condition-specific targets computationally by embedding information of gene expression profiles.</p

Use of a Generalized Additive Model to Investigate Key Abiotic Factors Affecting Microcystin Cellular Quotas in Heavy Bloom Areas of Lake Taihu

Lake Taihu is the third largest freshwater lake in China and is suffering from serious cyanobacterial blooms with the associated drinking water contamination by microcystin (MC) for millions of citizens. So far, most studies on MCs have been limited to two small bays, while systematic research on the whole lake is lacking. To explain the variations in MC concentrations during cyanobacterial bloom, a large-scale survey at 30 sites across the lake was conducted monthly in 2008. The health risks of MC exposure were high, especially in the northern area. Both Microcystis abundance and MC cellular quotas presented positive correlations with MC concentration in the bloom seasons, suggesting that the toxic risks during Microcystis proliferations were affected by variations in both Microcystis density and MC production per Microcystis cell. Use of a powerful predictive modeling tool named generalized additive model (GAM) helped visualize significant effects of abiotic factors related to carbon fixation and proliferation of Microcystis (conductivity, dissolved inorganic carbon (DIC), water temperature and pH) on MC cellular quotas from recruitment period of Microcystis to the bloom seasons, suggesting the possible use of these factors, in addition to Microcystis abundance, as warning signs to predict toxic events in the future. The interesting relationship between macrophytes and MC cellular quotas of Microcystis (i.e., high MC cellular quotas in the presence of macrophytes) needs further investigation

Influences of organic loading disturbances on the performance of anaerobic filter process to treat purified terephthalic acid wastewater

A lab-scale anaerobic filter process was operated for the treatment of purified terephthalic acid (PTA) wastewater, and the influences of organic loading disturbances on the process performance were investigated. After about 15 month operation, the COD removal efficiency was maintained at 79% under the volumetric loading rate of 5.05 kg-COD/m(3)/d and the hydraulic retention time (HRT) of 50 h. Interestingly, this performance Could be further enhanced over 85% by applying a step-increase/decrease of the HRT, which was mainly due to the increased p-toluate degradation. In the shock loading tests of four major pollutants (benzoate, acetate, terephthalate and p-toluate), it was found that the overall process performance was adversely affected by all the shock loadings, indicating that the syntrophic microbial consortium involved in the PTA wastewater treatment is highly sensitive to the organic loading disturbances. The complex inhibition effects of the benzoate and acetate on the terephthalate and p-toluate degradations were mainly responsible for this sensitivity. (c) 2008 Elsevier Ltd. All rights reservedX1139sciescopu

Intracellular Calcium and the Mechanism of Anodal Supernormal Excitability in Langendorff Perfused Rabbit Ventricles.

In pres