The genetic code is redundant as amino acids are encoded by synonymous codons that are unequally used.This codon usage bias (CUB) affects gene expression and cellular functions yet the underlying mechanisms have not been elucidated. We used a sequence-specific, stoichiometric model of metabolism and macromolecular synthesis for Escherichia coli K12 MG1655 to test the effect of randomly changed ...

INTRODUCTION Pseudomonas aeruginosa is a Gram-negative bacterium that considered as important opportunistic human pathogen. One of the mechanisms that help bacteria to tolerate survival in adverse conditions and resistance to antibiotics is biofilm formation through quorum sensing (QS) signals and toxin-antitoxin (TA) systems. QS and TA are two systems that have important roles in biofilm forma...

VapBC toxin-antitoxin (TA) systems are defined by the association of a PIN-domain toxin with a DNA-binding antitoxin, and are thought to play important physiological roles in bacteria and archaea. Recently, the PIN-associated gene pair PIN-COG2442 was proposed to encode VapBC-family TA system and found to be abundant in cyanobacteria. However, the features of these predicted TA loci remain unde...

This paper gives a p-adic analogue of the Mackey theory, which relates representations of a group of type G = H×tA to systems of imprimitivity.

Expression of bacterial type II toxin-antitoxin (TA) systems is regulated at the transcriptional level through direct binding of the antitoxin to pseudo-palindromic sequences on operator DNA. In this context, the toxin functions as a co-repressor by stimulating DNA binding through direct interaction with the antitoxin. Here, we determine crystal structures of the complete 90 kDa heterooctameric...

Bacterial toxin-antitoxin (TA) systems regulate key cellular processes to promote cell survival during periods of stress. During steady-state cell growth, antitoxins typically interact with their cognate toxins to inhibit activity presumably by preventing substrate recognition. We solved two x-ray crystal structures of the Proteus vulgaris tetrameric HigB-(HigA)2-HigB TA complex and found that,...

This paper presents a case study of the experience of a technical architecture team, the TA-CE Team, when developing an architectural design description (ADD) for an IT system focused on the communications engineering views of the technology viewpoint. The project charter and requirements for the assignments of the TA-CE Team project are based on a real-world initiative to improve electronic co...

The modelling and analysis of multi-component discrete event systems is a challenging research area. Over 30 years, modelling and simulation research of discrete event system specification (DEVS) has been developed with (1) dense-time, (2) the I/O concept, and (3) hierarchical model construction. Nevertheless, DEVS model verification research began relatively recently considering the whole DEVS...

Research on optimization of timed systems, as e.g. for computing optimal schedules of manufacturing processes, has lead to approaches that mainly fall into the following two categories: On one side, mixed integer programming (MIP) techniques have been developed to successfully solve scheduling problems of moderate to medium size. On the other side, reachability algorithms extended by the evalua...