Genome-Scale Analysis of Translation Elongation with a Ribosome Flow Model

We describe the first large scale analysis of gene translation that is based on a model that takes into account the physical and dynamical nature of this process. The Ribosomal Flow Model (RFM) predicts fundamental features of the translation process, including translation rates, protein abundance levels, ribosomal densities and the relation between all these variables, better than alternative (‘non-physical’) approaches. In addition, we show that the RFM can be used for accurate inference of various other quantities including genes' initiation rates and translation costs. These quantities could not be inferred by previous predictors. We find that increasing the number of available ribosomes (or equivalently the initiation rate) increases the genomic translation rate and the mean ribosome density only up to a certain point, beyond which both saturate. Strikingly, assuming that the translation system is tuned to work at the pre-saturation point maximizes the predictive power of the model with respect to experimental data. This result suggests that in all organisms that were analyzed (from bacteria to Human), the global initiation rate is optimized to attain the pre-saturation point. The fact that similar results were not observed for heterologous genes indicates that this feature is under selection. Remarkably, the gap between the performance of the RFM and alternative predictors is strikingly large in the case of heterologous genes, testifying to the model's promising biotechnological value in predicting the abundance of heterologous proteins before expressing them in the desired host

Neighbor Overlap Is Enriched in the Yeast Interaction Network: Analysis and Implications

The yeast protein-protein interaction network has been shown to have distinct topological features such as a scale free degree distribution and a high level of clustering. Here we analyze an additional feature which is called Neighbor Overlap. This feature reflects the number of shared neighbors between a pair of proteins. We show that Neighbor Overlap is enriched in the yeast protein-protein interaction network compared with control networks carefully designed to match the characteristics of the yeast network in terms of degree distribution and clustering coefficient. Our analysis also reveals that pairs of proteins with high Neighbor Overlap have higher sequence similarity, more similar GO annotations and stronger genetic interactions than pairs with low ones. Finally, we demonstrate that pairs of proteins with redundant functions tend to have high Neighbor Overlap. We suggest that a combination of three mechanisms is the basis for this feature: The abundance of protein complexes, selection for backup of function, and the need to allow functional variation

Ceramic restoration repair: report of two cases

The esthetic and functional rehabilitation of patients with multiple missing teeth can be performed with several techniques and materials. Ceramic restorations provide reliable masticatory function and good esthetics. However, fracture can occur in some cases due to their brittle behavior. In some cases, the replacement of an extensive prosthesis is a problem due to the high treatment cost. In this paper, two cases are presented, in which fractures occurred in extensive metal-ceramic fixed partial dentures, and their replacement was not possible. Ceramic repair was chosen and the sequences of treatment with and without presence of the ceramic fragment are also discussed. The cases illustrate that, in some situations, fractured metal-ceramic partial dentures can be successfully repaired when prosthetic replacement is not a choice. Prosthodontists must use alternatives that allow a reliable repair to extensive metal-ceramic fixed partial dentures. Surface preparation of the ceramic with hydrofluoric acid in conjunction with a silane coupling agent is essential for a predictable bonding of composite resin. The repair performed with composite resin is an esthetic and functional alternative when extensive fixed partial dentures cannot be replaced