Genetic evidence of a strong functional constraint of neurotrypsin during primate evolution

Neurotrypsin is one of the extra-cellular serine proteases that are predominantly expressed in the brain and involved in neuronal development and function. Mutations in humans are associated with autosomal recessive non-syndromic mental retardation (MR). We studied the molecular evolution of neurotrypsin by sequencing the coding region of neurotrypsin in 11 representative non-human primate species covering great apes, lesser apes, Old World monkeys and New World monkeys. Our results demonstrated a strong functional constraint of neurotrypsin that was caused by strong purifying selection during primate evolution, an implication of an essential functional role of neurotrypsin in primate cognition. Further analysis indicated that the purifying selection was in fact acting on the SRCR domains of neurotrypsin, which mediate the binding activity of neurotrypsin to cell surface or extracellular proteins. In addition, by comparing primates with three other mammalian orders, we demonstrated that the absence of the first copy of the SRCR domain (exon 2 and 3) in mouse and rat was due to the deletion of this segment in the murine lineage. Copyright (C) 2005 S. Karger AG, Basel.

Duplication and functional diversification of pancreatic ribonuclease (RNASE1) gene

Adaptation is one of the most fundamental issues in the studies of organismal evolution. Pancreatic ribonuclease is a very important digestive enzyme and secreted by the pancreas. Numerous studies have suggested that RNASE1 gene duplication is closely related to the functional adaptation of the digestive system in the intestinal fermentation herbivores. RNASE1 gene thus becomes one of the most important candidate genetic markers to study the molecular mechanism of adaptation of organisms to the feeding habit. Interestingly, RNASE1 gene duplication has also been found in some non-intestinal fermentation mammals, suggesting that RNASE1 gene may have produced novel tissue specificity or functions in these species. In this review, RNASE1 gene and its implications in adaptive evolution, especially in association with the feeding habit of organisms, are summarized.

Quantum master equation scheme of time-dependent density functional theory to time-dependent transport in nanoelectronic devices

In this work a practical scheme is developed for the first-principles study of time-dependent quantum transport. The basic idea is to combine the transport master equation with the well-known time-dependent density functional theory. The key ingredients of this paper include (i) the partitioning-free initial condition and the consideration of the time-dependent bias voltages which base our treatment on the Runge-Gross existence theorem; (ii) the non-Markovian master equation for the reduced (many-body) central system (i.e., the device); and (iii) the construction of Kohn-Sham master equations for the reduced single-particle density matrix, where a number of auxiliary functions are introduced and their equations of motion (EOMs) are established based on the technique of spectral decomposition. As a result, starting with a well-defined initial state, the time-dependent transport current can be calculated simultaneously along with the propagation of the Kohn-Sham master equation and the EOMs of the auxiliary functions.