Common Peptides Study of Aminoacyl-tRNA Synthetases

Aminoacyl tRNA synthetases (aaRSs) constitute an essential enzyme super-family, providing fidelity of the translation process of mRNA to proteins in living cells. They are common to all kingdoms and are of utmost importance to all organisms. It is thus of great interest to understand the evolutionary relationships among them and underline signature motifs defining their common domains.We utilized the Common Peptides (CPs) framework, based on extracted deterministic motifs from all aaRSs, to study family-specific properties. We identified novel aaRS–class related signatures that may supplement the current classification methods and provide a basis for identifying functional regions specific to each aaRS class. We exploited the space spanned by the CPs in order to identify similarities between aaRS families that are not observed using sequence alignment methods, identifying different inter-aaRS associations across different kingdom of life. We explored the evolutionary history of the aaRS families and evolutionary origins of the mitochondrial aaRSs. Lastly, we showed that prevalent CPs significantly overlap known catalytic and binding sites, suggesting that they have meaningful functional roles, as well as identifying a motif shared between aaRSs and a the Biotin-[acetyl-CoA carboxylase] synthetase (birA) enzyme overlapping binding sites in both families.The study presents the multitude of ways to exploit the CP framework in order to extract meaningful patterns from the aaRS super-family. Specific CPs, discovered in this study, may play important roles in the functionality of these enzymes. We explored the evolutionary patterns in each aaRS family and tracked remote evolutionary links between these families

Gene fusion in Helicobacter pylori: Making the ends meet

10.1007/s10482-005-9021-2Antonie van Leeuwenhoek, International Journal of General and Molecular Microbiology891169-18

Diffusion‐to‐Imbibition Transition in Water Sorption in Nanoporous Media: Theoretical Studies

The ability to predict multiphase fluid transport in nanoporous rocks such as shales is critical for many geoscience applications, for example unconventional hydrocarbon production, geologic carbon sequestration, and nuclear waste disposal. When the pore sizes approach nanoscales, the impact of the molecular interaction forces between fluids and solids becomes increasingly important. These forces can alter macroscopic fluid phase behavior and control transport. Recent experimental studies have shown that capillary condensation and subsequent imbibition of liquid water can occur in hydrophilic nanoporous media even if the vapor phase is at a critical relative humidity (rhcrit) well below vapor saturation. This study presents a theoretical investigation of the processes controlling adsorption, capillary condensation and imbibition in nanoporous media, using the square-gradient classical density functional theory. The proposed theoretical model explicitly includes the relevant interaction forces among fluids and solids in macroscopic porous media. Application of the model to a relative-humidity-controlled water adsorption experiment is presented to demonstrate the impact of water-pore wall attractive forces on multiphase water behavior in a hydrophilic silicon nanoporous medium. The model represents well the measured time-dependent evolution of the water imbibition front inside the nanoporous medium and also explains the diffusion-like water transport regimes observed at rh < rhcrit and the imbibition-like flow regimes observed at rh > rhcrit. The study furthermore gives an insight on hysteresis phenomenon in adsorption and desorption isotherms