Binding specificities of human RNA-binding proteins toward structured and linear RNA sequences

RNA-binding proteins (RBPs) regulate RNA metabolism at multiple levels by affecting splicing of nascent transcripts, RNA folding, base modification, transport, localization, translation, and stability. Despite their central role in RNA function, the RNA-binding specificities of most RBPs remain unknown or incompletely defined. To address this, we have assembled a genome-scale collection of RBPs and their RNA-binding domains (RBDs) and assessed their specificities using high-through-put RNA-SELEX (HTR-SELEX). Approximately 70% of RBPs for which we obtained a motif bound to short linear sequenc-es, whereas similar to 30% preferred structured motifs folding into stem-loops. We also found that many RBPs can bind to multiple distinctly different motifs. Analysis of the matches of the motifs in human genomic sequences suggested novel roles for many RBPs. We found that three cytoplasmic proteins-ZC3H12A, ZC3H12B, and ZC3H12C-bound to motifs resembling the splice donor sequence, suggesting that these proteins are involved in degradation of cytoplasmic viral and/or unspliced transcripts. Structural analysis revealed that the RNA motif was not bound by the conventional C3H1 RNA-binding domain of ZC3H12B. Instead, the RNA motif was bound by the ZC3H12B's PilT N terminus (PIN) RNase domain, revealing a po-tential mechanism by which unconventional RBDs containing active sites or molecule-binding pockets could interact with short, structured RNA molecules. Our collection containing 145 high-resolution binding specificity models for 86 RBPs is the largest systematic resource for the analysis of human RBPs and will greatly facilitate future analysis of the various bi-ological roles of this important class of proteins.Peer reviewe

Kinetic Assessment and Therapeutic Modulation of Metabolic and Inflammatory Profiles in Mice on a High-Fat and Cholesterol Diet

The kinetics of metabolic and inflammatory parameters associated with obesity were evaluated in a murine diet-induced obesity (DIO) model using a diet high in fat and cholesterol. Cellular infiltration and mediator production were assessed and shown to be therapeutically modulated by the PPARgamma agonist rosiglitazone. C57BL/6 mice were maintained on a 45% fat/ 0.12% cholesterol (HF/CH) or Chow diet for 3, 6, 16, or 27 weeks. Flow cytometry was employed to monitor peripheral blood monocytes and adipose tissue macrophages (ATM). Gene expression and protein analysis methods were used to evaluate mediator production from total epididymal fat (EF), stromal vascular fraction (SVF), and sorted SVF cells. To investigate therapeutic intervention, mice were fed a HF/CH diet for 12 weeks and then a diet formulated with rosiglitazone (5 mg/kg) for an additional 6 weeks. A HF/CH diet correlated with obesity and a dramatic proinflammatory state. Therapeutic intervention with rosiglitazone attenuated the HF/CH induced inflammation. In addition, a novel population was found that expressed the highest levels of the pro-inflammatory mediators CCL2 and IL-6

The origin of polyploids via 2n gametes in Vaccinium section Cyanococcus

The production of 2n pollen (pollen with the sporophytic chromosome number) was evaluated in 4x and 6x taxa of Vaccinium section Cyanococcus . Mean frequencies of 2n pollen producers were 17.1% and 8.3% in natural 4x and 6x populations, respectively. The frequency of 2n pollen producers in the 4x species ranged from 8.6% ( V. angustifolium ) to 23.8% ( V. pallidum ). Level of 2n pollen production was genotypically variable (1% to 37.4%). The widespread occurrence of 2n pollen in 2x, 4x and 6x taxa suggests that sexual polyploidization was widespread and responsible for the origin of the polyploid species found in this genus. The frequency of 2n pollen producers was not significantly different between the 4x species and their putative 2x ancestors. These results support the origin of 4x and 6x taxa as a consequence of sexual polyploidization. Polyploids derived from sexual polyploidization would be expected to have increased fitness and flexibility due to the mode of 2n pollen formation. In blueberry species the predominant mode of 2n pollen formation is genetically equivalent to a first division restitution mechanism (FDR). FDR 2n pollen transmits a high percentage of the heterozygosity and a large fraction of the epistasis from the 2x parent to the 4x offspring.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/42736/1/10681_2004_Article_BF00039664.pd

Internet Based Loss-of-Mains Detection for Distributed Generation

The cleaning of heat exchanging units is of a major concern for steam power plant. It has been proposed by the plant authority to install an on-line cleaning system at Callide Power Station located near Biloela, Queensland, Australia, on the steam condensing electrical generation units. The condenser is fitted with a waterbox to distribute the cooling water internally throughout. The cleaning system may incorporate the cycling of sponge balls throughout the cooling water circuit of the condenser, which through their abrasive action remove fouling. To predict the potential effectiveness of this cleaning system, it is important to determine the distribution of balls, i.e. the distribution of fluid velocity throughout the condenser tube systems is uniform and even. A Computational Fluid Dynamics (CFD) model is developed in this study in order to simulate and evaluate the fluid velocity distribution inside the condenser waterbox. The simulation results are presented and discussed, so that plant authority can realize the implementation of this cleaning system

Occurrence of unreduced pollen in diploid blueberry species, Vaccinium sect. Cyanococcus

A total of 1475 individuals belonging to 43 natural populations of seven diploid (2x) blueberry species ( Vaccinium section Cyanococcus ) and two natural interspecific 2x hybrid populations were evaluated for unreduced pollen production. Significant differences were found in the frequency of unreduced pollen producers between species and within and between populations of the same species. Individuals with 1% or more unreduced pollen were considered unreduced pollen producers. The average frequency of unreduced pollen producers in these diploid species was 13.5%, ranging from 7.4% ( V. corymbosum ) to 18.4% ( V. darrowii ). The frequency of unreduced pollen grains in individual clones varied from <-1% to 28.6%. The production of unreduced pollen was not associated with male fertility. The widespread occurrence of unreduced pollen in the diploid species should allow the introgression of this germ plasm to the tetraploid level via unilateral sexual polyploidization.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/46010/1/122_2004_Article_BF00223844.pd

Outcomes of implant-based oral rehabilitation in head and neck oncology patients—a retrospective evaluation of a large, single regional service cohort

Abstract Background The study reports on implant survival outcomes in head and neck cancer patients who received implant-based oral rehabilitation in a regional service centre. Methods A retrospective analysis of implant survival outcomes in patients treated in a regional service from 2012 to 2017 was performed. The primary outcome measure was implant survival. The secondary outcome measure was to assess the effect of covariates associated with implant failure including bone type, radiotherapy, chemotherapy, gender and surgical implant complications. Kaplan-Meier survival curves were applied to compare differences in the survival rates of groups of variables. Cox proportional hazards models were applied to identify covariates associated with implant failure. p value was set at 0.05. Results The sample was composed of 167 head and neck cancer patients who had 779 dental implants placed. Implant survival estimates were calculated: 3 years, 95.7% [95%CI 94.3–97.2%] and 5 years, 95.5% [95%CI 93.9–97.0%], with a median follow-up of 38 months. Gender (p = 0.09), radiotherapy (p = 0.16) and chemotherapy (p = 0.17) did not significantly influence implant survival, whereas implant failure was higher in transported (reconstructed) bone sites in comparison with native bone (p < 0.01). Conclusion The result of this study suggests that overall implant survival as part of the routine oral rehabilitation is high in this patient cohort; however, implant failure was found to be statistically higher for implant placed into transported bone in comparison to native bone